WO2008022332A2

WO2008022332A2 - System, method and kit for replicating a dna array

Info

Publication number: WO2008022332A2
Application number: PCT/US2007/076244
Authority: WO
Inventors: Richard M. Crooks; Kim Joohoon; Li Sun; Haohao Lin
Original assignee: Board Of Regents, The University Of Texas System
Priority date: 2006-08-18
Filing date: 2007-08-17
Publication date: 2008-02-21
Also published as: WO2008022332A3

Abstract

The present invention includes methods, systems and kits for replicating an oligonucleotide array. The replication includes hybridizing one or more biotin-functionalized oligonucleotides to one or more oligonucleotides on a first substrate and capturing the one or more biotin-functionalized oligonucleotides with streptavidin attached to a second substrate. The one or more biotin- functionalized oligonucleotides may be separated from the one or more oligonucleotides by mechanical force to form a replicated array.

Description

SYSTEM, METHOD AND KIT FOR REPLICATING A DNA ARRAY Technical Field of the Invention

The present invention relates in general to the field of nucleic acid array replication and specifically to nucleic acid array replication using positional hybridization that retains the location of the nucleic acids and allows numerous cycles using a single master nucleic acid array.

Background Art

Arrays of nucleic acids are of extremely useful in genomic characterization, genetic disease screening, drug and pharmaceutical compound screening, examination of protein/DNA/RNA or protein/protein interactions, solid support sequencing and numerous research applications; however, such arrays are expensive to produce and subject to errors due to the labor-intensive production.

For example, sequencing on solid supports includes hybridization of template nucleic acids to arrayed primers containing combinatorial sequences which hybridize to complementary sequences on the template strand. These methods combine the capture of the template, by formation of stable duplex structures, with sequence discrimination due to instability of mismatches between the template and the primer. In addition, other problems remain, e.g., specificity, reproducibility, specific localization of the oligonucleotides on the array and so forth.

United States Patent Number 5,795,714, to Cantor, et al., entitled, Method for replicating an array of nucleic acid probes reportedly provides for the replication of probe arrays and methods for replicating arrays of probes for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. The arrays are created using PCR technology with probes with 5'- and/or 3'-overhangs.

Another example includes British Patent application number GB2413555, to Alessandra et al., entitled, Replication of Nucleic Acid Arrays. The application reportedly provides a method of producing arrays of nucleic acids corresponding to a first set of nucleic acids immobilized on a first solid support and includes furnishing on said first set of nucleic acids a second set of nucleic acids, each nucleic acid of the second set having at least a portion which is complementary to at least a portion of respective nucleic acid of the first set and being hybridized to it thereby. This involve contact with a solution containing a mixture of nucleic acids, or synthesis using the first nucleic acids as primers and templates. The second set of nucleic acids are immobilized to a second solid support, either before or while they are hybridized to the first set of nucleic acids. Separation of the first and second solid supports provides said first support bearing the master array and said second support bearing a complementary array. United States Patent Number 6,511,803 to Church, et al., entitled, Replica Amplification of Nucleic Acid Arrays discloses methods of making and using immobilized arrays of nucleic acids, particularly methods for producing replicas of such arrays. Included are methods for producing high density arrays of nucleic acids and replicas of such arrays, as well as methods for preserving the resolution of arrays through rounds of replication. Also included are methods which take advantage of the availability of replicas of arrays for increased sensitivity in detection of sequences on arrays. Improved methods of sequencing nucleic acids immobilized on arrays utilizing single copies of arrays and methods taking further advantage of the availability of replicas of arrays are disclosed. The improvements lead to higher fidelity and longer read lengths of sequences immobilized on arrays. Methods are also disclosed which improve the efficiency of multiplex PCR using arrays of immobilized nucleic acids.

United States Patent Number 5,616,478 to Chetverin, et al., entitled, Method for amplification of nucleic acids in solid media reportedly provides an amplification of nucleic acids carried out in a medium immobilized by using a matrix penetrating the medium. However, the method of nucleic acid amplification provides pools of nucleic acid molecules positioned on a support matrix to which they are not covalently linked.

United States Patent Number 5,795,714, entitled, Method for replicating an array of nucleic acid probes provides for the replication of probe arrays and methods for replicating arrays of probes for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5'- and/or 3'-overhangs.

Disclosure of the Invention

The present inventors recognized a need in the art for improved methods and devices for oligonucleotide array design and production that provide specificity, reproducibility, specific localization of oligonucleotides on an array. The present invention provides a method of replicating an oligonucleotide array using very small amounts of reaction products and transferring about 10⁴⁴ to 10 ¹⁹ moles of DNA oligonucleotides. Additionally, the spatial relationship between reactant and product surfaces is preserved with micron- scale resolution after transfer. This approach is demonstrated for a DNA polymerase reaction, but other chemical and biological reactions may also be used. Applications to high-throughput screening and separation of very small amounts of reaction products from a complex milieu.

The present invention provides a method of replicating an oligonucleotide array by hybridizing one or more biotin-functionalized oligonucleotides to one or more oligonucleotides on a first substrate and capturing the one or more biotin-functionalized oligonucleotides with streptavidin attached to a second substrate. The present invention also includes an oligonucleotide array replication system. The system includes a first substrate having an oligonucleotide array, a second substrate having streptavidin attached thereto to capture one or more biotin-functionalized oligonucleotides and a biotin-functionalized oligonucleotides library. The first substrate and the second substrate can be separated mechanically. The oligonucleotide array includes oligonucleotide deposited, positioned or located in a specific area of the array. In some instances, the location and sequence of the individual oligonucleotides is associated with other information, e.g., function. The replicated array also replicates this association.

The present invention provides a method of replicating an oligonucleotide array by hybridizing one or more biotin-functionalized oligonucleotides to one or more oligonucleotides on a first substrate and capturing the one or more biotin-functionalized oligonucleotides with streptavidin attached to a second substrate. The one or more biotin-functionalized oligonucleotides may be separated from the one or more oligonucleotides by mechanical force to form a replicated array.

The present invention also includes an oligonucleotide array replication system. The system includes a first substrate having an oligonucleotide array, a second substrate having streptavidin attached thereto to capture one or more biotin-functionalized oligonucleotides and a biotin-functionalized oligonucleotides library. The first substrate and the second substrate can be separated mechanically. The oligonucleotide array includes oligonucleotide deposited, positioned or located in a specific area of the array. In some instances, the location and sequence of the individual oligonucleotides is associated with other information, e.g., function. The replicated array also replicates this association. An oligonucleotide array replication kit is provided by the present invention. The kit includes a first substrate having streptavidin for the capturing one or more biotin-functionalized oligonucleotides. An oligonucleotide array can be used to prepare oligonucleotide replicates having any functional sequence positioned anywhere on the oligonucleotide array. The first substrate having streptavidin is used to capture a biotin-functionalized oligonucleotide that is hybridized to an oligonucleotides library or array and subsequently separated mechanically.

In addition, the present invention provides a method of replicating oligonucleotide arrays by attaching one or more oligonucleotides onto a first substrate and hybridizing the one or more oligonucleotides to one or more biotin-functionalized oligonucleotides. The one or more biotin- functionalized oligonucleotides then may be captured with streptavidin attached to a second substrate. The array surface and the replication array may be separated mechanically.

A method of replicating an array of single-stranded nucleic acids on a solid support is also provided by the present invention. The method includes hybridizing one or more biotinylated nucleic acids to a nucleic acid set imobilized on a nucleic acid array and extending the one or more biotinylated nucleic acids using the nucleic acid set as a template. The one or more biotinylated nucleic acids are then captured with streptavidin attached to a substrate. This allows the spatial registration of the nucleic acid set to be replicated and the substrate and the nucleic acid array separated mechanically.

For example, the method includes synthesizing an array of one or more nucleic acids each comprising a non-variant sequence of length C at a 3 '-terminus and a variable sequence of length R at a 5'-terminus and fixing the array to a first solid support. A set of nucleic acids each having a sequence complementary to the non- variant sequence is synthesized and hybridized to the array of one or more nucleic acids. The set of one or more nucleic acids are enzymatically extended using the variable sequences of the array as templates. The enzymatically extend the set of one or more nucleic acids are fixed to a second solid support and separated mechanically to create the replicated array of single-stranded nucleic acids.

The present invention also provides a method for the fabrication of RNA microarrays using a surface ligase reaction and mechanical transfer. In one embodiment, eighteen replicas were prepared from a single master array with no detectable degradation of activity of the resulting replica RNA array or the master DNA array. The present invention provides a robust method for fabricating RNA microarrays in parallel with no requirement for RNA modification (e.g., biotin). The present invention provides microarray fabrication from DNA to RNA and protein arrays.

The present invention includes a method for replicating an array of single-stranded nucleic acids on a solid support by synthesizing an oligonucleotide array of a first set of one or more nucleic acids; fixing the oligonucleotide array to a first solid support; forming a complement set of one or more nucleic acids that hybridize to the first set of one or more nucleic acids; fixing the complementary set of one or more nucleic acids to a second solid support; mechanically separating the first set of one or more nucleic acids and complementary set of one or more nucleic acids to create a replicated array of single-stranded nucleic acids.

Description of the Drawings For a more complete understanding of the features and advantages of the present invention, reference is now made to the detailed description of the invention along with the accompanying figures and in which:

FIGURES 1 a- 1 d are schematics of the method for the replication of DNA microarrays as provided by one embodiment of the present invention; FIGURES 2a-2f show fluorescence micrographs demonstrating transfer of fluorescein labeled DNA from a master slide to a replica surface;

FIGURES 3a-3c are images that illustrate micrographs demonstrating replication of a 3 X 3 master array having just one DNA sequence; FIGURES 4a-4b are images of fluorescence micrographs demonstrating accurate replication of a master having multiple sequences;

FIGURE 5 is an image of a fluorescence micrograph demonstrating replication of multiple functional oligonucleotides; FIGURE 6 is an image of a schematic that illustrates ssDNA immobilization onto the reactant surface, primer annealing and extension and product transfer;

FIGURES 7a-7d are images of fluorescence micrographs obtained after immobilizing the ssDNA, annealing a primer to the template and then extending the primer;

FIGURES 8a-8d are images of fluorescence micrographs showing multiple primer-extension reactions and transfers using a single reactant surface and FIGURE 8e is a schematic of the method for the replication of DNA microarrays as provided by another embodiment of the present invention;

FIGURES 9a-9d are images of fluorescence micrographs demonstrating in-situ DNA primer extension on a master surface and subsequent mechanical transfer to a replica surface;

FIGURES 10a- 1Of are images of optical micrographs of the PDMS replicas; FIGURES 1 Ia-I Ic are images of fluorescence micrographs showing wide drainage canals;

FIGURES 12a-12e are images of micrographs demonstrating multiple replications of a single master array incorporating a single DNA template sequence;

FIGURES 13a-13h are images of micrographs demonstrating replication of a master array consisting of a single DNA template sequence; FIGURES 14a- 14c are images of micrographs demonstrating replication of a master array consisting of templates having long DNA sequences;

FIGURE 15 are images of fluorescence micrographs representing higher magnification views of spots;

FIGURES 16a- 16c are images of fluorescence micrographs demonstrating replication of a master array consisting of three different oligonucleotide sequences;

FIGURES 17a-17f are images of fluorescence micrographs representing higher magnification views of each replica spot;

FIGURE 18a-18d are images of fluorescence micrographs demonstrating replication of a high-density DNA microarray; FIGURE 19 is an image of a schematic that illustrates a method for parallel conversion of

DNA master arrays into RNA replicate arrays using an enzymatic reaction followed by mechanical transfer; FIGURE 20a is an image of a fluorescence micrograph obtained from the master after co- hybridization and ligation of a short, biotinylated DNA oligonucleotide and a labeled RNA probe onto a DNA template;

FIGURE 20b is an image of a fluorescence micrograph obtained from the master array after transfer of the ligated DNA/RNA oligonucleotide to the replica surface;

FIGURE 20c is an image of a fluorescence micrograph obtained from the PDMS replica surface after transfer of the ligated DNA/RNA oligonucleotide;

FIGURE 2Od is a graph of the fluorescence intensity profiles shown in FIGURES 20a -20c;

FIGURE 21 is an image of an optical micrograph of the PDMS surface shown in FIGURE 20c;

FIGURE 22 is an illustration of a control in the absence of a 5'-phosphoryl group on the anchor DNA;

FIGURE 23 a is an image of a fluorescence micrograph obtained from a PDMS replica surface after hybridization, ligation, transfer and subsequent hybridization of a fluorescently labeled target;

FIGURES 23b-23e are images of a fluorescence micrograph prepared the same as FIGURE 23a, but after 2, 3, 17, and 18 iterations;

FIGURE 23f is a graph of the fluorescence intensity profiles;

FIGURE 23g is a scheme illustrating the approach used to obtain the data in FIGURES 23a- 23f;

FIGURE 24a is a scheme of a control in the absence of 5'-phosphoryl group of anchor DNA; FIGURE 24b is a scheme of a control obtained in the absence of the T4 DNA ligase;

FIGURE 24c is a graph of the fluorescence intensity profiles of the fluorescence micrographs; FIGURE 25 is an image of a fluorescence micrograph obtained from an RNA microarray having 2500 micro-scale spots; and

FIGURE 26 is an image of a fluorescence micrograph demonstrating fabrication of RNA microarrays from a master DNA array having multiple different DNA template sequences.

Description of the Invention While the making and using of various embodiments of the present invention are discussed in detail below, it should be appreciated that the present invention provides many applicable inventive concepts that can be embodied in a wide variety of specific contexts. The specific embodiments discussed herein are merely illustrative of specific ways to make and use the invention and do not delimit the scope of the invention.

To facilitate the understanding of this invention, a number of terms are defined below. Terms defined herein have meanings as commonly understood by a person of ordinary skill in the areas relevant to the present invention. Terms such as "a", "an" and "the" are not intended to refer to only a singular entity, but include the general class of which a specific example may be used for illustration. The terminology herein is used to describe specific embodiments of the invention, but their usage does not delimit the invention, except as outlined in the claims. As used herein the term "Nucleic Acids" and "oligonucleotides" include sequences of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) which may be isolated from natural sources, produced using recombinant DNA technology or artificially synthesized. They also might include polyamide nucleic acid (PNA) or any nucleic acid analogues that have the ability to hybridize with a complementary chemical structure. Although it is not limiting, the optimal length of nucleic acid sequences in both variable and non-variable parts is about 1 to 500 nucleotides.

DNA microarrays have been increasingly used in high-throughput analysis for a wide range of applications, including monitoring gene expression, drug screening and fundamental studies of genetic diseases and cancers. The present invention makes it possible to use a master DNA array to produce replicates of any other material (e.g., proteins, carbohydrates, or inorganic nanoparticles) that can be labeled with a short oligonucleotide code.

The present invention provides a method of replicating an oligonucleotide array by hybridizing one or more biotin-functionalized oligonucleotides to one or more oligonucleotides on a first substrate and capturing the one or more biotin-functionalized oligonucleotides with streptavidin attached to a second substrate. The one or more biotin-functionalized oligonucleotides may be separated from the one or more oligonucleotides by mechanical force to form a replicated array. The mechanical force may be used in conjunction with chemical treatments to reduce the hybridization forces. Generally, the substrate may be a porous glass, non-porous glass, silicon, silicon dioxide, silicon nitride, one or more metals, one or more polymers, one or more plastics, one or more resins, one or more ceramics, one or more gels, one or more beads, one or more semiconductors and a combination thereof. In some instances the substrate may be a chip, a semiconductor, or a semiconductor component.

The one or more biotin-functionalized oligonucleotides include a code sequence complementary to one of the one or more oligonucleotides and a biotin modification. In some embodiments, the one or more oligonucleotides, the one or more biotin-functionalized oligonucleotides or both may be connected to a linker. The linker may be an alkyl group, alkylene group, alkenyl group, alkynyl group, aryl group, alkoxy group, alkylcarbonyl group, alkylcarboxyl group, amido group, carboxyl group or combinations thereof. In addition, the substrate, the oligonucleotide array, the oligonucleotides or combination thereof may be functionalized by the addition, removal or substitution of one or more alkyl groups, alkylene groups, alkenyl groups, alkynyl groups, aryl groups, alkoxy groups, alkylcarbonyl groups, alkylcarboxyl groups, amido groups, carboxyl groups, halogens, hydrogens or combinations thereof. Optionally, a fluorescent tag may be used with the one or more biotin-functionalized oligonucleotides.

Generally, the oligonucleotides may include a code sequence complementary to one of the one or more oligonucleotides and a biotin modification. The oligonucleotides may include other sequences or regions that provide a specific function. For example, restriction sites may be incorporated into the sequences or added as linkers, protein binding sites and chemical modifications may also be added. The present invention provides as an example biotin-functionalized oligonucleotides; however, other proteins, metals, compounds or surfaces may be used. As an example, T4 polymerase is used to extend the one or more biotinylated nucleic acids; however, the enzymatic treatment of the present invention is not limited to polymerases but may be any enzyme given the appropriate conditions and concentrations. In addition, chemical treatments may be used with the present invention to provide cleavage and modifications.

The present invention provides an efficient and accurate method for the replication of DNA microarrays as illustrated in the schematic of FIGURE 1. A master array sequence is prepared by depositing different single-stranded oligonucleotides onto an appropriate surface. Each spot represents a different sequence that will direct the placement of a second oligonucleotide.¹'² The master array sequence is exposed to a solution containing biotin-functionalized oligonucleotides that includes two parts: a code sequence and a functional sequence. Because each code sequence is designed to be complementary to just one specific sequence on the master array sequence, the biotin- functionalized oligonucleotides will be directed to their appropriate locations on the master array sequence. A replica surface-modified with streptavidin is brought into conformal contact with the master array sequence and results in binding of the replica surface to the biotinylated DNA to form a replica array sequence. The replica array sequence is separated from the master array sequence by mechanical force to transfer the biotinylated oligonucleotide from the master array sequence to the replica array sequence. The replica array sequence can now be used as a DNA array, and the master sequence array sequence can be rehybridized to generate additional replica array sequences. The oligonucleotides spotted onto a master array sequence surface will hybridize to their biotin- functionalized complements and then the complement can be transferred to a streptavidin-modified replica surface.

The best known in-situ method integrates photolithography and solid-state synthesis.¹² Each synthesis cycle consists of protection, photodeprotection, and addition of a nucleotide to directly grow oligonucleotides on a substrate. The growth of oligonucleotides is spatially defined by photolithographic masks, and the number of synthesis cycles required is proportional to the length of the oligonucleotides. This method has the advantages of small spot size (about 8 μm spot) and design flexibility,¹⁴ but the inefficiency of solid-state reactions limits the maximum oligonucleotide length to about 60 base pairs (bps)¹³'¹⁴ and leads to increased cost. The second general method for fabricating microarrays is ex-situ spotting of presynthesized oligonucleotides.¹⁵ Spotting to a DNA chip surface can be implemented by either contact printing using rigid pins¹⁶ or by projection through microfabricated nozzles.¹⁷ Spotting does not impose length restrictions on the patterned oligonucleotides.¹⁸ However, the expense and time required to prepare an array is proportional to the dimensionality of the array and the size of the individual array elements, which are large (about 75-500 μm) compared to those prepared by in situ methods.¹³ Moreover, as for any sequential process involving multiple repetitive steps, both in situ synthesis and ex-situ spotting are subject to an accumulation of errors.¹³ Other ex-situ methods for delivering presynthesized oligonucleotides include patterning using micro fluidic channels,¹⁹ microcontact printing,²⁰ and dip-pen nanolithography;²¹'²² however, all these methods involve manual loading of the oligonucleotides and therefore, at least for now, are not well-suited for creating largescale, complex microarrays.

One example, slides are used to fabricate master array sequences are CodeLmk slides (Amersham Bioscience, Piscataway, NJ). CodeLmk slides are coated with a three-dimensional polymeric scaffold functionalized with N-hydroxysuccinimide (NHS). The skilled artisan will recognize that many different surfaces and substrates may be used. The surfaces and substrates may be metal, polymer, alloys, glass and so forth. For example, the surfaces and substrates may be a long- chain, hydropbilio polymer containing amine-rcactive groups to eovalentSy immobilize aminc-roodified DNA for array p. The polymer raay be ocrvalctitiy crosslink to itself and/or to the surface of the slide and include end-point attachment to orient the DNA away from the siufkce of the slide. The poly(dimethylsiloxane) (PDMS) replicas were prepared from liquid precursors (Sylgard Silicone Elastomer- 184 from Dow Corning, Midland, MI). 3-Mercaptopropyltrimethoxysilane (97% from Alfa Aesar, Ward Hill, MA) and streptavidin-maleimide (from Sigma-Aldrich, St. Louis, MO) were used as received. All chemicals used to prepare buffers were purchased from Sigma-Aldrich: sodium phosphate monobasic (Sigma S0751), sodium phosphate dibasic (Sigma S0876), Trizma Base (Sigma T6791), Trizma HCl (Sigma T6666), ethanolamine (Sigma E9508), sodium dodecyl sulfate (SDS) (Sigma L4522), and 2Ox SSC (Sigma S6639). All the oligonucleotides were obtained from Integrated DNA Technologies (Coralville, IA). The sequences of the oligonucleotides are provided in Table 1.

Table 1

Fluorescence micrographs were captured using an inverted microscope (e.g., Eclipse TE300, Nikon) equipped with a CCD camera (Cascade, Photometries, Tucson, AZ). The filter set (XC 102: 475 nm excitation filter, 505 nm dichroic mirror, and 510 nm longpass emission filter) was purchased from Omega Optical, Inc. (Brattleboro, VT). The master slides were fabricated using CodeLink slides according to the instructions provided by the vendor (Amersham Bioscience, Piscataway, NJ). Twenty- five micromolar solutions of 5'-amine- modified oligonucleotides in 50 mM pH 8.5 phosphate buffer were spotted onto a CodeLink slide using a pipet (Pipettor 40000-264, VWR) or a microarrayer (Omnigrid Microarrayer, San Carlos, CA). After spotting, the slide was placed inside a sealed chamber above a saturated NaCl solution and incubated at 22 + 2°C for 15-20 hours. Next, the slide was placed in a solution containing 50 mM ethanolamine and 0.1 M TRIS buffer (pH 9.0) at 50⁰C for 30 minutes to block residual reactive NHS groups. After rinsing with purified water twice, the slide was placed in a buffer containing 4 X SSC and 0.1% SDS, which was pre -warmed at 50⁰C for 30 minutes. After rinsing with water again, the slide was dried under a stream of N₂. Only about 50% of the masters prepared using the microarrayer could be replicated, but the masters spotted manually worked 100% of time. Apparently, the contact spotting configuration used by the microarrayer causes some damage to the surface of CodeLink slides; however, that when an array can be replicated, the replica is always 100% faithful to the master and can always be hybridized to the complement of the functional sequence. No false positive signals were ever observed. Fabrication of Streptavidin-Functionalized PDMS. Following our previously reported procedures, thiol groups were first introduced onto a PDMS surface by silanization with 3- mercaptopropyltrimethoxysilane (MPS), and then streptavidin was immobilized onto MPS-modified PDMS through the reaction between maleimide and thiol groups.

Replication of DNA Microarrays. The master was exposed to a solution containing 10 μM oligonucleotide for at least 4 hours, and then replication was achieved by contacting the hybridized master with a streptavidin- functionalized PDMS surface. In a typical replication process, 10 μL of pH 7.2 buffer was used to wet the master surface, and then the streptavidin-functionalized PDMS was placed on top of the master with a pressure of 1.4 N/cm at 22 + 2 ⁰C. Although a pH 7.2 buffer solution was used to wet the master surface, water (no buffer) works just as well. After 10 minutes of contact, the PDMS replica was manually peeled off the master, rinsed and blown dry. FIGURE 2 are images of fluorescence micrographs demonstrating transfer of fluorescein labeled DNA from a master slide to a PDMS replica surface to show that multiple replicas can be prepared from a single master array sequence. The master array sequence was prepared by applying a solution of amine -modified oligonucleotide SEQ ID No.: 1 onto a slide. FIGURE 2a is an image that illustrates fluorescence micrographs demonstrating the master slide modified with SEQ ID No.: 1 and hybridized to fluorescein and biotin-labeled oligonucleotides SEQ ID No.: 4 whose code sequence is complementary to oligonucleotide having SEQ ID No.l. FIGURE 2b is an image that demonstrates the master slide after transfer. FIGURE 2c is an image that demonstrates the PDMS replica after transfer. FIGURE 2d is an image that demonstrates the second replica obtained after rehybridization of the master with SEQ ID No.: 4. FIGURE 2e is an image that demonstrates the third replica obtained after rehybridization of the master with SEQ ID No.: 4. FIGURE 2f is an image that demonstrates the fluorescence intensity profiles obtained along the dashed lines shown in FIGURES 2a-e. For clarity, FIGURE 2c and FIGURE 2d are offset by 6000 and 3000 counts, respectively. The image integration time was 30 seconds for all frames. The gray scale is 5000-25000 counts for FIGURE 2a and FIGURE 2b, and 4500-6500 counts for FIGURES 2c-2e.

The master array was exposed to oligonucleotide SEQ ID No.: 4. The first 18 bases from the 3' end of oligonucleotide SEQ ID No.: 4 are the exact complement of SEQ ID No.: 1, and SEQ ID No.: 4 is labeled with fluorescein at the 3' end and biotin at 5' end. Following hybridization, the master array sequence was thoroughly rinsed, and the fluorescence micrograph shown in FIGURE 2a was obtained.

Uniform fluorescence emission from the master surface confirms homogeneous hybridization of SEQ ID No.: 4 to the zip master array sequence. FIGURE 2b and FIGURE 2c are fluorescence micrographs of the master and replica, respectively, following replication. Fluorescence intensity is clearly transferred from the surface of the master to the replica after contact. The checkerboard pattern results from drainage canals (20 μm on center, 10 μm wide and 3 μm deep) present on the replica surface that direct buffer solution away from the contact area during replication. Controls showed that these canals were essential for successful DNA transfer.

Specifically, if both the master and the PDMS were dry, then no transfer of DNA was observed. Additionally, no transfer was observed in the absence of drainage canals regardless whether buffer was present. In the absence of drainage canals, solvent trapped between the two surfaces prevents molecular contact between the biotin-functionalized oligonucleotides on the master and streptavidin present on the replica.

FIGURE 2f is an image that provides a quantitative representation of the data shown in FIGURE 2b and FIGURE 2c. After replication, the contrast between the light and dark areas on the master of FIGURE 2b (about 1300 counts) is very close to that of the replica of FIGURE 2c (about 1100 counts), indicating that only a small fraction of the DNA is lost during transfer. FIGURE 2d and FIGURE 2e show the second and the third replicas obtained from the same master after rehybridization with oligonucleotide SEQ ID No.: 4 labeled with fluorescein and biotin. The contrast between the light and dark areas for the three consecutive replicas is 1100, 900, and 1200 counts, respectively, indicating good reproducibility and that there is no progressive loss of DNA from the master after formation of three replicas. The data presented thus far indicate that replication is a consequence of molecular contact and binding between the biotin groups present on the slide and streptavidin on the PDMS replica surface.

Because the binding force between biotin and streptavidin is stronger than between DNA base pairs, the DNA duplexes separate, and the biotin- functionalized oligonucleotides transfer to the replica surface. For very long DNA duplexes, however, it is important to separate the two surfaces slowly to avoid breaking the biotin/streptavidin bond as a result of the force required to separate a DNA duplex is independent of its length if the separation rate is appropriately controlled.⁶'⁷ For single - oligonucleotide replicas, the spot size is defined by the spacing of the canals on the replica surface. For example, each replica spot shown in panels FIGURE 2c-e is about 10 μm X lO μm, which is comparable to the smallest feature sizes obtained by in situ synthesis (about 8 μm),¹⁴ and much smaller than those obtained by ex-situ spotting (about 75 μm).¹³ However, for replicas patterned with multiple DNA oligonucleotides, the important size parameter is defined by the dimensions of the master, not the replica. To demonstrate replication from a master array instead of from a homogeneous surface, a microarrayer was used to print a 3 X 3 array of nine about 100 μm-diameter spots of SEQ ID No.: 1, and then the master array was copied onto a PDMS replica surface using the procedure discussed earlier for FIGURE 2.

FIGURE 3 are images that illustrate micrographs replication of a 3 X 3 master array having just one DNA sequence. FIGURE 3a is an image of a fluorescence micrograph obtained from a master array spotted with SEQ ID No.: 1 and subsequently hybridized to fluorescein- labeled and biotin-labeled oligonucleotide SEQ ID No.: 4 whose code sequence is the complement of oligonucleotide having SEQ ID No.: 1. FIGURE 3b is an image of a fluorescence micrograph obtained from the PDMS surface after replication of the master. FIGURE 3c is an optical micrograph of the replica surface showing the drainage canals. The integration time for both FIGURE 3a and FIGURE 3b was 30 seconds. The gray scale is 2000-20000 counts for FIGURE 3a, and 2000-8000 counts for FIGURE 3b. In FIGURE 3b, all three spots in the right column are cut off because they happen to intersect a major drainage canal as shown in the optical image, FIGURE 3c.

FIGURE 3 a is an image of a fluorescence micrograph obtained from the master after hybridization with fluorescein- labeled and biotinfunctionalized DNA sequence SEQ ID No.: 4. The presence of fluorescence, which is absent prior to hybridization, confirms hybridization of the code sequence. The fluorescence micrograph image shown in FIGURE 3b was obtained from the PDMS replica surface after conformal contact of the two substrates. The 3 X 3 array observed on the replica (FIGURE 3b) exactly mirrors the master array (FIGURE 3 a), except for the presence of the drainage canals. An optical image of the replica surface (FIGURE 3c) shows the drainage design of the replica. We have successfully replicated master arrays having up to 100 elements using this procedure.

FIGURE 4 is an image of a fluorescence micrograph demonstrating accurate replication of a master having multiple sequences. FIGURE 4a is a 4 X 3 master array having three sequences (row 1, SEQ ID No.: 1; row 2, SEQ ID No.: 2; and row 3, SEQ ID No.: 3; as seen in Table 1) after hybridization with fluorescein- labeled and biotin- labeled oligonucleotides SEQ ID No.: 4 whose code sequence is only complementary to SEQ ID No.: 1. FIGURE 4b is an image of a PDMS replica of the master showing only one row of transferred oligonucleotides. The integration time for both FIGURE 4a and FIGURE 4b was 30 seconds. The gray scale is 5000-13000 counts for FIGURE 4a, and 5000-8000 counts for FIGURE 4b.

Replication from a master having multiple sequences. To demonstrate this function, a 4 X 3 master array containing three different zip codes was prepared using a microarrayer. Each row is composed of four spots having a nominal diameter and edge-to-edge distance of about 100 μm. With reference to Table 1, the first, second, and third rows correspond to SEQ ID No.: 1, SEQ ID No.: 2, and SEQ ID No.: 3, respectively. Hybridization was carried out for at least 4 hours with 10 μM fluorescein- labeled and biotin- functionalized oligonucleotide SEQ ID No.: 4, which has a code sequence that only matches SEQ ID No.: 1, and afterward fluorescence was observed only from the four spots in the first row (FIGURE 4a). This result clearly shows that the master correctly directs the proper code sequence to the appropriate location on the master.¹'² Following replication (FIGURE 4b), fluorescence is only observed from the top row of spots, corresponding to SEQ ID No.: 1. This confirms that only the correct functional sequence is transferred to the replica surface.

Preparation and functionality of replica microarrays having multiple sequences. A master array having multiple sequences can direct placement of multiple sequences. Functional sequences could be transferred to the replica and the replica functional sequences remain active. First, a 4 X 3 master array having three sequences was prepared as described for FIGURE 4. A solution containing a mixture of three nonfluorescent, biotin- functionalized oligonucleotides (SEQ ID No.: 4, SEQ ID No.: 5, and SEQ ID No.: 6, Table 1; 10 μM each) was introduced onto the master surface for at least 4 hours. The sequence of each of the three oligonucleotides is complementary to exactly one of the sequences present on the master surface. Thus, oligonucleotides SEQ ID No.: 4, SEQ ID No.: 5, and SEQ ID No.: 6 are directed to oligonucleotides SEQ ID No.: 1, SEQ ID No.: 2, and SEQ ID No.: 3, respectively. Following replication, the replica array was exposed to a solution containing a mixture of three fluorescein- labeled targets, oligonucleotides SEQ ID No.: 7, SEQ ID No.: 8, and SEQ ID No.: 9, at a concentration of 10 μM each for at least 4 hours. Each target was chosen to match the functional sequence of one of the three oligonucleotides present on the replica surface.

FIGURE 5 is an image of a fluorescence micrograph demonstrating replication of multiple functional oligonucleotides. First, a 4 X 3 master array having three sequences, row 1, SEQ ID No.: 1; row 2, SEQ ID No.: 2; and row 3, SEQ ID No.: 3; was prepared and hybridized by exposure to a solution containing a mixture of three non- fluorescent, biotin-functionalized oligonucleotides: SEQ ID No.: 4, SEQ ID No.: 5, and SEQ ID No.: 6 whose sequences are complementary to oligonucleotides SEQ ID No.: 1, SEQ ID No.: 2, and SEQ ID No.: 3, respectively. After replication, the resulting PDMS surface was exposed to a mixture of fluorescein- labeled oligonucleotides SEQ ID No.: 7, SEQ ID No.: 8 and SEQ ID No.: 9 that are complementary to the functional sequences of SEQ ID No.: 4, SEQ ID No.: 5, and SEQ ID No.: 6, respectively. The integration time was 30 seconds, and the gray scale was 5000-8000 counts. The fluorescence image obtained from the replica clearly shows a 4 X 3 array in FIGURE 5 that a having multiple sequences for hybridization-based applications. The present invention provides an efficient and accurate method for replication of DNA microarrays from a sequence master. For arrays containing multiple DNA sequences, the replica spots can be as small as 100 μm. Three consecutive replications from the same master were successfully achieved with no significant decrease of oligonucleotide density on the replica surface. Replication from a 4 X 3 master array having three sequences proved to be accurate, and there was no observable cross- reactivity. The present invention provides for larger-scale arrays, smaller spot sizes, and replication of more complex biological materials (proteins and viruses) and inorganic nanomaterials.

The present invention also provides a method for directly transferring the product of a biological surface reaction from a primary reactant surface (or first substrate) to a secondary product surface (or second substrate). For example, a single-strand DNA (ssDNA) modified with a reactive amine group on the 5' end is spotted onto an epoxy-modified glass surface results in immobilization of the DNA template onto the reactant surface. Biotinylated primer oligonucleotides are hybridized to the ssDNA template and the primers are extended via a T4 polymerase reaction. A streptavidin-coated PDMS monolith is brought into contact with the reactant surface resulting in the binding of the reaction product (the extended DNA complement) to the PDMS product surface via biotin/streptavidin interaction. The reactant and product surfaces are mechanically separated from one-another, resulting in transfer of the product of the polymerase reaction to the PDMS surface. The product surface is able to selectively bind its complementary DNA and that a single reactant surface can be used multiple times to generate isolated product. Importantly, spatial registration is maintained between the reactant and product surfaces. The present invention provides a method for directly transferring small amounts of reaction products from one surface to another. The approach is illustrated using a T4 DNA polymerase reaction to extend primers hybridized to a surface-confined DNA template; however, the skilled artisan will recognize that other enzymes may be used and other types of nucleic acids may be used. The nucleic acids may be modified by the skilled artisan to include modifications, substitutions, replacements and combinations thereof to the sugar, the phosphate group, the base and a combination thereof. Following the extension reaction, the resulting oligonucleotide is transferred to a product surface. The present invention provides (1) the spatial registration of the product is preserved after transfer; (2) the same reactant surface can be used to generate and transfer multiple iterations of products; and (3) the reaction products are biologically active after transfer.

FIGURE 6 is an image of a schematic that illustrates ssDNA immobilization onto the reactant surface, primer annealing and extension, and product transfer. Specifically, FIGURE 7a is an image of a fluorescence micrograph obtained after immobilizing the ssDNA template onto an epoxy- modified glass surface, annealing the primer to the template, and then extending the primer. In this case, the polymerase reaction mixture included dye-labeled deoxycytidine triphosphate (Cy3-dCTP), and therefore the extended primer is fluorescent. Controls indicated that no fluorescence could be detected from the reactant surface after immobilization of the template and annealing of the primer, but before addition of Cy3-dCTP and primer extension. Likewise, no fluoresence was observed when the primer-annealed reactant surface was exposed to all reactants (including Cy3-dCTP) except for the T4 DNA polymerase and then rinsed with buffer. This indicates no detectable level of nonspecific adsorption of the dye.

FIGURES 7b and 7c are images of fluorescence micrographs of the reactant and product surface, respectively, after transfer of the extended primer. The dark regions on the reactant surface in FIGURE 7b correspond to DNA incorporating Cy3-dCTP that was transferred to the product surface, and the light regions in FIGURE 7c correspond to the transferred DNA on the product surface. The checkerboard pattern results from drainage canals (20 μm on center, 10 μm wide and 3 μm deep) on the product surface. These canals are necessary for successful DNA transfer, because they provide a means for buffer solution trapped between the reactant and product surfaces to escape.¹'² FIGURE 7d is an image that shows fluorescence intensity profiles obtained along the dotted lines in FIGURES 7a- 7c. The average intensity difference between the bright and dark regions on the reactant surface (6.8 ± 0.2) x 10³ counts, shown in FIGURE 7b is an image that is very close to that on the product surface ((6.0 ± 0.4) x 10³ counts) as seen in FIGURE 7c, indicating little net loss of extended primers during transfer.

FIGURES 7a-7d are images of fluorescence micrographs demonstrating extension of primers and transfer of the extended primers. FIGURE 7a is an image of a fluorescence micrograph obtained from a reactant surface after a polymerase reaction incorporated Cy3-dCTP into the extended primers. FIGURE 7b is a fluorescence micrograph obtained from the reactant surface after transfer of the extended primers. FIGURE 7c is an image of a fluorescence micrograph obtained from the product surface after transfer of the extended primers. FIGURE 7d is an image of a fluorescence intensity profiles obtained along the dotted lines shown in FIGURES 7a-7c. Integration time was 100 ms. Gray scales are 16000-42000 counts for FIGURES 7a and 7b and 2500-15000 counts for FIGURE 7c.

FIGURE 8 shows that multiple primer- extension reactions and transfers can be carried out using a single reactant surface. After annealing the primers to the immobilized template DNA, the polymerase reaction was performed using an unlabeled mixture of deoxyribonucleotide triphosphates (dNTP). This results in a surface that is not fluorescent. Next, the extended and nonfluorescent primers were transferred to a product surface. Finally, a fluorescently labeled oligonucleotide, complementary to only the extended sequence (not to the primer), was exposed to the product surface. This process was carried out three times using the same reactant surface, and fluorescence micrographs of the three resulting product surfaces are shown in FIGURES 8a-8c. Note that in the absence of the T4 polymerase, no fluorescence was detected on the product surface.

The present invention demonstrates that multiple product transfers can be carried out using the same reactant surface. FIGURE 8d provides line scans corresponding to the three micrographs. These show that the average modulation in fluorescence is 1040 ± 110, 920 ± 50, and 1190 ± 190 for the first, second, and third transfers, respectively. There was more variation between the first (1070 ± 90), second (1090 ± 110), and third (630 ± 50) replicates using different reactant surfaces. Second, when this was carried out in the absence of internal spacers between the template oligonucleotide and the surface (18-carbon internal spacers repeated five time: iSpl8₅, Integrated DNA Technologies, Coralville), no detectable hybridization of the fluorescently labeled complement was observed, likely a consequence of steric hinderance between the T4 polymerase and the glass surface, which results in incomplete primer extension. Third, FIGURE 8 clearly shows that the transferred reaction product is functional, because it hybridizes to its fluorescent complement.

First, very small amounts of reaction products can be transferred from the reactant surface to the product surface, e.g., the present invention provides transfer of ~10^~14 moles of DNA oligonucleotides,⁷'⁸ but there is no technological barrier for reducing this to as few as ~10^~19 moles.³ Second, the spatial relationship between reactant and product surfaces are preserved with micron- scale resolution after transfer, and it seems likely that this could be reduced still further. This approach is demonstrated for a DNA polymerase reaction, but it should be useful for other chemical and biological reactions too. Applications to high-throughput screening and separation of very small amounts of reaction products from a complex milieu are easily envisioned. FIGURES 8a-8d are images of fluorescence micrographs demonstrating multiple transfers of extended primers from a single reactant surface. FIGURE 8a is a fluorescence micrograph obtained from a product surface after primer extension, transfer of the extended primers, and hybridization of a fluorescent probe complementary to the extended primer (but not to the primer itself). FIGURE 8b is an image that is the same as FIGURE 8a, but after a second round of primer extension, transfer, and hybridization. FIGURE 8c is an image that is the same as FIGURE 8a, but after a third round of primer extension, transfer, and hybridization. FIGURE 8d is an image that shows Fluorescence intensity profiles obtained along the dotted white lines shown in FIGURES 8a-8c. FIGURE 8e shows the approach used to obtain the data in FIGURES 8a-8d. The star symbols represent the fluorescent dye. The integration time was 1000 ms. The gray scale is 2500-5500 counts for FIGURES 8a-8c.

FIGURE 8 shows that multiple primer-extension reactions and transfers can be carried out using a single reactant surface. This approach is shown in FIGURE 8e. After annealing the primers to the immobilized template DNA, the polymerase reaction was performed using an unlabeled mixture of deoxyribonucleotide triphosphates (dNTP). This results in a surface that is not fluorescent. Next, the extended and non- fluorescent primers were transferred to a product surface. Finally, a fluorescently labeled oligonucleotide, complementary to only the extended sequence (not to the primer), was exposed to the product surface. This process was carried out three times using the same reactant surface, and fluorescence micrographs of the three resulting product surfaces are shown in FIGURES 8a-8c. In the absence of the T4 polymerase, no fluorescence was detected on the product surface.

The present invention provides multiple product transfers can be carried out using the same reactant surface. FIGURE 8d provides line scans corresponding to the three micrographs that show the average modulation in fluorescence is 1040 ± 110, 920 ± 50, and 1190 ± 190 for the first, second, and third transfers, respectively. In the absence of internal spacers between the template oligonucleotide and the surface (e.g., 18-carbon internal spacers repeated five time: iSpl8₅, Integrated DNA Technologies, Coralville), no detectable hybridization of the fluorescently labeled complement was observed. The skilled artisan will recognize that the linker may be of different lengths by altering the numbers of carbons in the linker and/or the number of repeats of the linkers. In addition the linker may be of a different composition including other atoms or compounds, polymers, inorganic molecules and so forth. This is likely a consequence of steric hinderance between the T4 polymerase and the glass surface, which results in incomplete primer extension. FIGURE 8 clearly shows that the transferred reaction product is functional, because it hybridizes to its fluorescent complement. Another embodiment of the present invention includes a method for replication of DNA microarrays that involves in-situ, enzymatic synthesis of a DNA complement array using a prefabricated master array, followed by mechanical transfer of the complement array to a second substrate.

The DNA sample size can be faithfully replicated from about 100 μm or larger samples. In addition the replica arrays consisting of several different oligonucleotide sequences can be prepared, and such arrays are active toward hybridization of their complements. For example, 1 to 10 or more than 10 replicas can be prepared from a single master with no detectable progressive degradation of their activity. DNA master arrays consisting of long DNA templates (80mers or more) can be replicated, as can large-scale master arrays consisting of about 2300 spots. Glass slides coated with an epoxy monolayer (NEXTERION^® Slide E, SCHOTT North America, Inc., Elmsford, NY) were used to fabricate master DNA microarrays. The poly(dimethylsiloxane) (PDMS) monoliths were prepared from Sylgard 184 (Dow Corning, Midland, MI). Streptavidin- maleimide conjugates (Sigma S9415), 3-mercaptopropyltrimethoxysilane (MPS) (Fluka 63800), and other chemicals for buffers or blocking solutions were obtained from Sigma-Aldrich: 2Ox saline- sodium citrate (SSC) buffer (Sigma S6639), 10% sodium dodecyl sulfate (SDS) solution (Sigma L4522), sodium phosphate monobasic (Sigma S0751), sodium phosphate dibasic (Sigma S0876), TRITON^® X-100 (Sigma T8787), Trizma base (Sigma T6791), Trizma HCl (Sigma T6666), ethanolamine (Sigma E9508), 2-mercaptoethanol (Sigma M6250), and N-ethylmaleimide (Sigma E3876). T4 DNA polymerase (EP0061) supplied with 5x reaction buffer (335 mM TRIS-HCl pH 8.8 at 25 DC, 33 mM MgC12, 5 mM DTT, 84 mM (NH4)2SO4), deoxyribonucleotide triphosphate (dNTP) mix (R0241), dNTP set (RO 181), and nuclease-free water were used as received from Fermentas Inc. (Hanover, MD). Cy3 fluorescent dye-labeled deoxycytidine triphosphate (Cy3-dCTP) was obtained from Amersham Biosciences Corp. (Piscataway, NJ). DNA oligonucleotides were obtained from Integrated DNA Technologies (Coralville, IA). The sequences and modifications are provided in Table 2. Table 2

Characterization included a fluorescence microscope (Nikon TE2000, Nikon Co., Tokyo, Japan) equipped with appropriate filter sets (filter numbers 41001 for fluorescein, 31002 for Cy3, and 41008 for Cy5, Chroma Technology Corp., Rockingham, VT), a mercury lamp (X-CiteT 120, Nikon Co), and a CCD camera (Cascade, Photometries Ltd., Tucson, AZ) was used to acquire optical and fluorescence micrographs. Micrographs were processed using V++ Precision Digital Imaging software (Digital Optics, Auckland, New Zealand). High-density master arrays were scanned using a microarray scanner (GenePix 4000B, Molecular Devices Corp., Sunnyvale, CA).

The master arrays were fabricated using epoxy-modified glass slides (Nexterion Slide E) as previously described ^{" 5} but with some modifications. Briefly, template oligonucleotide solutions (25 μM in 50 mM sodium phosphate buffer, pH 8.5) were spotted onto the glass slides using a micropipette, a manual microarrayer (Xenopore Corp., Hawthorne, NJ) in a home -built humidity chamber, or a home-built robotic microarrayer. Next, the spotted slide was placed in a chamber in which the humidity was in equilibrium with a saturated NaCl solution at about 20 to about 25 °C. After incubation, the slide was washed (at about 20 to about 25 "C) to remove unbound templates and buffer residue using the following protocol: 1 x 5 minute in 0.1% TRITON ^® X-100 solution, 2 x 2 minute in 1 mM HCl solution, 1 x 10 minute in 100 mM KCl solution, and 1 x 1 min in Milli-Q water (18 MΩ*cm, Millipore, Bedford, MA). Next, the slide was placed in a blocking solution (50 mM ethanolamine and 0.1 % SDS in 0.1 M TRIS buffer, pH 9.0) for about 15 minute at about 50 "C. After washing with Milli-Q water for 1 minute, the slide was blown dry by a N₂ stream to avoid visible drying marks on the slide surface.

Fabrication of streptavidin-modified PDMS monoliths. Nanoscale, conformal contact between the master and replica surfaces is required for transfer of the replicate DNA array. This requires the use of micron-scale canals to direct buffer solution away from the interface during contact. These canals were introduced into the PDMS surface using a micromolding process^23"26 and then the entire PDMS surface was functionalized with streptavidin. Streptavidin functionalization was carried out as follows. First, the microstructured PDMS surface was silanized with 3- mercaptopropyltrimethoxysilane (MPS). Second, a streptavidin-maleimide conjugate was covalently linked to the PDMS surface via the resulting thiol groups. The unreacted maleimide and thiol groups were blocked by incubating the functionalized PDMS in a 1.5 mM 2-mercaptoethanol solution and then in a 3 mM N-ethylmaleimide solution.

The master slide was exposed to a primer solution, which was then extended for 5 minutes in a polymerase solution at 25 °C. The polymerase reaction mixture contained a T4 DNA polymerase (0.05 u/ μL) and a dNTP mixture (0.1 mM) in a polymerase reaction buffer (Ix: 67 mM TRIS-HCl (pH 8.8), 6.6 mM MgCl₂, 1 mM DTT, 16.8 mM (NH₄)₂SO₄). Polymerase solutions incorporating Cy3-dCTP were prepared the same way, except using a dNTP mixture containing Cy3-dCTP (0.1 mM) unless specifically mentioned otherwise. For polymerase reactions on high-density master arrays, incubation chambers (CoverWell, Grace Bio-Labs, Inc., OR) were used to ensure uniform spreading of the reaction mixture on the surface. Following primer extension, 4x SSC buffer (10 μL) was dropped on the master to wet the surface, and then the streptavidin-functionalized PDMS monolith was brought into contact with the surface. A pressure of 1.4 N/cm2 was applied at 20 to 25 °C for 10 minute. Next, the PDMS monolith was peeled off the master surface at constant separation speed (400 μm/s) using a linear motion actuator (CMA-25CC, Newport Corp., Irvine, CA), and then both surfaces were washed in buffer and blown dry.

FIGURES 9a-9d are images of fluorescence micrographs demonstrating in-situ DNA primer extension on a master surface and subsequent mechanical transfer to a replica surface. FIGURE 9a is an image of a fluorescence micrograph obtained from a master after a surface T4 DNA polymerase reaction incorporated Cy3-dCTP into the extended DNA primer. FIGURE 9b is an image of a fluorescence micrograph obtained from the master surface after transfer of the extended primer. FIGURE 9c is an image of a fluorescence micrograph obtained from the replica surface after transfer of the extended primer. FIGURE 9d is an image of a similar to FIGURE 9c, but after a third round of primer extension and transfer. The integration time was 500 ms, and the gray scales are 2000- 60000 counts for FIGURE 9a and FIGURE 9b and 1500-10000 counts for FIGURE 9c and FIGURE 9d.

FIGURE 9 demonstrates template-driven DNA polymerization on a master and subsequent transfer onto PDMS surfaces. The Template I solution from Table 2 was spotted onto a glass master using a manual microarrayer. This resulted in formation of about 200 μm-diameter Template I spot. After annealing, the biotinylated primers were extended using the polymerase reaction mixture including dye-labeled deoxycytidine triphosphate (Cy3-dCTP). The extended primers were then transferred to a PDMS replica surface as previously reported. ^{" 5} FIGURE 9a shows a fluorescence micrograph obtained from a single about 200 μm spot on the glass master after primer extension of Template I and subsequent washing. The extended primer is fluorescent because of Cy3-dCTP incorporation. A control confirmed that no fluorescence was detectable when the primer-annealed glass surface was exposed to the reaction mixture in the absence of the T4 DNA polymerase and washed using the same protocol used for the surface shown in FIGURE 9a.²³ FIGURES 9b and 9c are fluorescence micrographs of the glass master and PDMS replica, respectively, after transfer of the extended primers. The grid pattern visible on the PDMS surface in FIGURE 9c corresponds to microfabricated drainage canals (e.g., 20 μm on center, 10 μm wide, and 3 μm deep), which are necessary to direct buffer solution away from the glass/PDMS interface during conformal contact.^23" ²⁵ FIGURE 9d shows a PDMS replica obtained after two additional rounds of primer annealing, extension, and mechanical transfer from the same master. The average fluorescence intensities from the raised squares on the replica surfaces are 4200 ± 1100, 2200 ± 800, and 3400 ± 700 for the first, second, and third replicas, respectively, prepared from this master (fluorescence and optical micrographs of the second replica, and fluorescence intensity profiles are shown in FIGURE 1 Oc- 1Oe). The fluorescence intensity profile obtained from the glass master after transfer shows that about 25% of the extended primers were transferred from the master to a replica surface shown in FIGURE 1Of. Optical micrographs of the images shown in FIGURES 9c and 9d are shown in FIGURE 10a and 10b respectively.

FIGURES 10a- 1Of are images of optical micrographs of the PDMS replicas. Fluorescence and optical micrographs of the replica obtained after a second round of primer extension and transfer from the same master. Relatively low intensity on the leftmost area of the second replica spot was observed. The optical micrograph of the second replica shows some abnormal surface residue in this same region, which could be responsible for the lower intensity. The integration time was 500 ms, and the gray scale is 1500-10000 counts for FIGURE 1OC. FIGURE 1Oe is an image of a fluorescence intensity profiles obtained from the raised squares on the replica surfaces. FIGURE 1 Of is an image of a fluorescence intensity profile obtained from the master spot of FIGURE 1 Ob after transfer of the extended primer. FIGURES 1 Ia-I Ic are images of fluorescence micrographs showing that wide drainage canals appear bright in the images. FIGURE 11 a is an image of a fluorescence micrograph obtained from a streptavidin-coated PDMS surface. FIGURE l ib is an image of a fluorescence micrograph obtained from streptavidin-coated PDMS after incubation with hybridization buffer (no fluorescently labeled Target I) and post-hybridization washing. FIGURE l ie is an image of a fluorescence micrograph obtained from streptavidin-coated PDMS after incubation with Target I in hybridization buffer and post- hybridization washing. Integration time was 1 second, and the gray scale is 2100-3200 counts.

The drainage canals restrict contact between the glass and PDMS surfaces to multiple square areas (10 x 10 μm²) that reside between the canals. The dark areas within the spot on the master surface in FIGURE 9b correspond to primer-extended DNA incorporating Cy3-dCTP that was subsequently transferred to the PDMS surface.

FIGURE 11 is a schematic of up to 10 functional replicas can be prepared from a single master. Here, the primer extension reaction was carried out using Template I in the absence of a fluorescently labeled nucleotide, and consequently the resulting master surface is not fluorescent. However, after primer extension and transfer to the PDMS surface, the replica was exposed to fluorescently labeled DNA Target I (10 μM from Table 2), which is complementary to the extended DNA sequence but not to the primer. In contrast to the approach used to obtain the results shown in FIGURE 9, the method depicted in FIGUREl Ib avoids continuous photobleaching of fluorescent dyes present on the master surface. Moreover, this approach demonstrates that the replica array is functional in that it can hybridize its complement. FIGURES 12a-12e are images of micrographs demonstrating multiple replications of a single master array incorporating a single DNA template sequence (DNA Template I, Table 2). FIGURE 12a is an image of a fluorescence micrograph obtained from a replica after primer extension, transfer of the polymerized DNA, and hybridization of fluorescent Target I (Table T), which is complementary to the extended sequence (but not to the primer itself). FIGURES 12b-12e are images of samples that are the same as FIGURE 12a, but after 2, 3, 9, and 10 rounds of primer extension, transfer, and hybridization, respectively. FIGURE 12f is an image of a fluorescence intensity profiles obtained along the dotted white lines shown in FIGURES 12a-12e. The integration time was 1 second, and the gray scale is 2500-5000 counts for FIGURES 12a-12e. FIGURE 12a is a fluorescence micrograph obtained from a replica surface obtained after carrying out the three steps outlined in FIGURE 1 Ib. The presence of the fluorescent grid pattern indicates that extended primers transfer and able to bind labeled DNA Target I on the replica surface. Controls showed that there is no detectable fluorescence on the replica surface if the T4 polymerase is omitted during the primer-extension step.²³ This replication cycle, consisting of primer extension, transfer, and hybridization with labeled DNA Target I, was repeated a total 10 times using the same master. Micrographs corresponding to the second, third, ninth, and tenth cycles are presented in FIGURES 12b-12e, respectively. The fluorescence line profiles in FIGURE 12f show that the contrast in fluorescence between the light and dark areas on the surfaces of these replicas were 900 + 80, 1200 + 90, 1210 + 120, 1070 + 80, and 1120 + 100 counts, respectively. This indicates that there is no significant or progressive degradation of the functionality of the replicas up to the tenth round of replication from a single master.

First, a 3 x 2 master array having a single DNA template sequence (Template I from Table 2) was fabricated. The primer extension reaction was carried out using unlabeled nucleotides. After transfer of the nonfluorescent extended primers, the replica was exposed to fluorescently labeled DNA Target I (i.e., Table T). FIGURE 13a is a fluorescence micrograph obtained from a replica surface following this series of steps. This result clearly shows that six functional spots are transferred from the master array to the replica.

FIGURES 13a-13h are images of micrographs demonstrating replication of a 3 x 2 master array consisting of a single DNA template sequence (Template I, Table T). FIGURE 13a is an image of a fluorescence micrograph obtained from a replica after primer extension, transfer of the polymerized DNA, and hybridization of a fluorescent target (Target I, Table T) complementary to the extended sequence (but not to the primer itself). Integration time was 1 second. The gray scale is 2100-3200 counts. FIGURE 13b is an image of an optical micrograph obtained from the replica showing the drainage canal pattern. The cross-like structures are large drainage canals that are connected to the smaller canals to facilitate removal of buffer during contact of the two surfaces. FIGURES 13c-13h are images of a higher magnification views of the six spots shown in FIGURE 13 a. The registration of the spots in FIGURES 13c-13h is the same as in part FIGURE 13a. The integration time was 1 second, and the gray scale is 3000-13000 counts.

The cross-like feature in FIGURE 9a is a large drainage canal that is fed by the smaller canals discussed earlier.²³'²⁵ Consistent with intuition the smaller canals always appear dark, but these large canals appear bright. Indeed, they also appear bright in the optical micrograph of the replica surface as seen in FIGURE 13b. However, a series of controls confirmed that this is an optical effect unrelated to fluorescence as seen in FIGURE 11. FIGURES 13c-13h are higher magnification fluorescence micrographs of the six spots shown in FIGURE 13 a. The replica spot shown in

FIGURE 13d was truncated because of the wide drainage canal apparent in FIGURE 13a and 13b. The characteristic grid pattern arising from the smaller canals is also apparent at this magnification.

Replication of a 3 x 2 master array having a long template sequence (80mer, Long Template, Table 2) was also performed using the approach shown in FIGURE 11a. The sequence of this longer template was designed to incorporate a single dye-labeled nucleotide (Cy3-dCTP) exclusively at the bottom (3 ' end) of the extended primer. This confirms that the primer is fully extended along the length of the template, and that the complete extended primer is transferred to the replica surface.

FIGURES 14a- 14c are images of micrographs demonstrating replication of a 3 x 2 master array consisting of templates having long (80mer) sequences (Long Template, Table 2). FIGURE 14a is an image of a fluorescence micrograph obtained from a master array after a surface T4 DNA polymerase reaction incorporated Cy3-dCTP into the polymerized DNA. FIGURE 14b is an image of a fluorescence micrograph obtained from the master array after transfer of the extended DNA primer. FIGURE 14c is an image of a fluorescence micrograph obtained from a replica array after transfer of the extended primer. The integration time was 1 second, and the gray scales are 2500- 4500 counts for FIGURE 14a and FIGURE 14b and 2300-3500 counts for FIGURE 14c.

FIGURE 14a- 14c are images of fluorescence micrographs of the master array. FIGURE 14a shows six extended primer spots incorporating Cy3-dCTP on the master array. FIGURES 14b and 14c are images of fluorescence micrographs of the master and a PDMS replica, respectively, after transfer of the extended primers. A more highly magnified image of each spot shown in FIGURES 14b and 14c is presented in FIGURE 15.

FIGURE 15 are images of fluorescence micrographs representing higher magnification views of each spot shown in FIGURES 14b and 14c. FIGURE 15 images of the fluorescence micrographs representing higher magnification views of each spot shown in FIGURES 14b and 14c. The registration of the spots in these images corresponds to those in Figure 14. For example, FIGURE

15a corresponds to the top, left spot in FIGURE 14a. The integration time was 1 second, and the gray scales are 2200-15000 counts for FIGURES 15a-15f and 2400-12000 counts for FIGURE 15g- 151. Replication of a master array consisting of multiple template sequences. Replication of a master array having three different template sequences was also carried out using the approach shown in FIGURE 1 Ib. First, a 3 x 2 master array having three DNA templates (left column, Template I; middle column, Template II; right column, Template III, Table 2) was fabricated. After polymerization of DNA and transfer of the polymerized DNA, the replica PDMS surface was exposed to a mixture of fluorescent targets (Targets I, II, and III; 10 μM each, of Table 2) complementary to each extended sequence (but not to the primer). Three fluorescence micrographs were obtained from this single replica using a different filter set for each fluorescent target.

FIGURES 16a- 16c are images of fluorescence micrographs demonstrating replication of a 3 x 2 master array consisting of three different oligonucleotide sequences (Templates I, II, and III, Table 2). FIGURE 16a is an image of a fluorescence micrograph obtained from the replica using a fluorescence filter for Target I labeled with fluorescein. FIGURE 16b is an image of a sample that is the same as FIGURE 16a, but using a filter for Target II labeled with Cy3. FIGURE 16c is an image of a sample that is the same as FIGURE 16a, but using a filter for Target III labeled with Cy5. The integration time was 1 second, and the gray scales are 2400-3800 counts for FIGURE 16a and FIGURE 16b and 1800-3200 counts for FIGURE 16c. The fluorescence micrographs shown in FIGURE 16 indicate that each of the three sequences present on the replica surface hybridizes with a different fluorescent target. Higher magnification images of each replica spot are presented in FIGURE 17. FIGURES 17a- 17f are images of fluorescence micrographs representing higher magnification views of each replica spot shown in FIGURE 16. The registration of the spots in these images corresponds to that in FIGURE 16. For example, FIGURE 17a corresponds to the topmost spot in FIGURE 16a and FIGURE 16b corresponds to the topmost spot in FIGURE 16b. The integration time was 1 second, and the gray scales are 3700-6000 counts for FIGURE 17a and FIGURE 17d, 3000-30000 counts for FIGURE 17b and FIGURE 17e, and 2000-8000 counts for FIGURE 17c and FIGURE 17f. A very weak fluorescence signal from Target II labeled with Cy3 was observer in FIGURE 17a because of a slight overlap of the bandpass of the filter (no. 41001, Chroma Technology Corp.) used for detecting the fluorescein label on Target I with the emission spectrum of the Cy3 label on Target II. Therefore, the in-situ DNA polymerization is correctly carried out on each template sequence, and the resulting replica spots selectively hybridize their complements.

Replication of a high-density master array. Replication of a high-density master array was demonstrated using the approach shown in FIGURE l la. A master array consisting of 2304 DNA spots (Template I, Table 2) was fabricated using a robotic microarrayer. After annealing the primers, a polymerase reaction mixture, including dye-labeled Cy3-dCTP, was introduced onto the master slide. Finally, the polymerized DNA incorporating Cy3-dCTP was transferred onto a replica surface. FIGURE 18a-18d are images of fluorescence micrographs demonstrating replication of a high- density DNA microarray. The polymerase reaction mixture included a T4 DNA polymerase (0.05 u/μL), a dNTP mixture without dCTP (0.1 mM), and a dilute, labeled dCTP mixture (Cy3-dCTP: 10 μM, unlabeled dCTP: 90 μM) in a polymerase reaction buffer (Ix: 67 mM Tris-HCl (pH 8.8), 6.6 mM MgCl₂, 1 mM DTT, 16.8 mM (NFLO₂SO₄). FIGURE 18a is an image of afluorescence micrograph obtained by scanning the entire master (with a microarray scanner) after the surface T4 DNA polymerase reaction incorporated Cy3-dCTP into the polymerized DNA. FIGURE 18b is an image of a fluorescence micrograph obtained from the master after transfer of the polymerized DNA. FIGURE 18c is an image of a higher magnification view of a section of the micrograph in FIGURE 18b. FIGURE 18d is an image of a fluorescence micrograph of the replica after transfer of the polymerized DNA. The integration time was 1 second, and the gray scales are 2600-4000 counts in FIGURE 18c, and 2000-4500 counts in FIGURE 18d.

FIGURE 18a is an image of a fluorescence micrograph obtained by scanning the entire master array after extending the primers and rinsing the surface. The fluorescence from the DNA spots on the master array is qualitatively homogeneous, indicating that the polymerase reaction on the high- density master is uniform. FIGURE 18b is an image of a fluorescence micrograph of the entire master obtained after transfer. FIGURES 18c and 18d are expanded views of the indicated section of the master and the corresponding replica after transfer. FIGURE 18c is an image of fluorescence micrographs shows that a dark grid pattern is superimposed on each DNA spot, which confirms transfer of the polymerized DNA from the master array to the replica. This indicates that this method results in faithful replication of quite large DNA microarrays.

The present invention provides a method for in-situ synthesis and subsequent mechanical transfer of DNA to replica surfaces. For example, DNA spots as small as about 100 μm can be faithfully replicated; that replica arrays consisting of several different oligonucleotide sequences can be prepared, and that such arrays are active toward hybridization of their complements; and that up to about 10 replicas can be prepared from a single master with no significant progressive degradation of their activity. Moreover, DNA master arrays consisting of long DNA templates (e.g., about 80mers) could also be replicated, as could master arrays consisting of about 2300 spots. Forthcoming reports will focus on quantitative measurements of transfer efficiency and replication of arrays consisting of other biological materials (proteins, RNA, and cells).

In addition, the present invention provides a method for fabrication of RNA microarrays by co- hybridization of a short, biotinylated DNA oligonucleotide and an RNA probe sequence to DNA templates spotted onto a master array. Next, the short DNA sequence and the RNA probe are linked using T4 DNA ligase. Finally, a poly(dimethylsiloxane) (PDMS) monolith modified on the surface with streptavidin is brought into conformal contact with the master array. This results in binding of the biotinylated DNA/RNA oligonucleotides to the PDMS surface. When the two substates are mechanically separated, the DNA/RNA oligonucleotides transfer to the PDMS replica, and the DNA oligonucleotides remaining on the master array are ready to template another RNA replica array. This sequence can be repeated for at least 18 cycles using a single master arrays. RNA arrays consisting of up to 3 different oligonucleotide sequences of up to about 2500 individual about 70 μm spots.

FIGURE 19 provides a method for parallel conversion of DNA master arrays into RNA replicate arrays. The approach is based on a surface enzymatic reaction followed by mechanical transfer. The RNA replicate microarrays consist of single-strand RNA (ssRNA) oligonucleotides (probe RNA) ligated to short ssDNA oligonucleotides (anchor DNA). First, amine-modified ssDNA templates are immobilized on an epoxy-modified glass slide. The distal ends of all the DNA templates are configured to be identical. Second, this master slide is exposed to single-sequence biotinylated anchor ssDNA, which hybridizes to the distal ends of the templates and to the unmodified probe ssRNA, which is complementary to each ssDNA sequence of the master array. Third, the nick between the anchor ssDNA and the probe RNA is ligated using a T4 DNA ligase. Next, a streptavidin-coated poly(dimethylsiloxane) (PDMS) monolith is brought into conformal contact with the master to bind the biotin anchor (now linked to the RNA probe) to the streptavidin-modified PDMS surface. When the PDMS monolith is mechanically separated from the master, the RNA array is transferred to the PDMS surface while the DNA templates remain on the master surface. This series of steps can be repeated many times without loss of fidelity, resulting in multiple RNA replicate arrays from a single master.

RNA microarrays are a powerful tool for the analysis of nucleic acids and proteins. For example, ultrasensitive detection of DNA oligonucleotides was reported using RNA microarrays in conjunction with the enzyme RNase H.29,30 The use of RNA aptamer microarrays also allowed simultaneous detection of multiple proteins31 for diagnosis of cancers.32,33 RNA microarrays are normally fabricated by tethering modified RNA oligonucleotides on functionalized surfaces. For example, biotinylated RNA oligonucleotides on streptavidin- functionalized glass slides31,34,35 or thiol-modified RNA oligonucleotides on maleimide-terminated gold surfaces.29,30

The present invention provides replicating DNA arrays can be used to prepare many RNA replica arrays from a single DNA master using unmodified RNA oligonucleotides. The surface ligase reaction is required to link the anchor DNA to the RNA oligonucleotides using T4 DNA ligase. The present invention can be executed at least 18 times using a single DNA master array without loss of fidelty of the replicate RNA array. RNA microarrays consisting of about 121 spots and consisting of up to three different RNA sequences were prepared, and no evidence of cross-hybridization was detected. Streptavidin-maleimide conjugates (Sigma S9415), 3-mercaptopropyltrimethoxysilane (MPS) (Fluka 63800), and other chemicals for buffers or blocking solutions were obtained from Sigma-Aldrich: 2Ox saline-sodium citrate (SSC) buffer (Sigma S6639), 10% sodium dodecyl sulfate (SDS) solution (Sigma L4522), sodium phosphate monobasic (Sigma S0751), sodium phosphate dibasic (Sigma S0876), TRITON® X-100 (Sigma T8787), Trizma base (Sigma T6791), Trizma HCl (Sigma T6666), ethanolamine (Sigma E9508), 2-mercaptoethanol (Sigma M6250), and N-ethylmaleimide (Sigma E3876). The poly(dimethylsiloxane) (PDMS) precursor solution (Sylgard 184) was ordered from Dow Corning Inc. (Midland, MI). T4 DNA ligase (M0202S) provided with 10x reaction buffer (500 mM TRIS-HCl, 100 mM MgC12, 100 mM DTT, and 10 mM ATP at pH 7.5) at 25 ⁰C) was used as received from New England BioLabs Inc. (Ipswich, MA). Nuclease-free water was obtained from Fermentas Inc. (Hanover, MD). DNA and RNA oligonucleotides were obtained from Integrated DNA Technologies Inc. (Coralville, IA) and Dharmacon Corp. (Lafayette, CO), respectively. The sequences and modifications are provided in Table 3.

A fluorescence microscope (Nikon TE2000, Nikon Co., Tokyo, Japan) equipped with appropriate filter sets (filter #: 31002 for DY547 and Cy3, and 41008 for Cy5, Chroma Technology Corp.,

Rockingham, VT), a mercury lamp (X-CiteTM 120, Nikon Co), and a CCD camera (CASCADE®,

Photometries Ltd., Tucson, AZ) was used to acquire optical and fluorescence micrographs.

Micrographs were processed using V++ Precision Digital Imaging software (Digital Optics,

Auckland, New Zealand). High-density arrays were scanned using a microarray scanner (GenePix 4000B, Molecular Devices Corp., Sunnyvale, CA).

The master DNA arrays were fabricated using epoxy-modified glass slides (NEXTERION® Slide E, SCHOTT North America Inc., Elmsford, NY).²⁷'²⁸ Briefly, template DNA solutions (25 μM in 50 mM sodium phosphate buffer, pH 8.5) were spotted onto the glass slides. Next, the spotted slide was incubated in a chamber in which the humidity was in equilibrium with a saturated NaCl solution at 20 to 25 ⁰C. After incubation, the slide was washed as following (at 20 to 25 ⁰C): 1 x 5 min in 0.1% TRITON^® X-100 solution, 2 x 2 min in 1 mM HCl solution, 1 x 10 min in 100 mM KCl solution, and 1 x 1 min in Milli-Q water (18 MΩ«cm, Millipore, Bedford, MA). The slide was then placed in a blocking solution (50 mM ethanolamine and 0.1 % SDS in 0.1 M TRIS buffer, pH 9.0) for 15 min at 50 ⁰C. After washing with Milli-Q water for 1 minute, the slide was blown dry by a N₂ stream and stored under dark and dry condition.

The RNA arrays were fabricated by simultaneously exposing the DNA master array to the anchor DNA oligonucleotide, the RNA probe, and the T4 DNA ligase for 1 hour at 25 ⁰C. Specifically, the ligase reaction mixture contained the anchor DNA strands (0.5 μM), the probe RNA strands (0.5 μM), and T4 DNA ligase (20 u/μL) in a ligase reaction buffer (Ix: 50 mM TRIS-HCl, 10 mM MgC12, 10 mM DTT, 1 mM ATP, pH 7.5 at 25 ⁰C). Incubation chambers (Coverwelltm, Grace Bio- Labs Inc., OR) were used to ensure uniform spreading of the reaction mixture on the surface. Following ligation, the master slide was rinsed with buffer solutions (at 20 to 25 ⁰C): 2x SSC buffer containing 0.2 % SDS and 2x SSC buffer. The master slide was washed again as follows (at 20 to 25 0C): 10 minutes in 2x SSC buffer containing 0.2 % SDS, 10 minutes in 2x SSC buffer, and 10 min in 0.2x SSC buffer. Next, 4x SSC buffer (10 μL) was dropped on the master to wet the surface, and then a streptavidin-functionalized PDMS monolith was brought into contact with the surface. A pressure of 1.4 N/cm2 was applied at 20 to 25 ⁰C for 10 minutes. Note that the streptavidin- functionalized PDMS monolith was prepared as reported previously.27,2840 Finally, the PDMS monolith was peeled off the master surface at a constant separation speed (400 μm/s) using a linear motion actuator (CMA-25CC, Newport Corp., Irvine, CA), and then both surfaces were washed in buffer and blown dry.

FIGURE 20a is an image of a fluorescence micrograph obtained from the master after co- hybridization and ligation of a short, biotinylated DNA (DA, Table 3) oligonucleotide and a labeled RNA probe (RP I, Table 3) onto a DNA template (DT I, Table 3). FIGURE 20b is an image of a fluorescence micrograph obtained from the master after transfer of the ligated DNA/RNA oligonucleotide to the replica surface. FIGURE 20c is an image of a fluorescence micrograph obtained from the PDMS replica surface after transfer of the ligated DNA/RNA oligonucleotide. FIGURE 2Od is a graph of the fluorescence intensity profiles obtained along the dashed lines shown in FIGURES 20a -20c. FIGURE 2Oe is a scheme showing the approach used to obtain the data in FIGURES 20a-20d. The star symbols represent the fluorescent dye. Integration time was 100 ms. Gray scales are 5000-25000 counts for FIGURES 20a and 20b, and 1500-5000 counts for FIGURE 20c.

The fluorescence micrographs shown in Figure 20 demonstrate the viability of the replication procedure of the present invention. Template DNA (DT I; Table 3) immobilized on the master slide was exposed to a ligase reaction mixture composed of biotinylated anchor DNA (DA I; Table 3), fluorescently labeled probe RNA (dye-labeled RP I; Table 3), and T4 DNA ligase. This resulted in hybridization and ligation of the anchor DNA and probe RNA on the master surface. The ligated RNA/DNA conjugates were then transferred to a PDMS surface.27,28,40

Table 3. Sequences of the nucleic acids:

The abbreviations in the table correspond to the following modifications: 3AmM, an amino modifier on the 3' end of the DNA; DY547, a Cy3 alternate dye attached to the 5' end of the RNA; 5Phos, phosphorylation of the 5' end of the DNA; 3BioTEG, a biotin modifier with a tetraethyleneglycol (TEG) spacer on the 3' end of the DNA; 3Cy3Sp, a Cy3 dye attached to the 3' end of the DNA; and 3Cy5Sp, a Cy5 dye attached to the 3' end of the DNA. These are the same notations used by the DNA supplier (Integrated DNA Technologies, Coralville, IA) and the RNA supplier (Dharmacon Inc., Lafayette, CO).

FIGURE 20a is a fluorescence micrograph obtained from the glass master after exposure to the ligase reaction mixture and subsequent washing. The fluorescence intensity in this micrograph indicates that the labeled probe RNA hybridized with the template DNA. There was no detectable level of fluorescence when the master DNA template was treated identically to the surface shown in FIGURE 20a, but using probe RNA II (dye-labeled RP II, Table 3) which is not complementary to template DNA I. FIGURES 20b and 20c are fluorescence micrographs obtained from the glass master and PDMS surface, respectively, after transfer of the ligated RNA strands. Drainage canals (20 μm on center, 10 μm wide, and 3 μm deep) were microfabricated on the PDMS surface as reported previously27,28,40 to direct buffer solution away from the glass/PDMS interface during conformal contact.

FIGURE 21 is an image of an optical micrograph of the PDMS surface shown in FIGURE 20c. The drainage canals restrict contact between the glass and PDMS surfaces to multiple square areas (1O x 10 μm2), which results in the grid pattern present on both surfaces. The light areas on the PDMS surface in FIGURE 20c correspond to transfer of fluorescently labeled probe RNA from the darker regions apparent in FIGURE 20b. FIGURE 2Od shows fluorescence intensity profiles obtained along the dotted lines in FIGURES 20a-20c. Importantly, the average intensity difference between the bright and dark regions on the master surface (1540 ± 140 counts, FIGURE 20b) is close to the intensity difference measured from the PDMS surface (2010 ± 60 counts, Figure Ic), suggesting no significant loss of ligased RNA strands during the transfer. The fluorescence shown in FIGURE 20c results from transfer of probe RNA strands ligated to the biotinylated anchor DNA rather than from nonspecific adsorption of unligated RNA on the PDMS surface. FIGURE 22 is an illustration of a control in which a master surface was treated identically to that shown in FIGURE 2Oe, but in the absence of a 5'-phosphoryl group on the anchor DNA (DA, Table 3). The integration time was 100 ms. FIGURE 22b is an illustration of a control in which a master surface was treated identically to that shown in FIGURE 2Oe, but in the absence of treatment with the T4 DNA ligase. The integration time was 100 ms. FIGURE 22c is a graph comparing the fluorescence intensity profiles obtained for the two controls in FIGURES 22a and 22b with the profile along the dashed white line shown in FIGURE 20c.

Specifically, fluorescence micrographs were obtained from PDMS surfaces treated identically to that shown in FIGURE 20c, but in the absence of the 5'-phosphoryl group of the anchor DNA (FIGURE 22a, anchor DNA without PO4; Table 3) and the T4 DNA ligase (FIGURE 22b), respectively. In the absence of 5'-phosphoryl group of anchor DNA or the T4 DNA ligase, the ligation of the anchor DNA to the probe DNA is not expected to proceed. FIGURE 22c is a graph of the fluorescence intensity profiles from these two controls compared to the profile of the replica surface shown in FIGURE 2Od. On the basis, both the 5'-phosphoryl group of the anchor DNA and the T4 DNA ligase are required to transfer RNA to the PDMS surface and that there is no detectable level of nonspecific adsorption of RNA on the PDMS.

FIGURE 23 a is an image of a fluorescence micrograph obtained from a PDMS replica surface after hybridization of DA and RP onto the master DNA template, ligation, transfer of the DNA/RNA conjugate to PDMS, and subsequent hybridization of a fluorescently labeled target (DNA I, Table 3) complementary to the RNA sequence (but not to the sequence of anchor DNA). FIGURES 23b-23e are images of a fluorescence micrograph prepared the same as FIGURE 23 a, but after 2, 3, 17, and 18 iterations. FIGURE 23f is a graph of the fluorescence intensity profiles obtained along the dotted white lines shown in FIGURES 23a-23e. FIGURE 23g is a scheme illustrating the approach used to obtain the data in FIGURES 23a-23f. The star symbols represent the fluorescent dye. The integration time was 100 ms. The gray scale was 1800-5000 counts for FIGURES 23a-23e.

Multiple transfers of ligated RNA strands from a single master to different replica surface were demonstrated using the approach shown in FIGURE 23g. In contrast to the results shown in FIGURES 20 and 22, the surface ligase reaction here was carried out using unlabeled probe RNA (RP I; Table 3), and consequently the resulting master surface is not fluorescent. However, after transfer of the nonfluorescent and ligated RNA strands, the PDMS surface was exposed to fluorescently labeled target DNA (Target DNA I; Table 3) complementary to the probe RNA sequence but not to the anchor DNA.

FIGURE 23 a is an image of a fluorescence micrograph obtained from a PDMS surface after the ligation, transfer, and hybridization steps. The presence of the bright spots indicates that the unlabeled RNA sequence transferee! to the replica surface, and that the RNA is functional; that is, it is able to bind fluorescently labeled complementary DNA. Control analogous to those described earlier indicate no detectable level of fluorescence on the PDMS surfaces in the absence of 5'-phosphoryl group of the anchor DNA or the T4 DNA ligase during the ligation step.

FIGURE 24a is a scheme of a control with a fluorescence micrograph image was obtained from a PDMS surface treated identically to that shown in FIGURE 23 a, but in the absence of 5'-phosphoryl group of anchor DNA. Integration time was 100 ms. FIGURE 24b is a scheme of a control with a fluorescence micrograph image was obtained from a PDMS surface treated identically to that shown in FIGURE 23a, but in the absence of the T4 DNA ligase. Integration time was 100 ms. FIGURE 24c is a graph of the fluorescence intensity profiles obtained along lines on the fluorescence micrographs described in FIGURES 24a and 24b. Fluorescence intensity profile along the dotted white line shown in FIGURE 23 a is included as the top intensity profile for comparison.

This fabrication cycle, includes ligation, transfer, and hybridization with labeled, complementary DNA was repeated a total 18 times using the same master. Images of the micrographs corresponding to the first, second, third, seventeenth, and eighteenth cycles are presented in FIGURES 23a-23e, respectively. As shown in the fluorescence line scans in FIGURE 23 f, the contrasts in fluorescence between the light and dark areas on the surfaces of these replicas were 1860 ± 130, 2070 ± 180, 2310 ± 90, 2120 ± 180, and 2460 ± 530 counts, respectively. These indicate that there is no significant or progressive degradation of the master up to the eighteenth round of replication. The master slide was stable, and produced replicas indistinguishable from those shown in FIGURE 23, for more than 1 month when stored in dark and dry conditions.

The present invention also provides for large-scale RNA microarrays of a single probe RNA sequence (RP I; Table 3) using the hybridization, ligation, and transfer steps of FIGURE 23. For example, a master DNA array having 2500 spots (-70 μm-diameter) of template DNA I (Table 3) was fabricated using a robotic microarrayer. The T4 DNA ligase reaction was performed on the master surface using unlabeled probe RNA (RP I; Table 3) as shown in FIGURE 23g. Finally, the ligated RNA strands were transferred to a PDMS surface.

FIGURE 25 is an image of a fluorescence micrograph obtained from an RNA microarray (PDMS surface), which was fabricated using a master DNA array (DT I) having 2500 micro-scale spots (nominally 70 μm in diameter). For clarity, only 121 of the 2500 spots are shown. The data were obtained after hybridization of DA and RP onto the master DNA template, ligation, transfer of the DNA/RNA conjugate to PDMS, and subsequent hybridization of a fluorescently labeled target (DNA I, Table 3) complementary to the RNA sequence (but not to the sequence of anchor DNA). RNA microarrays having multiple probe sequences were fabricated using the approach illustrated in FIGURE 23g. A master DNA array having three different template sequences (DT I, DT II, and DT III; Table 3) using a robotic microarrayer. The three different DNA templates were spotted in consecutive rows as shown in FIGURE 26.

FIGURE 26 is an image of a fluorescence micrographs demonstrating fabrication of RNA microarrays from a master DNA array having multiple different DNA template sequences. A master array having three different template sequences (DT I, DT II, and DT III; Table 3) in each repetitive row was fabricated. After ligation and transfer, the PDMS surface was exposed to a mixture of fluorescently labeled DNA targets (Target DNA I and target II; Table 3) complementary to the sequence of each probe RNA (RP I and RP II; Table 3), respectively. FIGURE 26a is an image of a fluorescence micrograph obtained by scanning a part of the PDMS surface after ligation, transfer, and hybridization. FIGURE 26b is an image of a fluorescence micrograph obtained from the PDMS surface using a filter for target DNA I labeled with Cy3. The integration time was 500 ms. Gray scale is 2000- 10000 counts. FIGURE 26c is an image of a fluorescence micrograph of a sample prepared the same as FIGURE 26b, but using a filter for target DNA II labeled with Cy5. The integration time was 500 ms. Gray scale is 200-3000 counts.

After hybridization and ligation of a mixture of unlabeled RNA probes (RP I, RP II, and RP III; Table 3) on the master, the probe RNA strands were transferred to a PDMS replica surface. Finally, the PDMS surface was exposed to a mixture of fluorescently labeled DNA targets (Target DNA I and target DNA II; Table 3) which are complementary to probe RNA I (RP I) and probe RNA II (RP II), respectively. Note that only two different target sequences were introduced on the PDMS surface.

FIGURE 26a is an image of a fluorescence micrograph obtained by scanning a part of the PDMS surface. It shows that the correct, labeled DNA complement hybridized to the appropriate probe RNA sequences, e.g., Cy3-labeled DNA I hybridized with Rp I, Cy5-labeled DNA II hybridized with Rp II, and neither of the labeled DNA targets hybridized with Rp III, as no cross-hybridization was observed.

It is contemplated that any embodiment discussed in this specification can be implemented with respect to any method, kit, devices of the invention, and vice versa. Furthermore, compositions of the invention can be used to achieve methods of the invention.

It will be understood that particular embodiments described herein are shown by way of illustration and not as limitations of the invention. The principal features of this invention can be employed in various embodiments without departing from the scope of the invention. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, numerous equivalents to the specific procedures described herein. Such equivalents are considered to be within the scope of this invention and are covered by the claims.

All publications and patent applications mentioned in the specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

The use of the word "a" or "an" when used in conjunction with the term "comprising" in the claims and/or the specification may mean "one," but it is also consistent with the meaning of "one or more," "at least one," and "one or more than one." The use of the term "or" in the claims is used to mean "and/or" unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and "and/or." Throughout this application, the term "about" is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.

As used in this specification and claim(s), the words "comprising" (and any form of comprising, such as "comprise" and "comprises"), "having" (and any form of having, such as "have" and "has"), "including" (and any form of including, such as "includes" and "include") or "containing" (and any form of containing, such as "contains" and "contain") are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. The term "or combinations thereof as used herein refers to all permutations and combinations of the listed items preceding the term. For example, "A, B, C, or combinations thereof is intended to include at least one of: A, B, C, AB, AC, BC, or ABC, and if order is important in a particular context, also BA, CA, CB, CBA, BCA, ACB, BAC, or CAB. Continuing with this example, expressly included are combinations that contain repeats of one or more item or term, such as BB, AAA, MB, BBC, AAABCCCC, CBBAAA, CABABB, and so forth. The skilled artisan will understand that typically there is no limit on the number of items or terms in any combination, unless otherwise apparent from the context.

All of the compositions and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims. References

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Claims

CLAIMS: 1. A method for replicating an array of single- stranded nucleic acids on a solid support comprising the steps of: a) synthesizing an array of one or more nucleic acids each comprising a non- variant sequence of length C at a 3'-terminus and a variable sequence of length R at a 5'-terminus; b) fixing the array to a first solid support; c) synthesizing a set of nucleic acids each comprising a sequence complementary to the non- variant sequence; d) hybridizing the nucleic acids of the set of nucleic acids to the array of one or more nucleic acids; e) enzymatically extending the set of one or more nucleic acids using the variable sequences of the array as templates; f) fixing the enzymatically extended set of one or more nucleic acids to a second solid support; and g) mechanically separating the first and second solid supports and their attached single- stranded nucleic acids to create the replicated array of single-stranded nucleic acids.

2. A method for replicating an array of single- stranded nucleic acids on a solid support comprising the steps of: synthesizing an oligonucleotide array of a first set of one or more nucleic acids; fixing the oligonucleotide array to a first solid support; forming a complement set of one or more nucleic acids that hybridize to the first set of one or more nucleic acids; fixing the complementary set of one or more nucleic acids to a second solid support; mechanically separating the first set of one or more nucleic acids and complementary set of one or more nucleic acids to create a replicated array of single-stranded nucleic acids.

3. The method of claim 2, wherein the complement set of one or more nucleic acids are formed by adding one or more primers that at least partially hybridize to a portion of the first set of one or more nucleic acids and extending enzymatically the complement set of one or more nucleic acids using a polymerase and the set of one or more nucleic acids as a template.

4. The method of claim 2, wherein the polymerase is a T4 polymerase.

5. The method of claim 2, wherein the complement set of one or more nucleic acids are formed by adding a two or more complementary sequences and ligasing the two or more complementary sequences.

6. The method of claim 2, wherein the first substrate comprises porous glass, non-porous glass, silicon, silicon dioxide, silicon nitride, one or more metals, one or more polymers, one or more plasties, one or more resins, one or more ceramics, one or more gels, one or more beads, one or more semiconductors and a combination thereof.

7. The method of claim 2, wherein the one or more nucleic acids comprise a variant sequences.

8. A method of replicating an oligonucleotide array comprising the steps of: hybridizing one or more biotin- functionalized oligonucleotides to one or more oligonucleotides on a first substrate; and capturing the one or more biotin-functionalized oligonucleotides with streptavidin attached to a second substrate.

9. The method of claim 8, further comprising the step of separating the one or more biotin- functionalized oligonucleotides to one or more oligonucleotides by mechanical force to form a replicated array.

10. The method of claim 8, wherein the first substrate comprises porous glass, non-porous glass, silicon, silicon dioxide, silicon nitride, one or more metals, one or more polymers, one or more plastics, one or more resins, one or more ceramics, one or more gels, one or more beads, one or more semiconductors and a combination thereof.

11. The method of claim 8, wherein the first substrate comprises an oligonucleotide chip surface.

12. The method of claim 8, wherein the one or more oligonucleotides comprise variant sequences.

13. The method of claim 8, wherein the one or more oligonucleotides are single-stranded.

14. The method of claim 8, wherein the one or more oligonucleotides, the one or more biotin- functionalized oligonucleotides or both are connected to a linker.

15. The method of claim 8, wherein the one or more biotin-functionalized oligonucleotides comprise a code sequence complementary to one of the one or more oligonucleotides and a biotin modification.

16. The method of claim 8, wherein the one or more biotin-functionalized oligonucleotides further comprises a fluorescent tag.

17. The method of claim 8, wherein the one or more oligonucleotides comprise DNA, RNA, PNA and a combination thereof.

18. An oligonucleotide array replication system comprising: a first substrate comprising an oligonucleotide array; a second substrate having streptavidin attached thereto to capture one or more biotin- functionalized oligonucleotides; and a biotin-functionalized oligonucleotides library, wherein the first substrate and the second substrate can be separated.

19. The system of claim 18, wherein the first substrate, the second substrate or both comprise glass, one or more metals, one or more polymers, one or more beads and a combination thereof.

20. The system of claim 18, wherein the first substrate, the second substrate or both comprises an oligonucleotide chip surface.

21. The system of claim 18, wherein the oligonucleotide array comprises variant sequences.

22. The system of claim 18, wherein the oligonucleotides array, the one or more biotin- functionalized oligonucleotides or both are connected to a linker.

23. The system of claim 18, wherein the one or more biotin- functionalized oligonucleotides comprise a code sequence complementary to one of the one or more oligonucleotides and a biotin modification.

24. The system of claim 18, wherein the one or more biotin- functionalized oligonucleotides further comprises a fluorescent tag.

25. An oligonucleotide array replication kit comprising: a first substrate comprising streptavidin to capture one or more biotin-functionalized oligonucleotides, wherein an oligonucleotide array can be used to prepare oligonucleotide replicates that retains the positioning of the positioned anywhere on the oligonucleotide array.

26. The kit of claim 25, further comprising one or more oligonucleotides attached to a second substrate.

27. The kit of claim 25, wherein the first substrate comprises glass, one or more metals, one or more polymers, one or more beads and a combination thereof.

28. The kit of claim 25, wherein the first substrate comprises an oligonucleotide chip surface.

29. The kit of claim 25, wherein the one or more biotin-functionalized oligonucleotides comprise variant sequences.

30. The kit of claim 25, wherein the one or more biotin-functionalized oligonucleotides are single-stranded.

31. The kit of claim 25, wherein the one or more oligonucleotides, the one or more biotin- functionalized oligonucleotides or both are connected to a linker.

32. The kit of claim 25, wherein the one or more biotin-functionalized oligonucleotides comprise a code sequence complementary to one or more oligonucleotides and a biotin modification.

33. The kit of claim 25, wherein the one or more biotin-functionalized oligonucleotides further comprises a fluorescent tag.

34. The kit of claim 25, wherein the one or more oligonucleotides comprise DNA, RNA, PNA and a combination thereof.

35. A method of replicating oligonucleotide arrays comprising the steps of: attaching one or more oligonucleotides onto a first substrate; hybridizing the one or more oligonucleotides to one or more biotin-functionalized oligonucleotides; capturing the one or more biotin-functionalized oligonucleotides with streptavidin attached to a second substrate; and separating the array surface and the replication array.

36. The method of claim 35, further comprising the step of separating the first substrate and the second substrate by mechanical force to form a replicated array.

37. The method of claim 35, wherein the one or more biotin-functionalized oligonucleotides comprise a code sequence complementary to one of the one or more oligonucleotides and a biotin modification.

38. The method of claim 35, wherein the one or more biotin-functionalized oligonucleotides further comprises a fluorescent tag.

39. The method of claim 35, wherein the one or more oligonucleotides comprise DNA, RNA, PNA and a combination thereof.

40. A method for replicating an array of single-stranded nucleic acids on a solid support comprising the steps of: hybridizing one or more biotinylated nucleic acids to a nucleic acid set imobilized on a nucleic acid array; extending the one or more biotinylated nucleic acids using the nucleic acid set as a template; capturing the one or more biotinylated nucleic acids with streptavidin attached to a substrate, wherein the spatial registration of the nucleic acid set is replicated; and mechanically separating the substrate and the nucleic acid array.

41. The method of claim 40, wherein a T4 polymerase is used to extended the one or more biotinylated nucleic acids; 42. The method of claim 40, wherein the substrate is a streptavidin-coated PDMS monolith..