CA2292896A1 - Attachment of unmodified nucleic acids to silanized solid phase surfaces - Google Patents

Abstract

The invention relates to a simple, cost effective method for immobilizing synthetic nucleic acid molecules onto a solid support. The invention further concerns the use of such immobilized molecules in nucleic acid hybridization assays, sequencing by hybridization assays, and genetic analyses and combinatorial analyses involving nucleic acids or proteins for screening applications.

Description

TITLE OF THE INVENTION:
ATTACHMENT OF UNMODIFIED NUCLEIC ACIDS TO
SILANIZED SOLID PHASE SURFACES
F1ELD OF THE INVENT10N:
The invention relates to a simple, and preferably cost effective, method for immobilizing nucleic acid molecules onto a solid support The invention further concerns the use of such immobilized molecules in nucleic acid hybridization assays, sequencing by hybridization assays, and genetic analyses and combinatorial analyses involving nucleic acids or proteins for screening applications BACKGROUND OF THE INVENTION:
The analysis of the structure, organization and sequence of nucleic acid molecules is of profound importance in the prediction, diagnosis and treatment of human and animal disease, in forensics, in epidemiolo~~y and public health, and in the elucidation of the factors that control gene expression and development Methods for immobilizing nucleic acids are often important in these types of analyses Three areas of particular importance involve hybridization assays, nucleic acid sequencing, and the analysis of genomic polymorphisms I. Nucleic Acid Hybridization The capacity of a nucleic acid "probe" molecule to hybridize (i a base pair) to a complementary nucleic acid "target" molecule forms the cornerstone for a wide array of diagnostic and therapeutic procedures Hybridization assays are extensively used in molecular biology and medicine Methods of performing such hybridization reactions are disclosed by, for example, Sambrook, J. et al. (In. Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1989)), Haymes, B.D , et al. (In Nucleic Acid Hybridization~ A Practical Approach, IRL Press, Washington, DC (1985)) and Keller, G.H and Manak, M M (In. DNA Probes, Second Edition, Stockton Press, New York, NY (1993)) which references are incorporated herein by reference Many hybridization assays require the immobilization of one component.
Nagata et al described a method for quantifying DNA which involved binding SUBSTITUTE SHEET (RULE 26~

n

-2-unknown amounts of cloned DNA to microtiter wells in the presence of 0 1 M
MgCl2 (Nagata et al , FEBS Letters 1 ~ 3 379-382, 1985) A complementary biotinylated probe was then hybridized to the DNA in each well and the bound probe measured colorimetrically Dahlen, P et al. have discussed sandwich hybridization in microtiter wells using cloned capture DNA adsorbed to the wells (Dahlen, P et al , Mol.
Cell.
Probes 1. 159-16S, 1987) An assay for the detection of HIV-1 DNA using PCR
amplif cation and capture hybridization in microtiter wells has also been discussed (Keller, G H et al , J. Clin. Microbiol 29 638-641, 1991) The NaCI-mediated binding of oliwomers to polystyrene wells has been discussed by Cros et al (French patent no 2,663,040) and very recently by Nikiforov et al (PCR Methods A~plic

3 285-291, 1994) The cationic deterrent-mediated binding of oligomers to polystyrene wells has very recently been described by Nikiforov et al , Nucleic Acids Res I1. Analysis Of Single Nucleotide DNA Polymorhhisms Many genetic diseases and traits (i a hemophilia, sickle-cell anemia, cystic fibrosis, etc ) reflect the consequences of mutations that have arisen in the genomes of some members of a species through mutation or evolution (Gusella, J F , Ann.
Rev.
Biochem. 55 831-854 (1986)) In some cases, such polymorphisms are Linked to a genetic locus responsible for the disease or trait, in other cases, the polymorphisms are the determinative characteristic of the condition Such single nucleotide polymorphisms differ si~,nificantly from the variable nucleotide type polymorphisms ("VNTRs"), that arise from spontaneous tandem duplications of di- or tri-nucleotide repeated motifs of nucleotides (Weber, J
L., U S
Patent 5,075,217, Armour, J A L et al., FEBS Lett. 307 113-115 (1992), Jones, L et al., Eur. J. Haematol. 39 144-147 (1987), Horn, G T et al., PCT Application W091/14003, Jeffreys, A J., U S Patent 5,175,082), Jeffreys A J et al., Amer.
J.
Hum. Genet. 39.11-24 (1986), Jef~reys A.J et al., Nature 316'76-79 (1985), Gray, LC et al., Proc. R. Acad. Soc. Lond. 243 241-253 (1991), Moore, S S et al., Genomics 10.654-660 (1991), Jeffreys, A.J et al., Anim. Genet. 18 1-15 (1987), Hillel, J et al., Anim. Genet. 20 145-155 (1989), Hillel, J et al., Genet. 124 783-789 (1990)), and from the restriction fragment length polymorphisms ("RFLPs") that comprise SUBSTITUTE SHEET (RULE 2f) variations which alter the lengths of the fragments that are generated by restriction endonuclease cleavage (Glassberg, 3 , UK patent application 2135774, Skolnick, M H
et al., Cvtog_en Cell Genet. 32 58-67 (1982), Botstein, D et al., Ann. J. Hum.
Genet.
32.314-331 (1980), Fischer, S G et al. (PCT Application W090/13668), Uhlen, M
, PCT Application W090/I 1369)) Because single nucleotide polymorphisms constitute sites of variation flanked by regions of invariant sequence, their analysis requires no more than the determination of the identity of the single nucleotide present at the site of variation, it is unnecessary to determine a complete gene sequence for each patient Several methods have been developed to facilitate the analysis of such single nucleotide polymorphisms Mundy, C R (U S Patent No 4,656,127), for example, discusses a method for determining the identity of the nucleotide present at a particular polymorphic site that employs a specialized exonuclease-resistant nucleotide derivative A primer complementary to the allelic sequence immediately _~' to the polymorphic site is I S permitted to hybridize to a target molecule obtained from a particular animal or human If the polymorphic site on the tarjet molecule contains a nucleotide that is complementary to the particular exonuclease-resistant nucleotide derivative present, then that derivative will be incorporated onto the end of the hybridized primer Such incorporation renders the primer resistant to exonuclease, and thereby permits its detection Since the identity of the exonuclease-resistant derivative of the sample is known, a finding that the primer has become resistant to exonucleases reveals that the nucleotide present in the polymorphic site of the target molecule was complementary to that of the nucleotide derivative used in the reaction The Mundy method has.
the advantage that it does not require the determination of large amounts of extraneous sequence data It has the disadvantages of destroying the amplified target sequences, and unmodified primer and of being extremely sensitive to the rate of polymerise incorporation of the specific exonuclease-resistant nucleotide being used Cohen, D et al (French Patent 2,650,840, PCT Appln No W091/02087) discuss a solution-based method for determining the identity of the nucleotide of a polymorphic site As in the Mundy method of U.S Patent No 4,656,127, a primer is employed that is complementary to allelic sequences immediately 3' to a polymorphic site The method determines the identity of the nucleotide of that site using labeled dideoxynucleotide derivatives, which, if complementary to the nucleotide of the polymorphic site will become incorporated onto the terminus of the primer SUBSTITUTE SHEET (RULE 26) WO 98/55593 PCT/US98i11662 _4_ An alternative method, known as Genetic Bit AnalysisT"' or GBA''~'' is described by Goelet, P et al (PCT Appln No 92/1 x712) The method of Goelet, P et al uses mixtures of labeled terminators and a primer that is complementary to the sequence 3' to a polymorphic site The labeled terminator that is incorporated is thus determined by, and complementary to, the nucleotide present in the polymorphic site of the target molecule being evaluated In contrast to the method of Cohen et al (French Patent 2,650,840, PCT Appln No W091/02087) the method of Goelet, P et al is preferably a heterogeneous phase assay, in which the primer or the target molecule is immobilized to a solid phase It is thus easier to perform, and more accurate than the method discussed by Cohen Cheesman, P (U S Patent No S, 302,509) describes a method for sequencing a single stranded DNA molecule using fluorescently labeled 3'-blocked nucleotide triphosphates An apparatus for the separation, concentration and detection of a DNA
molecule in a liquid sample has been recently described by Ritterband, et al.
(PCT
1 _S Patent Application No W095/17676) An alternative approach, the "Oligonucleotide Li<~ation Assay" ("OLA") (Landegren, U. et al., Science 241 1077-1080 (1988)) has also been described as capable of detecting single nucleotide poiymorphisms The OLA protocol uses two oligonucleotides which are designed to be capable of hybridizing to abutting sequences of a single strand of a target One of the oligonucleotides is biotinylated, and the other is detectably labeled If the precise complementary sequence is found in a tar=et molecule, the oli~,onucleotides will hybridize such that their termini abut, and create a ligation substrate Ligation then permits the labeled oligonucleotide to be recovered using avidin, or another biotin ligand Nickerson, D A et al. have described a nucleic acid detection assay that combines attributes of PCR and OLA (Nickerson, D A
et al., Proc. Natl. Acad. Sci. (U.S.A.) 87 8923-8927 (1990) In this method, PCR is used to achieve the exponential amplification of target DNA, which is then detected using OLA In addition to requiring multiple, and separate, processing steps, one problem associated with such combinations is that they inherit all of the problems associated with PCR and OLA
Recently, several primer-guided nucleotide incorporation procedures for assaying polymorphic sites in DNA have been described (Komher, J S et al , Nucl.
Acids. Res. I7 7779-7784 (1989); Sokolov, B P , Nucl. Acids Res. 18 3671 (1990), Syvanen, A -C , et al , Genomics 8'684 - 692 ( 1990), Kuppuswamy, M N et al , Proc.
SUBSTITUTE SHEET (RULE 26) __ _._ ~_~~.- ~ ._. .

Natl. Acid. Sci. ~U.S.A.) 88 1143-1147 (1991), Prezant, T R. et al , Hum.
Mutat.
1 ~ 159-164 (1992), Ugozzoli, L et al , GATA 9 107-1 12 ( 1992), Nyren, P et al , Anal.
Biochem. 208 171-175 (1993)) These methods differ from GBAT"' in that they all rely on the incorporation of labeled deoxynucleotides to discriminate between bases at a polymorphic site In such a format, since the signal is proportional to the number of deoxynucleotides incorporated, polymorphisms that occur in runs of the same nucleotide can result in signals that are proportional to the length of the run (Syvanen, A -C , et al , Amer. J. Hum. Genet. 52 46-59 (1993)) Such a range of locus-specific signals could be more complex to interpret, especially for heterozygotes, compared to the simple, ternary (2 0, 1 l, or 0 2) class of signals produced by the GBA"' method In addition, for some loci, incorporation of an incorrect deoxynucleotide can occur even in the presence of the correct dideoxynucleotide (Komher, J S et al , Nucl.
Acids. Res. 17 7779-7784 ( 1989)). Such deoxynucleotidemisincorporation events may be due to the Km of the DNA polymerise for the mispaired deoxy-substrate being comparable, in some sequence contexts, to the relatively poor Km of even a correctly base paired dideoxy-substrate (Kornberg, A , et al , In DNA Replication, Second Edition (1992), W H Freeman and Company, New York, Tabor, S et al , froc.
Natl.
Acid. Sci. (U.S.A~ 86'4076-4080 (1989)) This effect would contribute to the background noise in the polymorphic site interrogation III. Methods of Immobilizing Nucleic Acids to a Solid Phase Several of the above-described methods involve procedures in which one or more of the nucleic acid reactants are immobilized to a solid support Currently, 96-well polystyrene plates are widely used in solid-phase immunoassays, and several PCR
product detection methods that use plates as a solid support have been described The most specific of these methods require the immobilization of a suitable oligonucleotide probe into the microtiter wells followed by the capture of the PCR product by hybridization and colorimetric detection of a suitable hapten It would be desirable to have an improved immobilization method that could be used to bind oligonucleotides to polystyrene such that their capacity to be used for hybridization, sequencing, or polymorphic analysis would be retained, and which would be rapid, convenient to use and inexpensive The present invention provides such in improved method The means by which macromolecules bind non-covalently to polystyrene and glass surfaces is not well understood Nevertheless, these adsorption phenomena have SUBSTITUTE SHEET (RULE 26) proven to be important in the development and manufacturing of immunoassays and other types of diagnostic tests where one component needs to be immobilized Polystyrene is a very hydrophobic material because it normally contains no hydrophilic groups Microtiter plate manufacturers have developed methods of introducing such groups (hydroxyl, carboxylate and others) onto the surface of microwells to increase the hydrophilic nature of the surface Theoretically, this allows macromolecules to bind through a combination of hydrophobic and hydrophilic interactions (Baier et al , Science 162 1360-1368 ( 1968), Baier et al , J.
Biomed.
Mater. Res lb 335-355 (1984), Good et al , in L H Lee (ed ) Fundamentals of Adhesion, Plenum, New York, chapter 4 ( 1989)) (Figure 1 ) In practice, some proteins do bind more efficiently to the treated hydrophilic pt~lystyrene than to the untreated material Covalent binding to polystyrene, especially microtiter wells, has however proven to be difficult, so passive adsorption remains the most commonly used method of binding macromolecules to such wells The term "polystyrene" may also be used to describe styrene-containing copolymers such as styrene/divinyl benzene, styrene/butadiene, styrene/vinyl benzyl chloride and others While polystyrene is an organic hydrophobic substrate, glass provides an inorganic hydrophilic surface The most common glass format in immunoassays is the microscope slide Laboratory-grade glasses are predominantly composed of Si02, but they also may contain B203, A1~0~ as well as other oxides (Figure 2) Interfaces involving such materials have thus become a dynamic area of chemistry in which surfaces have been modified in order to generate desired heterogeneous environments or to incorporate the bulk properties of different phases into a uniform composite structure Our purpose here then is to use organosilanes for tailoring surfaces with chemically reactive groups mercapto (SH) and/or epoxy While numerous methods for the attachment of oligonucleotides and proteins on surfaces have been described, the methods are both expensive and time consuming The reported covalent attachments of pre-made oligonucleotides onto modified glass surfaces have been always using modified oligonucleotides in order to increase reactivity and selectivity of oligonucleotides towards surfaces Typical modifications involved the introduction of amino groups, or thio groups into 3'- and/or 5'-oligonucleotides For example, Stimpson et al. (P.N.A..S. 926379-6383 (1995)) reported covalent attachment of 3'-amino oligonucleotides onto epoxy silanized surfaces with acid catalysis but with only 1/10 the density achieved in this invention SUBSTITUTE SHEET (RULE 26) _... ___._.~....~.

-7_ Beanie et al (C:lirr. C.'herrr 41 700-706 ( 1995)) reported attachment of 3'-and/or 5'-amino oli~onucleotides onto epoxy silanized surfaces under elevated temperature Lamture et al (Nucleic Acids Res. 22 2121-2125 (1994)) reported the methods for attaching 3'-amino-oligonucleotides onto epoxy silanized slides under 0 1 M
KOH
Hetero bifunctional cross-linkages have been used to couple the 3' or 5'-thio-modified oligonucleotides or aminoanodified onto amino-propyl silanized surfaces as reported by Chrisey et al (Nucleic Acids Reas 24 303103039 (1996)) and Guo et al (Nucleic Acids Res 22 4556-5465 ( 1994)) All of these reported methods however, require modified oli~onucleotides The present invention describes a novel method for immobilizing nucleic acid molecules to a solid-phase by means of a covalent ether or thioether linkage This simple, two-step method has the specificity and efficiency needed to prepare DNA
arrays.
SUMMARI' OF THE 1N'VENTION:
The present invention provides an improved immobilization method that permits the rapid, and inexpensive immobilization of nucleic acid molecules to a solid phase The invention allows immobilization of oligonucleotides by incubation with a siiane-containin~ or silane-treated solid phase The immobilized molecules can be used for nucleic acid hybridization assays, sequencing hybridization assays, genetic analyses, combinatorial analyses involving nucleic acids or proteins, and other screening applications such as protein-DNA binding assays In detail, the invention provides a method for immobilizing a nucleic acid molecule to a solid phase, the method comprising the steps of (A) coating said solid phase with a silane and allowing said silane-coated solid phase to cure; and (B) coupling unmodified nucleic acid molecules having either a terminal 3' OH or a terminal S' OH to said silane-coated solid phase The invention particularly concerns the embodiments of the above method wherein, in step A, the silane is selected from the group consisting of 3-mercapto-propyl-trimethoxysilane and 3-glycidoxy propyl-trimethoxysilane SUBSTITUTE SHEET (RULE 26) _g_ The invention further pertains to oligonucleotide coated surfaces useful in genetic analysis and other screening applications such as protein-DNA bindin~, assays The invention particularly concerns oligonucleotide arrays comprising epoxy-or mercapto-silane coated surfaces and unmodified oligonucleotides covalently attached to the epoxy or mercapto-silane, such arrays being useful for nucleic acid hybridization assays, sequencing hybridization assays, genetic analyses, combinatorial analyses involving nucleic acids or proteins, and other screening applications such as protein-DNA binding assays The features of the coated surface enable standardized patterning of unique oligonucleotides onto silane surface coatings The invention further pertains to simultaneous patterning of multiple DNA
probes in a high density and in a variety of array formats DETAILED DESCRIPTION OF THE INVENTION:
I. The Immobilization of Nucleic Acid Molecules The present invention concerns a method for immobilizing nucleic acid molecules onto a solid-phase Recently, several methods have been proposed as suitable for immobilizing an oligonucleotide to a solid support Holmstrom, K
et al., for example, exploit the affinity of biotin for avidin and streptavidin, and immobilize biotinylated nucleic acid molecules to avidin/streptavidin coated supports (Hohnstrom, K et al., Anal. Biochem. 209 278-283 ( 1993)) Another method requires the precoating of the polystyrene or glass solid phases with poly-L-Lys or poly L-Lys, Phe, followed by the covalent attachment of either amino- or sulfhydryl-modified oligonucleotides using bi-functional crosslinking reagents Unlike the present invention, both methods require the use of modified oligonucleotides as well as a pretreatment of the solid phase, however, the present invention discloses a method to covalently bond oligonucleotides with an "unmodified" 5' or 3' -OH to a solid surface As used herein, the term "unmodified" refers to the absence of any requirement for specialized reactive groups It does not refer to the exclusion of nucleotides or oligonucleotides that have such groups, or that are biotinylated, flouresceinated, etc Kawai, S. et al describes an alternative method in which short oligonucleotide probes were Iigated together to form multimers and these were ligated into a phagemid vector (Kawai, S et al., Anal. Biochem. 209 63-69 (1993)) The oligonucleotides SUBSTITUTE SHEET (RULE 26) T..~.- ~..~.~....

_g_ were immobilized onto polystyrene plates and fixed by UV irradiation at 254 nm A
method for the direct covalent attachment of short, 5'-phosphorylated primers to chemically modified polystyrene plates ("Covalink" plates, Nunc) has also been proposed by Rasmussen, S R et al., (Anal. Biochem. 198 138-142 (1991)) The covalent bond between the modified oligonucleotide and the solid phase surface is created by a condensation reaction with a water-soluble carbodimide The Rasmussen method claims a predominantly 5'-attachment of the oli<~onucleotides via their 5'-phosphates, however, it requires the use of specially prepared, expensive plates The method of the present invention departs from such methods, in not requiring such unstable and difficult to manipulate crosslinking reagents Maskos, U et al. describes a method to synthesize oligonucleotides directly onto a glass support (Maskos, U et al., Nucl. Acids Res. 20 1679-1684 (1992)) According to this method, a flexible linker with a primary hydroxyl group is bound to the solid support via a glycidoxypropyl silane, wherein the primary hydroxyl group serves as the starting point for the oligonucleotide synthesis Numerous methods for the attachment of oligonucleotides and proteins on surfaces have been described The reported covalent attachments of pre-made oligonucleotides onto glass surfaces have been always using modified oligonucleotides in order to increase reactivity and selectivity of oligonucleotides towards surfaces Typical modifications involved the introduction of amino groups, or thio groups into 3'-and /or 5'- amino modified oligonucleotides onto epoxy surfaces Stimpson et a1.
(P.N.A.S. 92 6379-6383 (1995)) discloses the generation of DNA chips for use in automated DNA diagnostic applications To this effect, the Stimpson article discloses the immobilization of 3' amino-linked oligonucleotides into an organized array on a glycidoxypropyl silane treated glass slide Lamture et al. (N~rclc~ic Acids Res. 22 2121-2125 (1994)) describes the immobilization of 3' amino modified oligonucleotides to a 3-glycidoxypropyl-trimethoxysilane coated silicon wafer in the presence of 0 1 M KOH The oligonucleotides are covalently immobilized to the solid support by means of a secondary amine linkage Beattie et al. (Clrrr. Chem. -ll 700-706 ( 1995)) discloses the immobilization of either 3' and/or 5' amino modified oligonucleotides to 3-glycidoxypropyltrimethoxysilane coated glass slides at a temperature of 60° C
Additionally, several other references generally related to the immobilization of oligonucleotides to a solid-support. Chrisey et al. (Nucleic Acids Res.
2.13031-3039 SUBSTITUTE SHEET (RULE 26) ( 1996), Guo et al. (Nucleic Aciu'.~~ R~.~~. 2? 45456-5465 ( I 994), Fahy et al. (Nucleic Acids Res. 211819-1826 (1993), Sliwkowski et a1. (liiochenr. .l. 209 731-739 (1983) all disclose the immobilization of a 5' or 3' modified oligonucleotide to a solid-support The method of the present invention provides three distinct advantages over other covalent attachment chemistries for oligonucleotide array preparation First, while the above-identified prior art references require that the oiigonucleotide be either amino or thiol modified, the present invention discloses a method to covalently bond oligonucleotides with an "unmodified" 5' or 3' -OH to a solid surface The present invention thus differs from conventional methods for the covalent attachment of oligonucleotides to solid phases in that it permits the covalent attachment of "unmodified" oligonucleotides Accordingly, the present invention provides several significant improvements over the prior art In particular, the present invention provides a low-cost, stable method for the covalent attachment of "unmodified"
oligonucleotides to a silanized solid-phase wherein the covalently bound oligonucleotides have wide uses in genetic and combinatorial analysis involving nucleic acids or proteins Covalent attachment of oligonucleotides onto solid phase surfaces is therefore achieved without modification of oligonucleotides, thereby dramatically reducing the cost and eliminating the variation in quality of modified oligonucleotides Second, the silanized surface of the present method provides a very hydrophobic surface which allows oligonucleotide probe droplets to form at specific and localized positions on the solid surface Thus, for example, multiple probes can be patterned simultaneously on the surface using, for example, a robotic liquid delivery system or an ink jet printing technique with no cross contamination between probes, even at a high probe density ( 10,000 probes/cm2) Accordingly, the process can be easily automated and scaled-up using an off the-shelf robot or ink jet printing instrument Standard covalent attachment chemistries require the use of photolithographic and laser patterning techniques which require multiple masking and lifting steps for high density DNA array preparation Third, unlike traditional techniques, the present method does not require the use of expensive crosslinking agents These crossiinking agents are difficult to use because of their sensitivity to air and humidity Therefore, the present method provides a new, efFrcient and inexpensive method for DNA array preparation, and particularly for large scale DNA array preparation SUBSTITUTE SHEET (RULE 26) _~_..._ ~...... ...

-ll-In the preferred embodiment, this invention describes a method for immobilizing nucleic acids on silane coated solid phase surfaces which is useful in genetic analysis and other screening applications such as protein-DNA binding assays. The invention pertains to oligonucleotide arrays comprising silane coated solid phase surfaces and unmodified or modified oligonucleotides covalently attached to the silane coated solid phase, such arrays being useful for genetic analyses and combinatorial analyses involving nucleic acids or proteins The features of the coated surface enable standardized patterning of unique oligunucleotides onto silane surface coatings In the most preferred embodiment, the invention provides for methods of covalent attachment of unmodified oligonucleotides onto mercapto-silanized surface or epoxy-silanized surfaces with high density and high stability The ease of preparation of unmodified oligonucleotides coupled with stable ether (epoxy) or thio-ether (mercapto) linkage attachments renders this method the most cost effective, with little or no variation in terms of the quality of oligonucleotides, stability of attachment linkage and consistency in large scale batch to batch manufactures Additionally, the hydrophobic property of silane surfaces also allows simultaneous patterning of multiple DNA probes in a high density and in a variety of array formats Furthermore, a DNA
array that is stable to high salt and denaturing conditions such as DMF, urea and elevated temperatures, has wide uses in miniaturized biotechniques such as genetic testing, sequencing by hybridization and combinatory selection of DNA binding molecules The covalent attachment of the present invention can be distinguished from other means of attachment, such as van der Waals interaction and ion-ion interactions Thus, unlike other attachment means, the covalently immobilized oligonucleotide will not be released from the solid-phase during subsequent wash steps The covalent attachment generally provides more stable binding than noncovalent attachment under elevated temperatures and upon other chemical treatment, thus, giving more flexibility for use in biochemical processes II. The Immobilization of Nucleic Acid Molecules Using Epoxy Chemistry In a preferred embodiment of the present invention, a selective, highly efficient method is provided which employs an epoxy-based attachment chemistry to covalently attach nucleic acid molecules in an end selective manner to a solid-phase Oligonucleotides have two free hydroxyl groups at the 5'- and 3'- ends which allow SUBSTITUTE SHEET (RULE 26) oligonucleotides to undergo chemical and/or enzymatic elongation, ligation and circularization The differences in steric hindrances between these two end hydroxyl groups have enabled 5'-selective esterification, 5'-selective tritylation and 5'- selective oxidation in controlled conditions Unmodified oligonucleotides for attachment to solid phases under certain controlled conditions thus have the potential for the 5'-OH to react preferentially over the 3'-OH towards epoxy activated surfaces End-selective attachment is achieved in epoxy chemistry by taking advantage of differences in steric hindrance between the 5' and 3' end of the oligonucleotide Accordingly, one could block either terminus (via phosphorylation, etc ) and therefore obtain a directionally oriented attachment between the solid phase and the unblocked terminus The covalent bond described in the epoxy-based preferred embodiment of the present invention is a covalent ether linka~,e End selective attachment ensures that the full sequence of the immobilized oligonucleotide is accessible for any desired biochemical reaction. Since there is no need for any modification of oligonucleotides, this embodiment dramatically reduces the cost and variation in teens of the quality of oligonucleotides The epoxy-based attachment chemistry allows attachment of all forms of DNA including pcr products or genomic DNA to the silanized surface Furthermore, in the case of epoxy-based attachment chemistry, the chemical bonds between the silane layer and oligonucleotides are covalent ether linkages, which are stable to heat, high salt, and elevated temperatures III. The Immobilization of Nucleic Acid Molecules Using Mercapto Chemistry The present invention describes in another preferred embodiment a random, highly efficient method which employs a mercapto-based attachment chemistry to covalently attach nucleic acid molecules in a non-specific manner to a solid-phase The covalent bond described in this second preferred embodiment of the present invention is a covalent thioether linkage Because this embodiment relies on non-specific binding, the full sequence of the immobilized oli~onucleotide may not be accessible for all desired biochemical reactions Since the mercapto group is very reactive in terms of radical reactions and easily deionized under lower pH (pH
9), this allows a variety of reactions to occur with nucleic acids Heterocyclic purines (electron rich system stabilizing radicals, particularly at position 7 of purines) and pyrimidines (electron deficient, a nucleophile acceptor) in oligonucleotides are good acceptors for SUBSTITUTE SHEET (RULE 26) _ _.~

either nucleophilic attack or radical reactions In mercapto chemistry the highly reactive mercapto groups allow mild conditions for attachment The resulting array can undergo a variety of biochemical reactions and allows hybridization with high efficiency The mercapto-based attachment chemistry allows attachment of all forms of DNA including pcr products or genomic DNA to the silanized surface Furthermore, in the case of mercapto-based attachment chemistry, the chemical bonds between the silane layer and o ligonucleotides are covalent thioether linkages, which are stable to heat, high salt, and elevated temperatures The unmodified nucleic acid molecules, described in the present invention, may be either genomic DNA (i a , DNA containing a non-translated region), cDNA (i a , DNA lacking non-translated regions) or 1NA, the nucleic acid molecule may also be either single or double stranded While any unmodified nucleic acid molecule may be immobilized using the present invention, the preferred nucleic acid molecule of the present: invention is an unmodified single-stranded synthetic oli~Tonucleotide The method for making a synthetic oligonucleotide has been previously described by Gait, M J (Oli~onucleotide Synthesis A Practical Approach IRL Press Ltd , Oxford (1984)) and Sinha, N D et al. (Nucl. Acids Res. i2 4539-4557 (1984)) (herein incorporated by reference) Synthesis of unmodified oligonucleotides of about 10 to about 250 nucleotides in length may be performed on an ABI 392 DNA/RNA synthesizer according to phosphoramidite chemistry After synthesis, the unmodified oligonucleotides can be purified (for example, using an HPLC column) to separate the full-length oli~ronucleotides from any contaminating prematurely terminated (i a , shortened) oligonucleotides Prior to use in the coupling reaction, the oligonucleotides are concentrated, and, if desired, the molar concentration of the oligonucleotides can be determined Although any of a variety of glass or plastic solid supports can be used in accordance with the methods of the present invention, glass is the preferred support The support can be fashioned as a bead, dipstick, test tube, pin column, etc However, an especially preferred support is a glass slide Alternatively, the solid support can be a form of polystyrene plastic (e g , 96-well microtiter plate, etc ) Many different mercaptosilane compounds such as 3-mercapto-propyltrimethoxy-silane, 3-mercaptopropyltriethoxysilane, (mercapto-methyl) dimethoxysilane and (mercaptoethyl)ethyldimethoxysilane, etc can be used in the SUBSTITUTE SHEET (RULE 26) present invention for coating the solid support with sulfhydryl groups The general formula for a mercaptosilane that can be used in this invention is HS(CH2)"-SiX~
wherein X is a hydrolyzable group such as alkoxy, acyloxy, amine or halide, etc All of the mercaptosilanes mentioned above are commercially available from United Chemical, Inc or Aldrich Chemical Company, lnc The silane can be coated onto the solid-phase by any of a number of means For example, the mercaptosilane can be deposited onto the solid surface as an aerosol or a vapor Alternatively, the silane can be spread onto the solid-surface by mechanical means (e g , a spreader bar, a saturated cloth, etc ) An important feature of the present invention is the hydrophobic nature of silanes Because of this feature, it is possible for an aqueous solution to form extremely well defined beads on the surface of any solid support coated with mercaptosilane With an automated delivery system, such as a Hamilton robot or ink jet printing method, it is possible to form a very complex array of oligonucleotide probes on a mercaptosilane coated glass slide Such methods can deliver nano to pico-liter size droplets with sub-millimeter spacing Because the aqueous beads are extremely well defined, it is possible to create an array with an extremely hiy~h density of oli~onucleotide probes Thus, it is possible to create arrays having greater than about 10,000 probe droplets/cm2 IV. The Use of Immobilized Nucleic Acid Molecules Immobilized nucleic acid molecules, and more preferably, immobilized oligonucleotides, make an ideal diagnostic tool Specifically, their versatility and simplicity make them ideal diagnostic tools for the detection of infectious and genetic diseases, mutation analysis, etc Although the manner in which the nucleic acid molecules are immobilized to the solid support can be random, one of the preferred embodiments of the invention is to arrange the nucleic acid molecules into an ordered array As used herein, an array is an orderly arrangement of nucleic acid molecules, as in a matrix of rows and columns The chemistry of the present invention is such that an individual array can contain either a finite or an infinite number of unique immobilized nucleic acid molecules SUBSTITUTE SHEET (RULE 26) _ -..__..~ ___...

_15_ There are two preferred methods to make a nucleic acid array one is to synthesize the specific oligonucleotide sequences directly onto the solid-phase in the desired pattern (Southern, et al., Nucl. Acids Res. 22 1368-1373 ( 1994), Maskos, et al., Nucl. Acids Res. 20 1679-1684 (1992), and Pease, et al., Proc. Natl.
Aced. Sci.
91 ' 5022-5026 ( 1994), all of which are herein incorporated by reference) and the other is to pre-synthesize the oligonucleotides on an automated DNA synthesizer (such as an ABI 3~>2 and then attach the oligonucleotides onto the solid-phase at specific locations (Lamture, et al., Nucl. Acids Res. 22 2121-2125 ( 1994) and (Smith, et al., Nucl. Acids Res. 22'5456-5465 (1994) both herein are incorporated by reference) In the first method, the efficiency of the coupling step of each base will affect the quality and integrity of the nucleic acid molecule array This method generally yields a large percentage of undesired incomplete (shortened) sequences which can create problems in the analysis step and effect the integrity of the analysis Thus, the quality and integrity of an array synthesized according to the first method is inversely proportional to the length of the nucleic acid molecule Specifically, the synthesis of longer oligonucleotides results in a higher percentage of incomplete, shortened sequences A second, more preferred, method for nucleic acid array synthesis utilizes an automated DNA synthesizer for DNA synthesis The controlled chemistry of an automated DNA synthesizer allows for the synthesis of longer, higher quality DNA
molecules than is possible with the first method Also, the nucleic acid molecules synthesized according to the second method can be purified prior to the coupling step Therefore, the quaiity of the nucleic acid molecule array can be expected to be much higher than the quality of the nucleic acid array of the first method However, a simple, effective and specific oligonucleotide coupling chemistry is lacking for the attachment of presynthesized oligonucleotides The present invention describes a simple, effective and efficient method for coupling a pre-synthesized unmodified oiigonucleotide onto a solid-phase by means of either an ether or thioether covalent linkage A. Hybridization Detection Of PCR Products Thus, for example, covalently immobilized nucleic acid molecules may be used to detect specific PCR products by hybridization where the capture probe is immobilized on the solid phase (Ranki et al., Gene 21 77-85 (1983), Keller et al., J
Clin Microbiol. 29' 638-641 (1991), Urdea et al., Gene 61. 2_S3-264 (1987) A
preferred method would be to prepare a single-stranded PCR product before SUBSTITUTE SHEET (RULE 26) WO 9$/55593 PCT/US98/11662 hybridization A sample, suspected to contain the tar';et molecule, or an amplification product thereof, would then be exposed to the solid-surface and permitted to hybridize to the bound oligonucieotide The methods of the present invention do not require that the target nucleic acid contain only one of its natural two strands Thus, the methods of the present invention may be practiced on either double-stranded DNA, or on single-stranded DNA
obtained by, for example, alkali treatment of native DNA The presence of the unused (non template) strand does not affect the reaction Where desired, however, any of a variety of methods can be used to eliminate one of the two natural stands of the target DNA molecule from the reaction Sin~rle stranded DNA molecules may be produced using the single-stranded DNA
bacteriophage M 13 (Messing, .1 et al , Meth. Enzymol. 101 20 ( 1983), see also, Sambrook, J , et al. (In Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY ( 1989)) Several alternative methods can be used to ~~enerate single-stranded DNA
molecules Gyllensten, U et al., (I'roc Natl Acad. Sci (U.S.A.} ~S 7652-7656 (1988}
and Mihovilovic, M et al., (BioTechniques 7 14 ( 1989)) describe a method, termed "asymmetric PCR," in which the standard "PCR" method is conducted using primers that are present in different molar concentrations Higuchi, R G et al.
(Nucleic Acids Res. 17.5865 (1985)) exemplifies an additional method for generating single-stranded amplification products The method entails phosphorylating the _5'-terminus of one strand of a double-stranded amplification product, and then permitting a 5'--~3' exonuclease {such as T7 gene exonuclease) to preferentially degrade the phosphorylated strand Other methods have also exploited the nuclease resistant properties of phosphorothioate derivatives in order to generate single-stranded DNA
molecules (Benkovic et al., U S Patent No 4,521,509, June 4, 1985), Sayers, J R et aI.
(Nucl.
Acids Res. 16 791-802 (1988}, Eckstein, F et al., Biochemistry 15 1685-1691 (1976), Ott, J et al., Biochemistry 26 8237-8241 (1987)) Most preferably, such single-stranded molecules will be produced using the methods described by Nikiforov, T (commonly assigned U S Patent No 5,518,900, herein incorporated by reference) In brief, these methods employ nuclease resistant nucleotide derivatives, and incorporate such derivatives, by chemical synthesis or SUBSTITUTE SHEET (RULE 26) ....... _..r-....__ ,...... . .... ....

_17_ enzymatic means, into primer molecules, or their extension products, in place of naturally occurring nucleotides Suitable nucleotide derivatives include derivatives in which one or two of the non-bridging oxygen molecules of the phosphate moiety of a nucleotide has been replaced with a sulfur-containin; group (especially a phosphorothioate), an alkyl group (especially a methyl or ethyl alkyl group), a nitrogen-containing group (especially an amine)., and/or a selenium-containing group, etc Phosphorothioate deoxyribonucleotide or ribo-nucleotide derivatives are the most preferred nucleotide derivatives Methods of producing and using such phosphorothioate derivatives are disclosed by Nikiforov, T (U S Patent No 5,515,900) B. Soiid Phrase DNA Sequencing The methods of the present invention may also be used in the practice of solid-phase sequencing as described by Khrapko, K R et al. (DNA Seq , I 375-3F8 (1991) and Drmanac, R and Crkvenjakov, R , Int. J Genome Res , 1 1-1 1 (1992)), both herein are incorporated by reference C. GBAT"" Genetic Bit Analysis The methods of the present invention may also be used to immobilize the oligonucleotides that are used in the GBA'M Genetic Bit Analysis (Goelet, P et al , PCT Application No 92/15712), herein incorporated by reference GBATM Genetic Bit Analysis a solid-phase method for the typing of single-nucleotide polymorphisms Oligonucleotides having a defined sequence complementary to a region that lies immediately proximal or distal to the variable nucleotide of a polymorphism would thus be provided to a polystyrene microtiter well or glass plate, and incubated with a salt, in accordance with the above-described methods The immobilized primer is then incubated in the presence of a DNA molecule (preferably a genomic DNA molecule) having a single nucleotide polymorphism whose immediately 3'-distal sequence is complementary to that of the immobilized primer Preferably, such incubation occurs in the complete absence of any dNTP (i a dATP, dCTP, dGTP, or dTTP), but only in the presence of one or more chain terminating nucleotide derivatives (such as a dideoxynucleotide derivative), and under conditions sufficient to permit the incorporation of such a derivative onto the 3'-terminus of the primer As will be appreciated, where tire polymorphic site is such that only two or SUBSTITUTE SHEET (RULE 26) three alleles exist (such that only two or three species of ddNTPs, respectively, could be incorporated into the primer extension product), the presence of unusable nucleotide triphosphate(s) in the reaction is immaterial In consequence of the incubation, and the use of only chain terminating nucleotide derivatives, a single dideoxynucleotide is added to the 3'-terminus of the primer The identity of that added nucleotide is determined by, and is complementary to, the nucleotide of the polymorphic site of the polymorphism Using the method described in the present patent application, oligonucleotide primers can be immobilized on solid phases like polystyrene or glass, hybridized to PCR-derived, single-stranded templates, and subjected to enzymatic extension at their 3'-ends by a single, labeled ddNTf The nature of the incorporated ddNTP is determined by the nucleotide that is located in the opposite strand (the polymorphic nucleotide) This assay can be conveniently carried out both in polystyrene ELISA
plates, or on ~,=lass slides In this embodiment, the nucleotide of the polymorphic site is thus determined by assayin~, which of the set of labeled nucleotides has been incorporated onto the 3'-terminus of the bound oligonucleotide by a primer-dependent polymerase Most preferably, where multiple dideoxynucleotide derivatives are simultaneously employed, different labels will be used to permit the differential determination of the identity of the incorporated dideoxynucleotide derivative D. Lig~se-Mediated GBATM
The methods and reagents of the present invention can also be used in concert with a poiymerase/ligase mediated polymorphic interrogation assay This assay, termed ligase-mediated GBATM genetic bit analysis, is a more specific version of the GBATM
genetic bit analysis assay The additional specificity arises from the addition of a second hybridization step and a ligation step In this assay, two oligonucleotides are employed The first oligonucleotide is a primer that is complementary to the immediately 3'-distal invariant sequence of the polymorphism The 3'-end of the oligonucleotide is attached to the plate A
second linker oligonucleotide is complementary to the 5'-proximal sequence of the polymorphism being analyzed, but is incapable of hybridizing to the first oligonucleotide The second linker oligonucleotide is phosphorylated at both its 3' and 5' ends SUBSTITUTE SHEET (RULE 26) These oligonucleotides are incubated in the presence of DNA containing the single nucleotide polymorphism that is to be analyzed, and at least one 2'-deoxynucleotide 5'-triphosphate The incubation reaction further includes a DNA
polymerise and a DNA ligase The tethered and soluble oligonucleotides are thus capable of hybridizing to the same strand of the target molecule under analysis The sequence considerations cause the two oligonucleotides to hybridize to the proximal and distal sequences of the single nucleotide polymorphism (SNP) that flank the variable nucleotide of the polymorphism, and to be separated by a single nucleotide at the precise position of the variability The presence of a polymerise and the 2'-deoxynucleotide 5'-triphosphate complementary to the nucleotide present in the variable site of the polymorphism permits the extended primer to be ligated to the bound oligonucleotide, thereby immobilizing the primer The identity of the polymorphic site that was opposite the single nucleotide can then be determined by any of several means In a preferred embodiment, the 2'-deoxynucleotide 5'-triphosphate of the reaction is labeled, and its detection thus reveals the identity of the complementary nucleotide of the polymorphic site Several dif~'erent 2'-deoxynucleotide 5'-triphosphates may be present, each differentially labeled Alternatively, separate reactions can be conducted, each with a different 2'-deoxynucleotide 5'-triphosphate In an alternative sub-embodiment, the 2'-deoxynucleotide 5'-triphosphates are unlabeled, and the soluble oligonucleotide is labeled In this embodiment, the primer that is extended is immobilized on the polystyrene Separate reactions are conducted, each using a different unlabeled 2'-deoxyn.ucieotide 5'-triphosphate While the invention has been described in connection with specific embodiments thereof; it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features herein before set forth and as follows in the scope of the appended claims Having now generally described the invention, the same will be more readily understood through reference to the following examples which are provided by way of illustration, and are not intended to be limiting of the present invention unless specified SUBSTITUTE SHEET (RULE 26) All patents, patent applications and publications mentioned herein are incorporated by reference in their entirety EPOXY-BASED CHEMISTRY
Attachment was obtained by a two-step process of silane treatment and oligonucleotide binding Glass slides were etched in 25% aqueous ammonium hydroxide, rinsed in milliQ water, then in 95% ethanol They were treated for about 30 minutes in 3-glycidoxy propyl ethanol (95% ethanol, pH 4 5) Slides were cured at 65°C for at least 12 hours 2 5-10 uM conc of oligonucleotides in an alkaline solution (l2.Smm NaOH or KOH) were applied onto cured slides in any desired array formats, in a covered chamber overnight, afrer which they were stored in water or a covered chamber for later use A functional test with hybridization and enzymatic reactions gave the desired signal with 400>1 signal to noise ratio by ELF
indirect detection reading and radioisotope quantitation (Figure 1 ) Fi~~ure 1 shows the results of GBA functional assay of epoxy-based attachment chemistry The 25-mer primer with (T)10 spacer arm at 5' was used for attachment Standard GBA conditions were used in terms of nucleoside triphosphate concentration and enzyme concentration and reaction conditions Synthetic template 1 was desi,ned to give an "A" signal and synthetic template 2 was designed to give a "T" signal Single base extension (GBA
signal) was obtained only with appropriate template, by using ELF indirect detection and also by CCD camera imaging The signal to noise ratio (S/N) was greater than Additionally, an attachment experiment was designed with the following end-blocked oligonucleotides 5'-end blocked, 3'-end blocked, or both end blocked The end blocks were achieved by phosphorylation of the end hydroxyl groups during automated DNA synthesis The attachment for each type of oligonucleotides was quantified by phosphor image analysis and then the ratio of end selectivity was determined The 5'-end selective attachment of unmodified oligonucleotides to epoxy silanized surfaces was demonstrated with a selectivity ratio of at least 5 1 Attachment through heterocyclic aminos was minimal in certain conditions tested (Table 1 ) SUBSTITUTE SHEET (RULE 26) r ..._ .T.

Olio conc. used for att. 10 5 2 5 I 25 (uM) 5'-att (incl middle) mole/7mm21 0 1 6 1 4 0 9 3'-att (incl middle)pmoles/7mm20 14 0 29 0 42 0 4~
>

middle att mole/7mm2 0 13 0 09 0 35 0 235 S'-att /3'-att (after sub 87 7 SS 15 21 middle) 5'-att /middle att 6 7 16 3 2 g 3'att /middle att 0 077 2 2 0 2 1 04 3'-& 5-att /middle att 6 8 19 3 2 3 g Table 1 shows the end selective attachment of un-modified oligonucleotides by epoxy-based chemistry Attachment was performed on an epoxy silanized slide with various concentrations of oligonucleotides in 12 5 mM NaOH for overnight and washed sequentially with TNTw and SO nllvl NaOH S'-att refers to the attachment reading of 3'-phosphorylated oligonucleotides, 3'-att refers to the attachment reading of S'-phosphorylated oligonucleotides Middle att refers to the heterocyclic amino attachment reading of both 3'- and 5'-end blocked oli~,onucleotides The '''P
isotopes images were analyzed on phosphor image quanta software Attachment at a concentration of 10 uM gave the best selectivity ratio of 87 1 of 5'-end vs 3'-end attachment Attachment at concentration of 5 uM gave the best end selectivity ratio of I9 1 of 3'-plus 5'-vs middle attachment These results were based on one slide only, I S however, a number of slides expressed a trend of optimum concentration at 2 5-5 uM
for 5'-end selective attachment In addition, epoxy-silanized surfaces are air-, moisture and heat-stable and showed no nonspecific binding to proteins and oiigonucleotides under conditions tested In summary, 5'-end selective attachment of oligonucieotides was demonstrated without modification of oligonucleotides SUBSTITUTE SHEET (RULE 26) MERCAPTO-BASED CHEMISTRY
Attachment was obtained by a two-step process of silane treatment and oligonucleotide binding Glass slides were etched in 25% aqueous ammonium hydroxide, rinsed in milliQ water, then in 95% ethanol They were treated for about 30 minutes in 3-mercapto-propyl-trimethoxysilane (MPTS} Slides were cured for at least 24 hours under dry inert bas (Ar or N~) 2 5-i0 uM cone of oli~onucleotides in an alkaline solution were applied onto cured slides in any desired array formats, in a covered chamber for an overnight, after which they were stored in water or a covered chamber for later use A functional test with hybridization and enzymatic reactions gave the desired signal (Figure 2) Figure 2 shows the results of mercapto-based attachment chemistry and functional assay by hybridization and GBA The data was based on phosphor imaging quanta analysis The X axis represents the input concentration of oligonucleotides used for attachment from 0 3125 uM to 40 uM
Oligo attached is represented by the trian<Jle (pmole/7 mm'), the diamond represents hybridization and the square represents GBA signals (ddATP extension) 'zP
labeled oligonucleotides were used for determining the attachment density The ~ZP 5'-template was used for assessing the hybridization efficiency The GBA
efficiency was determined by incorporation of 'zP-ddATP with exo-klenow DNA polymerise without the presence of other cold dideoxynucleotides The GBA efficiency and hybridization reached saturation at the attachment input of 10 uM
Additionally, experiments were performed for attachment of dye-labeled nucleotides to mercapto propyl silanized slides which showed stronger si,nals for A
and G and weaker signals for C and T, which favors the hypothesis that radical mechanisms are more involved than nucleophilic attacks The attachment of ~zP
labeled oligonucleotides and fluorescein labeled oligonucleotides was demonstrated and quantified (Figure 2) The attachment results achieved in terms of attachment density, hybridization and genetic bit analysis efficiency were compatible with epoxy chemistry and chemistries reported by others SUBSTITUTE SHEET (RULE 26) .. ..T. ..._........ .,. .... _.

THE RELATIONSHIP BETWEEN PRIMER DENSITY
AND HYBRIDIZATION EFFICIENCY
Hybridization efl3ciency is positively related to the surface density of the attached primer In this study, increasing amounts of the BRAC 1 primer 5' (T),~, TCA
TTA ATG CTA TGC AGA AAA TCT TAG (SEQ ID No 1 ) are covalently attached to a solid surface according to the methods described above Table 2 shows the results for epoxy-based attachment vs hybridization efficiency The data was based on phosphor imaging quanta analysis 3'-phosphorylated oliv_=onucleotides were used for attachment and 5'-phosphorylated templates were used for hybridiation A low surface coverage would presumably yield a corresponding low hybridization signal Conversely, hi<~h surface densities might result in steric interference between the covalently immobilized oli~~onucleotides thereby impeding access to target DNA
The results indicated that with higher coverage up to 1 78 pmoles/7 mm2, a higher hybridization efficiency was obtained Increased primer density is associated with increased hybridization efficiency Accordingly, hybridization efficiency is affected by the stability of the primer attachment cone for att covalent att Hybridization 40uM 019 O1+0015 0 42 0 14+0 00 5 1 78 0 58+0 005 2 5 I .61 0 43+0.03 1.25 0.98 0 29+0 OS

0 625 0 42 0 17+0 O l SUBSTITUTE SHEET (RULE 26) EJ~AMPLE 4 GENETIC BIT ANALYSIS COMPATIBILITY
A GBA primer having a poly-T", residue long spacer arm is attached to the glass surface by means of the previously described epoxy-based chemistry or mercapto-based chemistry Standard GBA biochemistry is used to analyze two synthetic templates Each synthetic template is hybridized to GBA primer immobilized to the treated glass slide and treated with an extension mix containing all of the extension reaction components, exonuclease-tree Klenow fragment of the IJ cmli polymerase and each of four fluorescein-labeled ddNTP's and co-ddNTP's or ~'P-ddATP The signal was recorded by enzyme-mediated fluorescence usin;; a Cytoflour ll fluorescent plate reader (Figure 1 ) or phosphor image quanta analysis Figure 1 shows the results of GBA functional assay of epoxy-based attachment chemistry The 27-mer primer with (T}10 spacer arm at 5' was used for attachment {SEQ ID No 1 ) Standard GBA
conditions were used in terms of nucleoside triphosphate concentration and enzyme concentration and reaction conditions Synthetic template 1 5' ACA CTC TAA GAT
TTT CTG CAT AGC ATT AAT (SEQ ID No 2) was designed to give an "A" signal and synthetic template 2 5' GGA CAC TAA GAT TTT CGT CAT AGC ATT AAT
(SEQ ID No 3 ) was desi~,ned to give a "T" signal Single base extension (GBA
signal) was obtained only with the appropriate template, by using ELF indirect detection and also by CCD camera imajing The signal to noise ratio (S/N} was greater than 400' 1 DNA Samples Genomic DNA was isolated using the SDS/Proteinase I<
procedure (Maniatis, T Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor {1989)) from peripheral blood nucleated cells of humans or horses enriched from red blood cells by selective lysis accomplished by diluting blood with a three fold volume excess of ACK lysing buffer (0 I S M
ammonium chloride, 1 mM potassium bicarbonate, 0.1 mM EDTA) Oligonucleotides were prepared by solid-phase phosphoramidite chemistry using an Applied Biosystems, Inc. Model 391 automated DNA synthesizer (Foster City, CA) In the case of primers used in Genetic Bit Analysis (GBA) reactions, detritylation was not performed following the final cycle of synthesis and the full-length oligonucleotide was purified using the Applied Biosystems oligonucleotide purification cartridge (OPC) as SUBSTITUTE SHEET (RULE 26) t ..__._. _ __...~ _..

recommended by the manufacturer For most PCR reactions, primers were used directly by drying down the de-protection reaction Table 3 depicts the results of an experiment employing a synthetic template 1 5' ACA CTC TAA GAT TTT CTG CAT AGC ATT ATT (SEQ ID No 2)(designed to give a GBA signal in base A) and a synthetic template 2, 5' GGA CAC TAA GAT
TTT CGT CAT AGC ATT AAT (SEQ ID No 3)(designed to give a signal in base T) The primer used was (T),~ TCA TTA ATG CTA TGC AGA AAA TCT TAG (SEQ ID
No 1) Both signals give strong signals in the expected bases with virtually no noise observed in the other bases (the Signal to Noise Ratio ranged from 520 I to 600 1) Table 3 Nucleotide Inserted Fluorescent Counts Template 1 Template 2 A ~ 600 1 C ND ND

G ND ND

T 1 ~ 520 PREPARATION OF AN OLIGONUCLEOTIDE ARRAY
BY INK-JET PRINTING
Another method for the automated delivery of the oligonucleotide solution employs an ink-jet printing technique performed by MicroFab (MicroFab Technologies, Inc , Plano, Texas) In one experiment, four difFerent spot spacings (center to center) and eight different droplet sizes are tested on the mercaptosilane coated surface using an oligonucleotide labeled at the 3'-terminus with fluorescein The format of the slides, depicted in Table 4, are as follows SUBSTITUTE SHEET (RULE 26) Table

4 Row (Row Spacin~~
= 6 mm) Slide Spot Row 1 Row 2 Row 3 No S acin~>

Slide 1 mm S nl 10 nl 25 nl I

Slide 0 S mm I nl 2 nl S nl 2 i Slide 250 m 250 1 500 ~l 1 nl Slide 125 ym 12S 1 250 ~l N/A

The labeled oligonucleotides are detected using a Molecular Dynamic FIuorIma~er 595 The ink jet printing technique is a suitable method for the manufacture of oligonucleotide arrays with sub-millimeter spacing and nano to pico-liter droplet sizes As such, the ink-jet printing technique is suitable for large scale manufacture of oligo arrays EXAMPLE G
PREPARATION OF AND OLIGONUCLEOTIDE ARRAY WITH
AN AUTOMATIC PIPETING ROBOT
A Hamilton 2200 automated pipeting robot is used to make arrays of oligonucleotide drops, ranging in size from about 100 nl to about 250 nl, with I mm spacing between dots The small volumes of oligonucleotide solution used with the automated pipeting robot allows for rapid drying of the oligonucleotide drops As in the ink jet printing method, a Hamilton robot can be programmed to deliver nano to pico-liter size droplets with sub-millimeter spacing While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features herein before set forth and as follows in the scope of the appended claims SUBSTITUTE SHEET (RULE 26) _......

SEQUENCE LISTING
(1) GENERAL INFORMATION
S (i) APPLICANT: Shi, Jufang Boyce-Jacino, Michael (ii) TITLE OF THE INVENTION: Covalent Attachment of Unmodified Nucleic Acids to Silanized Solid Phase Surfaces (iii) NUMBER OF SEQUENCES: 3 (iv) CORRESPONDENCE ADDRESS:

(A) ADDRESSEE: Howrey & Simon IS (B) STREET: 1299 Pennsylvania Avenue, N.W.

(C) CITY: Washington (D) STATE: DC

(E) COUNTRY: USA

(F) ZIP: 20004-2402 (v) COMPUTER
READABLE
FORM:

(A) MEDIUM TYPE: Diskette (B) COMPUTER: IBM Compatible (C) OPERATING SYSTEM: DOS

~S (D) SOFTWARE: FastSEQ for Windows Version 2.0 (vi) CURRENT APPLICATION DATA:

(A) APPLICATION NUMBER:

(B) FILING DATE:

3O (C) CLASSIFICATION:

(vii) PRIOR APPLICATION DATA:

(A) APPLICATION NUMBER:

(B) FILING DATE:

(viii ) ATTORNEY/AGENT INFORMATION:

(A) NAME: Sira, Serge 40 (B) REGISTRATION NUMBER: 39,445 (C) REFERENCE/DOCKET NUMBER: 04990-0037 (ix) TELECOMMUNICATION INFORMATION:

(A) TELEPHONE: 202 383-6857 4S (B) TELEFAX: 202 383-6610 (C) TELEX:

(2 ) INFORMATION FOR SEQ ID NO:1:

SO

(i) S EQUENCE CHARACTERISTICS:

(A) LENGTH: 37 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single SS (D) TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:
E)O TTTTTTTTTT TCATTAATGC TATGCAGAAA ATCTTAG 37 (2) INFORMATION FOR SEQ ID N0:2:
SUBSTITUTE SHEET (RULE 26) (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 30 base pairs (B) TYPE: nucleic acid S (C) STRANDEDNESS: single (D) TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID N0:2:

(2) INFORMATION FOR SEQ ID N0:3:
1S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 30 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: cDNA
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:3:

SUBSTITUTE SHEET (RULE 26) ~.

Claims (31)

WHAT IS CLAIMED IS

1 A method for immobilizing a synthetic nucleic acid molecule to a solid phase, which comprises the steps of (A) coating said solid phase with a silane and allowing said silane-coated solid phase to cure, and (B) coupling unmodified nucleic acid molecules having either a terminal 3' OH or a terminal 5' OH to said silane-coated solid phase

2 The method of claim I, wherein in step A, said coating occurs in the presence of an acidic buffer of aqueous ethanol for at least about 30 minutes

3 The method of claim 1, wherein in step A, said silane is selected from the group consisting of mercapto-alkyl-trimethoxysilane and glycidoxy- alkyl-silane

4 The method of claim l, wherein in step A, said silane is 3-mercapto-propyl-trimethoxysilane

The method of claim I, wherein in step A, said silane is 3-glycidoxy propyl-silane

6 The method of claim 4, wherein in step A, said curing occurs for about 24 hours in the presence of a dry inert gas consisting of Ar or N2

7 The method of claim 5, wherein in step A, said curing occurs at a temperature of from about 60°C to about 70° C for about 10-14 hours

8 The method of claim 1, wherein in step B, said coupling occurs in alkaline solution

9 The method of claim 8, wherein in step B, said alkaline solution comprises from about 0 0001 M to about 5 M NaOH.

10. The method of claim 8, wherein in step B, said alkaline solution comprises NaOH, KOH, and LiOH

11 The method of claim 1, wherein in step B, said nucleic acid molecules comprise oligonucleotides

12 The method of claim 11, wherein said oligonucleotides have a concentration of from about 10 to about 10 µM

13 The method of claim 1, wherein in step B, said covalent linkage is selected from the group consisting of covalent ether and thioether linkages

14 The method of claim 4, wherein in step B, said covalent linkage is a covalent thioether linkage

15 The method of claim 5, wherein in step B, said covalent linkage is a covalent ether linkage

16 The method of claim 1, wherein said solid phase is glass

17 The method of claim 16, wherein said glass is a microscope slide

18 The method of claim 1, wherein said solid-phase is plastic

19 The method of claim 18, wherein said plastic is polystyrene plastic

20 The method of claim 1, wherein said solid-phase is selected from the group consisting of a bead, a plate, a column, a pin and a dipstick

21 The method of claim 1, wherein the coupling reaction creates an array of immobilized nucleic acid molecules

22 The method of claim 1, wherein said immobilized nucleic acid is a polynucleotide and wherein said method optionally further comprises the steps of (C) capturing from a solution at least one strand of a specific poiynucleotide analyte by hybridization to said immobilized polynucleotide, and (D) detecting the presence of the captured analyte

23. The method of claim 22, wherein step C further comprises the steps of (C'(1))amplifying a specific region of a specific genome using a polymerase chain reaction, said region having a sequence complementary to said immobilized polynucleotide, and (C'(2)) capturing from solution at least one strand of said amplification product by hybridization to said immobilized polynucleotide, and wherein step D
further comprises the step of (D') detecting the presence of the captured amplification product

24 The method of claim 23, wherein said method optionally further comprises the steps of (E) incubating a sample of nucleic acid of a target organism, containing a single nucleotide polymorphism in the presence of said immobilized polynucleotide primer and at least one dideoxynucleotide derivative, under conditions sufficient to permit a polymerase mediated, template-dependent extension of said primer, said extension causing the incorporation of a single dideoxynucleotide to the 3'-terminus of said primer, said single dideoxynucleotide being complementary to the single nucleotide of the polymorphic site of said polymorphism, (F) permitting said template-dependent extension of said primer molecule, and said incorporation of said single dideoxynucleotide, and (G) determining the identity of the nucleotide incorporated into said polymorphic site, said identified nucleotide being complementary to said nucleotide of said polymorphic site

25 The method of claim 19, wherein said polystyrene support is a microwell plate

26 The method of claim 19, wherein said polystyrene support is an array designed to fit into a microwell plate

27 The method of claim 1, wherein said coating step is by means of an aerosol, a vaporization means or any other mechanical means

28. A composition comprising an immobilized unmodified nucleic acid molecule wherein said nucleic acid molecule is coupled to a solid phase by means of a covalent linkage

29 The composition of claim 28, wherein said unmodified nucleic acid molecule is covalently attached to a silane-coated solid phase

30 The composition of claim 29, wherein said silane is selected from the group consisting of mercapto-alkyl-trimethoxysilane and glycidoxy alkyl silane

31 The composition of claim 28, wherein said composition is used for screening applications comprising genetic analysis, combinatorial analysis, nucleic acid hybridization analysis and sequencing by hybridization, and primer extension genotyping