# Patent

## Title
Methods and compositions for determining the purity of and purifying chemically synthesized nucleic acids

## Abstract

An antibody microarray is described comprising a plurality of antibodies immobilized on a substrate, wherein each antibody specifically binds to a synthetic oligomer (e.g., an oligonucleotide or oligopeptide) having an organic protecting group covalently bound thereto, which antibody does not bind to that synthetic oligomer when the organic protecting group is not covalently bound thereto. Methods of making and using such antibodies are disclosed, along with cells for making such antibodies. Methods of making and using such antibody microarrays are also disclosed.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a continuation of International Application No. PCT/US02/20418, filed Jun. 28, 2002, which designated the United States and was published in English on Jan. 9, 2003 as International Publication No. WO 03/003014, and which claims the benefit of U.S. Provisional Application No. 60/302,153, filed Jun. 29, 2001. The entire disclosures of International Application No. PCT/US02/20418 and U.S. Provisional Application No. 60/302,153 are hereby incorporated herein by reference.


FIELD OF THE INVENTION
The present invention relates to the detection, identification, and quantification of protecting groups remaining after chemical synthesis of oligomers, particularly oligonucleotides, and also relates to the purification of such oligomers.
BACKGROUND OF THE INVENTION
Over the past decade automated chemical synthesis of nucleic acids such as DNA and RNA on solid supports has been developed. These chemical processes include the use of agents to protect the exocyclic amines of the nucleotide bases adenine, thymine, cytosine and guanine and to direct the synthesis by blocking the 2′OH of RNA's ribose. The bases within the nucleic acid product of the synthesis are deprotected upon cleavage of the nucleic acid from the solid support. However, the extent of base deprotection is not easily determined.
For example, after base deprotection of synthetic RNA, products still contain the 2′-dimethylsilyl tert-butyl group as a protection of the 2′OH of the ribose moiety. This protecting group is removed carefully by chemical means so as not to effect the chemistry and structure of the RNA. However, the extent of deprotection of the 2′OH is not readily determined. The nucleic acid is purified by high pressure liquid chromatography or by gel electrophoresis. However, some of the unwanted products of the synthesis are complete nucleic acid sequences that still contain one or more protecting groups, and shorter than full length (aborted) sequences difficult to separate from full length sequences, especially for oligomers of longer than 50 nucleosides. At present, there is no easy method to determine how much of each protecting group, if any, still remains on the product, and what proportion of the product is full-length. See generally Davis, G. E., Gehrke, C. W., Kuo, K. C., and Agris, P. F. (1979) Major and Modified Nucleosides in tRNA Hydrolysates by High Performance Liquid Chromatography. J. Chromatogr. 173:281-298; Agris, P. F., Tompson, J. G., Gehrke, C. W., Kuo, K. C., and Rice, R. H. (1980) High-Performance Liquid Chromatography and Mass Spectrometry of Transfer RNA Bases for Isotopic Abundance. J Chromatogr. 194:205-212; Gehrke, C. W., Kuo, K. C., McCune, R. A., Gerhardt, K. O., and Agris, P. F. (1981) Quantitative Enzymatic Hydrolysis of tRNAs: RP-HPLC of tRNA Nucleosides. J. Chromatogr. 230:297-308; Chromatography and Modification of Nucleosides Volumes A, B and C (Gehrke, C. W. and Kuo, K. C. T., eds.), Elsevier Publishing Co. 1990; Agris, P. F. and Sierzputowska-Gracz, H. (1990) Three Dimensional Dynamic Structure of tRNA's by Nuclear Magnetic Resonance. In Chromatography and Modification of Nucleosides (Gehrke, C. W. and Kuo, K. C. T., eds.), Elsevier Publishing Co., pp. 225-253; Agris, P. F., Hayden, J., Sierzputowska-Gracz, H., Ditson, S., Degres, J. A., Tempesta, M., Kuo, K. C. and Gehrke, C. W. (1990) Compendium on Biological, Biochemical, Chemical, Physical and Spectroscopic Properties of RNA and DNA Nucleosides. In Chromatography and Modification of Nucleosides, Elsevier Publishing Co.
The incomplete removal of the protecting group and lack of a simple assay is a problem for two industries and for numerous researchers world wide: (i) the multitude of companies now providing nucleic acid sequence synthesis products by overnight delivery have difficulty telling their customers the extent to which the product is deprotected; (ii) pharmaceutical companies cannot easily verify for regulatory agencies the purity and/or length of the therapeutic or diagnostic oligonucleotide products they seek to introduce or market. Accordingly, there is a need for simple and reliable techniques for determining the purity of oligonucleotide products and for determining the proportion of full length oligonucleotide products.
SUMMARY OF THE INVENTION
The present invention relates to an antibody microarray that comprises a plurality of antibodies immobilized on a substrate and the use thereof. Each of the antibodies immobilized on the antibody microarray specifically binds to a synthetic oligomer having an organic protecting group covalently bound thereto, which antibody does not bind to the synthetic oligonucleotide when the organic protecting group is not covalently bound thereto.
An antibody chip according to the present invention may be used to detect incomplete deprotection of synthetic oligomers and/or separate protected synthetic oligomers from fully deprotected synthetic oligomers. Such an antibody chip may also be used to detect incomplete elongation of synthetic oligomers and/or separate full-length oligomers from incomplete synthetic oligomers. The methods described herein may be useful in high throughput assays of unbound oligomers or oligomers bound to a substrate such as an oligonucleotide microarray. For example, an antibody chip according to the present invention and methods of using such an antibody chip may be useful in a high throughput assay for detecting the insufficient deprotection or elongation of DNA used to form a DNA chip.
One aspect of the invention includes a method of detecting incomplete deprotection of a synthetic test oligonucleotide using an antibody microarray. The method comprises the following steps:
(a) providing an antibody microarray comprising a plurality of antibodies immobilized on a substrate, each antibody specifically binding to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to the synthetic oligonucleotide when the organic protecting group is not covalently bound thereto;
(b) contacting the synthetic test oligonucleotide with the antibodies immobilized on the antibody microarray; and
(c) detecting binding of the synthetic test oligonucleotide to the antibodies immobilized on the antibody microarray, the presence of binding indicating incomplete deprotection of the synthetic test oligonucleotide.
Another aspect of the invention includes a method of purifying a synthetic oligonucleotide mixture prepared using organic protecting groups. The method uses an antibody microarray and comprises the following steps:
(a) providing a synthetic oligonucleotide mixture comprising fully deprotected synthetic oligonucleotides, partially deprotected synthetic oligonucleotides, and/or fully protected synthetic oligonucleotides, the mixture having at least one partially or fully protected synthetic oligonucleotide with a protecting group covalently bound thereto;
(b) providing an antibody microarray comprising a plurality of antibodies immobilized on a substrate, each antibody specifically binding to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to the synthetic oligonucleotide when the organic protecting group is not covalently bound thereto, the plurality of antibodies including at least one antibody that is capable of binding at least one of the partially or fully protected synthetic oligonucleotides;
(c) contacting the synthetic oligonucleotide mixture with the antibodies immobilized on the antibody microarray such that at least one of the protected synthetic oligonucleotides from the mixture is bound to at least one of the antibodies immobilized on the antibody microarray, wherein at least a portion of the oligonucleotides in the synthetic oligonucleotide mixture do not bind to the plurality of antibodies; and
(d) separating the antibody microarray and the unbound synthetic oligonucleotides, thus separating the unbound synthetic oligonucleotides from any partially and/or fully protected synthetic oligonucleotide or oligonucleotides bound to the antibodies immobilized on the antibody microarray.
Yet another aspect of the present invention includes a method of preparing an oligonucleotide microarray using an antibody microarray. The method comprises the following steps:
(a) providing a synthetic oligonucleotide mixture prepared using organic protecting groups, the mixture comprising fully deprotected synthetic oligonucleotides, partially deprotected synthetic oligonucleotides, and/or fully protected synthetic oligonucleotides, the mixture having at least one partially or fully protected synthetic oligonucleotide with a protecting group covalently bound thereto;
(b) providing an antibody microarray comprising a plurality of antibodies immobilized on a first substrate, each antibody specifically binding to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to the synthetic oligonucleotide when the organic protecting group is not covalently bound thereto, the plurality of antibodies including at least one antibody that is capable of binding at least one of the partially or fully protected synthetic oligonucleotides;
(c) contacting the synthetic oligonucleotide mixture with the antibodies immobilized on the antibody microarray such that at least one of the protected synthetic oligonucleotides from the mixture is bound to at least one of the antibodies immobilized on the antibody microarray, wherein at least a portion of the oligonucleotides in the synthetic oligonucleotide mixture do not bind to the plurality of antibodies;
(d) separating the antibody microarray and the unbound synthetic oligonucleotides, thus separating the unbound synthetic oligonucleotides from any partially and/or fully protected synthetic oligonucleotide or oligonucleotides bound to the antibodies immobilized on the antibody microarray; and
(e) immobilizing the unbound synthetic oligonucleotides on a second substrate to form an oligonucleotide microarray.
According to a further aspect of the present invention, an oligonucleotide microarray impregnated with antibodies is provided. Each of the antibodies specifically binds to a synthetic oligomer having an organic protecting group covalently bound thereto. The antibodies are immobilized on a substrate along with an array of oligonucleotides. In some embodiments, the antibodies may be encapsulated or one or more blocking groups may be used to block the binding sites on the antibodies until such time as detection of incomplete deprotection and/or insufficient elongation is desired. In such embodiments, the antibodies may be contacted with the oligonucleotides on the oligonucleotide microarray when desired by releasing the antibodies from the capsules or removing the blocking groups from the antibodies. A suitable assay may then be performed to determine incomplete deprotection of the synthetic oligonucleotides and/or incomplete elongation of the synthetic oligonucleotides.
In summary, the antibodies, the antibody microarrays, the oligonucleotide microarrays impregnated with antibodies, and the methods of the present invention are useful in immunoassays, such as for the qualitative and quantitative detection of protecting groups used in organic synthetic processes, with particular application to oligonucleotides or peptides in research, therapeutics, diagnostics and biomedical science. The present invention can be used in purification techniques, such as for the separation of final products from by-product contaminants. The instant invention can be used in the course of quality control of oligonucleotide and peptide synthesis, such as in the quality control of drugs for gene therapy, antisense, antigene and control of gene expression, in the quality control of biomedical polymers that may contain protecting groups, and as probes or devices for purification and characterization of synthetic oligomers, particularly oligonucleotides or peptides. The present invention advantageously provides high sensitivity in such quality control, purification, and immunoassay techniques, even when using a low volume of antibodies. In addition, the use of the present invention may be helpful in producing improved oligonucleotide products such as, for example, improved DNA chips with lower amounts of incompletely deprotected/insufficiently elongated DNA.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a dot-blot immunoassay of monoclonal antibody 1H11, which selectively binds to oligoIbu-dG20mers.
FIG. 2 is a dot-blot immunoassay of monoclonal antibody 7H3, which selectively binds to oligoBz-dC20mers.
FIG. 3 shows ELISA (FIG. 3A) and dot-blot (FIG. 3B) results demonstrating specificity and detection sensitivity of a monoclonal antibody (mAb) of the commonly used protecting group, benzoyl (Bz), for the chemical synthesis of nucleic acids. Partially deprotected oligomer oligo Bz-dC (center column) can be re-treated to remove the remaining protecting groups, and re-tested with mAb (FIG. 3C). An RNA standard with protecting groups Bz, ibu and ipr-Pac was synthesized and assayed for identification of the protecting groups with the mAb against Bz (FIG. 3D).
FIG. 4 shows ELISA (FIG. 4A) and dot-blot (FIG. 4B) results demonstrating specificity and sensitivity of a monoclonal antibody (mAb) and its detection of the commonly used protecting group, isobutryl (ibu), for the chemical synthesis of nucleic acids. Dot-blot assay with high amounts of DNA demonstrates that the ibu protecting group was recognized by the mAb no matter which nucleobase was protected (FIG. 4C). Partially deprotected oligomer oligo Ibu-dg (center column) can be re-treated to remove the remaining protecting groups, and re-tested with mAb (FIG. 4D). An RNA standard with protecting groups Bz, ibu and ipr-Pac was synthesized and assayed for identification of the protecting groups with the mAb against ibu (FIG. 4E).
FIG. 5 shows ELISA (FIG. 5A) and dot-blot (FIG. 5B) results demonstrating specificity and sensitivity of a monoclonal antibody (mAb) and its detection of the commonly used protecting group, isopropyl-phenoxyacetyl (ipr-Pac), for the chemical synthesis of nucleic acids. Partially deprotected oligomers oligo ibr-Pac-dG and oligo ibu-dG (columns second from left and forth from left, respectively) can be re-treated to remove the remaining protecting groups, and re-tested with mAb (FIG. 5C). An RNA standard with protecting groups Bz, ibu and ipr-Pac was synthesized and assayed for identification of the protecting groups with the mAb against ipr-Pac (FIG. 5D).
FIG. 6 shows a mAb dot-blot assay of protecting groups demonstrating the sensitivity and quantifiable response of the technology as related to HPLC. Dot-blot detection of Bz groups remaining on a standardized 20mer oligo dC molecule was analyzed (FIG. 6A) and a quantitation of the mAb response (FIG. 6B) was determined. The mAb response was analyzed with an increase in the amount of DNA on the dot-blot membrane (FIG. 6C). The column on the left is just the protected Bz-dC 20mer. The column on the right is the protected Bz-dC together with a 2500-fold excess of the completely deprotected oligo dC(Bz).
FIG. 7 shows a direct comparison of the mAb and HPLC detection of Bz in the pmole (FIG. 7A) and nmol range (FIG. 7B), respectively.
FIG. 8 shows a blind study demonstrating the detection of remaining protecting groups in commercial samples. dA-dC oligos were analyzed with anti-Bz mAb (FIG. 8A) and dG-dT oligos were analyzed with anti-ipr-Pac mAb (FIG. 8B). The oligo dA-dC samples from companies #2 and #6 were tested in higher amounts to confirm the presence of the Bz protecting group (FIG. 8C). In addition, the samples were treated to remove the remaining protecting groups using a standard protocol. The oligo dG-dT samples were assayed for the ipr-Pac protecting groups (FIG. 8D). The samples were re-treated to remove remaining protecting groups and re-analyzed as in (FIG. 8C).
FIG. 9 shows the production and analyses of polyclonal antibody against the 5′ terminal protecting group, dimethyltritgl (DMT), including (DMT)3-d(T)20-Biotin and DMT-d(T)20-Biotin. (Seq. ID No.:1).
FIG. 10 shows a substrate carrying different oligonucleotides of the same sequence, but with varying degrees of deprotection, that may be used as a testing standard to screen similar oligonucleotides of the same sequence for varying degrees of protection or deprotection.
FIG. 11 illustrates an oligonucleotide array that may be screened for the presence of protecting groups or insufficient elongation with antibodies of the present invention.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
1. General Definitions
“Antibody” as used herein refers to both monoclonal and polyclonal antibodies, refers to antibodies of any immunoglobulin type (including but not limited to IgG and IgM antibodies), and including antibody fragments that retain the hypervariable or binding regions thereof. Antibodies may be of any species of origin, but are typically mammalian (e.g., horse, rat, mouse, rabbit, goat). Antibodies may be bound to or immobilized on solid supports such as nitrocellulose, agarose, glass, organic polymers (“plastics”) and the like in accordance with known techniques, and may be labeled with or joined to other detectable groups in accordance with known techniques.
“Binding” as used herein with respect to the selective binding of an antibody to an oligomer has its usual meaning in the art. In general, to obtain useful discrimination in an immunoassay or an affinity purification technique, the antibody should bind to the protected oligomer at an affinity of at least about kd=10−6, 10−7, or 10−8 M, and should bind to the unprotected oligomer at an affinity of not greater than about kd=10−2, 10−3, or 10−4 M.
“Oligomer” as used herein refers to synthetic oligonucleotides and synthetic oligopeptides, including synthetic oligomers in the naturally occurring form such as DNA and RNA, and modified backbone chemistries as discussed below. Oligonucleotides are currently preferred in carrying out the present invention, and the instant invention is primarily explained with reference to oligonucleotides herein. However, the methods and techniques described herein may also be applied to oligopeptides, oligosaccharides, etc. (i.e., any synthetically produced polymer requiring protecting groups for synthesis).
“Nucleotide” as used herein refers to a subunit of an oligonucleotide comprising a pentose, a nitrogenous heterocyclic base (typically bound to the 1 position of the pentose), and a phosphate or phosphoric acid group (typically bound at the 5′ position of the pentose) but absent, or considered bound at the 3′ position, in the 5′ terminal nucleotide of an oligonucleotide. These structures are well known. See, e.g., A. Lehninger, Biochemistry, 309-320). “Nucleoside” typically refers to a nucleotide, absent a phosphoric acid or phosphate group.
“Protecting group” as used herein has its conventional meaning in the art and refers to a chemical moiety, group or substituent that is coupled, typically covalently coupled, to an atom in a molecule prior to a chemical reaction involving that molecule (typically in an organic synthesis), so that the chemical reaction is averted at the atom to which the protecting group is coupled. Typically, the protecting group is then chemically removed from the intermediate molecule for preparation of the final product, although removal techniques may not be entirely successful leading to only partial deprotection of the final product (i.e., the presence of at least one protecting group remaining on that molecule). Protecting groups may be intentionally left on a molecule for purposes of generating or testing an antibody as described herein.
“Deprotection” or “deprotected” as used herein refers to the absence of protecting groups employed during chemical oligonucleotide synthesis from a molecule. Such protecting groups are described below. The presence of such a protecting group may indicate insufficient elongation of the oligonucleotide, when the protecting group is chain terminating. Chemically synthesized oligonucleotides are ideally fully deprotected, but the present invention is employed to detect partial or incomplete deprotection of such oligonucleotides (that is, the presence of at least one protecting group as described below in the oligonucleotide).
“Base” as used herein with respect to oligonucleotides refers to a nitrogenous heterocyclic base which is a derivative of either purine (e.g., adenine, guanine) or pyrimidine (e.g., uracil, thymine, cytosine). Pyrimidine bases are bound to the pentose by the 1 ring nitrogen; Purine bases are bonded to the pentose by the 9 ring nitrogen. Preferred bases are those that contain a free amino group, such as guanine, adenine, and cytosine (the protecting group is then covalently bound to the free amino group by substitution of one, or both, of the hydrogens on the free amino group). However, the present invention may be used with any purine or pyrimidine base, whether standard or modified/rare, that contains a free amino group for protection, or other group requiring protection during synthesis thereof in an oligonucleotide. Examples of standard and modified/rare bases are those found in the nucleosides set forth in Table 1 below.







TABLE 1







Standard and modified nucleosides and their standard


abbreviations.










abbreviation
base






U
uridine



C
cytidine



A
adenosine



G
guanosine



T
thymidine



?A
unknown modified adenosine



m1A
1-methyladenosine



m2A
2-methyladenosine



i6A
N6-isopentenyladenosine



ms2i6A
2-methylthio-N6-isopentenyladenosine



m6A
N6-methyladenosine



t6A
N6-threonylcarbamoyladenosine



m6t6A
N6-methyl-N6-threonylcarbomoyladenosine



ms2t6A
2-methylthio-N6-threonylcarbamoyladenosine



Am
2′-O-methyladenosine



I
Inosine



m1I
1-methylinosine



Ar(p)
2′-O-(5-phospho)ribosyladenosine



io6A
N6-(cis-hydroxyisopentenyl)adenosine



?C
Unknown modified cytidine



s2C
2-thiocytidine



Cm
2′-O-methylcytidine



ac4C
N4-acetylcytidine



m5C
5-methylcytidine



m3C
3-methylcytidine



k2C
lysidine



f5C
5-formylcytidine



f5Cm
2′-O-methyl-5-formylcytidine



?G
unknown modified guanosine



Gr(p)
2′-O-(5-phospho)ribosylguanosine



m1G
1-methylguanosine



m2G
N2-methylguanosine



Gm
2′-O-methylguanosine



m22G
N2N2-dimethylguanosine



m22Gm
N2,N2,2′-O-trimethylguanosine



m7G
7-methylguanosine



fa7d7G
archaeosine



Q
queuosine



manQ
mannosyl-queuosine



galQ
galactosyl-queuosine



Yw
wybutosine



o2yW
peroxywybutosine



?U
unknown modified uridine



mnm5U
5-methylaminomethyluridine



s2U
2-thiouridine



Um
2′-O-methyluridine



s4U
4-thiouridine



ncm5U
5-carbamoylmethyluridine



mcm5U
5-methoxycarbonylmethyluridine



mnm5s2U
5-methylaminomethyl-2-thiouridine



mcm5s2U
5-methoxycarbonylmethyl-2-thiouridine



cmo5U
uridine 5-oxyacetic acid



mo5U
5-methoxyuridine



cmnm5U
5-carboxymethylaminomethyluridine



cmnm5s2U
5-carboxymethylaminomethyl-2-thiouridine



acp3U
3-(3-amino-3-carboxypropyl)uridine



mchm5U
5-(carboxyhydroxymethyl)uridinemethyl ester



cmnm5Um
5-carboxymethylaminomethyl-2′-O-methyluridine



ncm5Um
5-carbamoylmethyl-2′-O-methyluridine



D
Dihydrouridine



ψ
pseudouridine



m1ψ
1-methylpseudouridine



ψm
2′-O-methylpseudouridine



m5U
ribosylthymine



m5s2U
5-methyl-2-thiouridine



m5Um
5,2′-O-dimethyluridine









See Sprinzl et al., Nucleic Acids Res. 26, 148 (1998).
Applicants specifically intend that the disclosures of all United States patent references cited herein be incorporated by reference herein in their entirety.
2. Protecting Groups
The particular protecting group will depend upon the oligomer being synthesized and the methodology by which that oligomer is synthesized.
For the synthesis of oligonucleotides, suitable protecting groups include alkyl, aryl, alkylaryl, arylalkyl groups, which may contain one or more hetero atoms such as N, O, or S, and which may be substituted or unsubstituted (e.g., a carbonyl group). Examples of protecting groups include, but are not limited to, the following: acetyl; isobutyryl; 2-(t-butyldiphenyl-silyloxymethyl)benzoyl; naphthaloyl; iso-butyryloxycarbonyl; levulinyl; fluorenylmethoxycarbonyl; 2-nitrothiophenyl; 2,2,2-trichloro-t-butoxycarbonyl, ethoxycarbonyl; benzyloxycarbonyl; p-nitrophenyl-ethyloxycarbonyl; N′N-dimethylformamidine; formyl; benzoyl, toluyl; 2,4-6-trimethylbenzoyl; anisoyl; 2,4-dimethylphenyl; 2,4,6-trimethylphenyl; triphenylthiomethyl; pivoloiloxymethyl; t-butoxycarbonyl; p-nitrophenylethyl; methoxyethoxymethyl; butylthiocarbonyl; 2-methyl-pyridine-5-yl; 2-nitrothiophenyl; 2,4-dinitrothiophenyl; 2-nitro-4-methylthiophenyl; p-nitrophenylsulphonylethyl; 5-chloro-8-hydroxyquinoline; thiophenyl; β-cyanoethyl; phenylethyl; p-nitrophenylethyl; pyridylethyl; 2-N-methylimidazolylphenyl; methyl; allyl; trichloroethyl; dibenzoyl; p-nitrophenylethoxycarbonyl; benzoyl and substituted derivatives thereof; 2(acetoxymethyl) benzoyl; 4,4′,4′′-tris-(benzyloxy)trityl; 5-methylpyridyno-2-yl; phenylthioethyl; dipehylcarbamoyl; 3,4-dimethoxybenzyl; 3-chlorophenyl; 2-nitrophenyl; 9-phenylxanthen-9-yl; 9-(p-methoxyphenyl)xanthen-9-yl; 9-(p-ocatadecyloxyphenyl)xanthen-9-yl; “bridged” bis-dimethoxytrityl groups; phthaloyl; succinyl; benzensulphonylethoxycarbonyl; 4,4′,4′′-tris(bevulinyloxy)trityl; p-phenylazophenyloxycarbonyl; o-substituted benzoyl; 4,4′4′′-tris-(4,5-dichlorophalimidin)trityl; levelinyl; alkyloxy and aryloxyacetyl; 1,3-benzodithiol-2-yl; tetrahydrofuranyl; [2-(methylthio)phenyl]thiomethyl; 1-(2-chloroethyoxy)ethyl; 1-[(2-fluorophenyl]4-methoxy piperidin-4-yl; 4-methoxytetrahydropyran-4-yl; (1-methyl-1-methoxy)ethyl; tetrahydropyranyl; 3-methoxy-1,5-dicarbomethoxypentam-3-yl; 2-nitrobenzyl; benzyl; 4-nitrophenylethyl-sulphonyl; t-butyldimethylsilyl; 4-methoxybenzyl; 3,4-dimethoxybenzyl; 9-p-methoxyphenylthioxanthen-9-yl; compounds of the formula X1X2X3C—, wherein X1, X2, and X3 are each independently selected from the group consisting of phenyl, p-monomethoxyphenyl, o-monomethoxphenyl, biphenyl, p-fluoropnehyl, p-chlorophenyl, p-methylphenyl, p-nitrophenyl, etc.
3. Oligonucleotides
Synthetic oligonucleotides that contain protecting groups and may be used to carry out the present invention include both the naturally occurring forms such as DNA and RNA, and those with modified backbone chemistries, such as poly (phosphate derivatives) such as phosphonates, phosphoramides, phosphonamides, phosphites, phosphinamides, etc., poly (sulfur derivatives) e.g., sulfones, sulfonates, sulfites, sulfonamides, sulfenamides, etc. It is noted that antibodies of the invention may be characterized by their selective binding to particular “reagent” or “benchmark” oligonucleotides, but the same antibodies may also bind to a variety of other oligonucleotides (e.g., longer or shorter nucleotides) or other compounds that contain the same protecting group.
For example, an oligonucleotide to which the antibody selectively binds may consist of from 3 to 20 nucleotides, and wherein one of said nucleotides is a protected nucleotide according to Formula (I) below:




wherein:

R is H or a protecting group, such as dimethoxytrityl; subject to the proviso that R is a covalent bond to an adjacent nucleotide when said protected nucleotide is not a 5′ terminal nucleotide in said oligonucleotide;
R1 is H or a protecting group such as β-cyanoethyl; subject to the proviso that R1 is a covalent bond to an adjacent nucleotide when said protected nucleotide is not a 3′ terminal nucleotide in said oligonucleotide;
R2 is H or —OR3;
R3 is H or a protecting group such as tert-butyldimethylsilyl;
Base is a purine or pyrimidine base; and
R4 is a protecting group substituted for a hydrogen on an amino group of the base, such as a protecting group selected from the group consisting of acetyl (Ac), benzoyl (Bz), dimethylformamidine (dmf), isobutyrl (Ibu), phenoxyacetyl (Pac), and isopropyl-phenoxyacetyl (Ipr-pac), subject to the proviso that R4 is not present in Formula (I) when R, R1, or R3 is a protecting group or when the base does not include an amino group; and
further subject to the proviso that only one of R, R1, R3, and R4 is a protecting group and the others of R, R1, R3, and R4 are not protecting groups.
In one particular embodiment of the foregoing, the antibody may be one that selectively binds to an oligonucleotide that consists of from 3 to 20 nucleotides and has a 5′ nucleotide, and wherein said 5′ nucleotide is a protected nucleotide according to Formula (IA):




wherein:

R5 is a protecting group such as dimethoxytrityl;
R6 is a covalent bond to an adjacent nucleotide;
R7 is H or —OH; and
Base is a purine or pyrimidine base.
In another particular embodiment of the foregoing, the antibody may be one that selectively binds to an oligonucleotide that consists of from 3 to 20 nucleotides and has a 3′ nucleotide, and wherein said 3′ nucleotide is a protected nucleotide according to Formula (IB):




wherein:

R8 is a covalent bond to an adjacent nucleotide;
R9 is a protecting group such as β-cyanoethyl;
R10 is H or —OH; and
Base is a purine or pyrimidine base.
In another particular embodiment of the foregoing, the antibody may be one that selectively binds to an oligonucleotide that consists of from 3 to 20 nucleotides, and wherein one of said nucleotides is a protected nucleotide according to Formula (IC):




wherein:

R11 is a covalent bond to an adjacent nucleotide;
R12 is a covalent bond to an adjacent nucleotide;
R13 is —OR14;
R14 a protecting group such as tert-butyldimethylsilyl; and
Base is a purine or pyrimidine base.
In still another particular embodiment of the foregoing, the antibody may be one that selectively binds to an oligonucleotide that consists of from 3 to 20 nucleotides, and wherein one of said nucleotides is a protected nucleotide according to Formula (ID):




wherein:

R15 is a covalent bond to an adjacent nucleotide;
R16 is a covalent bond to an adjacent nucleotide;
R17 is H or —OH;
Base is a purine or pyrimidine base; and
R18 is a protecting group bonded to an amino group of said base, such as acetyl, benzoyl, dimethylformamidine, isobutyryl, phenoxyacetyl, and isopropyl-phenoxyacetyl.
Thus, examples of protected bases that may be employed in the structures shown above include, but are not limited to, adenine, guanine, and cytosine, as follows:




wherein Y1 and Y2 are both H in an unprotected base, and either or both Y1 and/or Y2 are a protecting group as described above (e.g. Pac, Ipr-pac, Ibu, Bz, Ac, dmf) for a protected base. Likewise, modified nucleosides have protecting groups at the modifications that are chemically reactive.

In one embodiment of the invention, the oligonucleotides are peptide nucleic acids, and the protecting groups are those protecting groups employed in the synthesis of peptide nucleic acids, including but not limited to those described in U.S. Pat. No. 6,133,444.
In still another particular embodiment of the foregoing, the antibody may be one that selectively binds to an oligonucleotide that consists of from 3 to 20 nucleotides, and wherein one of said nucleotides is protected with a photolabile protecting group, including but not limited to those described in U.S. Pat. Nos. 5,744,101 and 5,489,678.
4. Antibodies
As noted above, the present invention provides antibodies (e.g., a monoclonal or polyclonal antibody) that specifically bind to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to said synthetic oligonucleotide when said organic protecting group is not covalently bound thereto.
The antibody may be provided immobilized on (or bound to) a solid support in accordance with known techniques, or may be provided in a free, unbound form (e.g., lyophilized, frozen, in an aqueous carrier, etc.). Whether or not an antibody is immobilized will depend upon the particular immunoassay or affinity purification technique in which the antibody is used, and is determined by the known parameters for such techniques. Similarly, the antibody may be bound to or conjugated with suitable detectable groups, such as an enzyme (e.g., horseradish peroxidase), a member of a binding pair such as biotin or avidin, a radioactive group or a fluorescent group such as green fluorescent protein, also in accordance with known techniques, typically depending upon the immunoassay format in which the antibody is used.
5. Immunoassay Methods
The present invention provides a method for detecting incomplete deprotection of a synthetic oligonucleotide (including aborted sequences that still contain a protecting group) by immunoassay. In general, such an immunoassay comprises the steps of: (a) contacting a synthetic oligonucleotide to an antibody as described above, and then (b) detecting the presence or absence of binding of said antibody to said oligonucleotide, the presence of binding indicating incomplete deprotection of said synthetic oligonucleotide. Any suitable assay format can be employed, including heterogeneous and homogeneous immunoassays. For example, the immunoassay may be an immunodot-blot assay, or may be a sandwich assay. The oligonucleotides being tested for deprotection may be in any suitable form, such as in solution or immobilized on a solid support.
In a preferred embodiment, the detection method employs a “dip stick” or the like, in which binding of the antibody to the test oligonucleotide is compared to binding of the antibody to a set of known oligonucleotides, all immobilized on a common solid support. Such an article, as illustrated in FIG. 10, useful for determining incomplete deprotection of a synthetic oligonucleotide in an immunoassay, comprises: (a) a solid support (e.g., a nitrocellulose strip) 25 having a surface portion, said surface portion having at least two separate discrete regions 26, 27 formed thereon; (b) a first oligonucleotide bound to one of said separate discrete regions, said first oligonucleotide having a protecting group bound thereto (e.g., at least one protecting group); and (c) a second oligonucleotide bound to another of said separate discrete regions, said second oligonucleotide not having said protecting group bound thereto; wherein the nucleotide sequence of said first and second oligonucleotides are the same. In a preferred embodiment, the article further comprises (d) a third oligonucleotide bound to another of said separate discrete regions 28; said third oligonucleotide also having said protecting group bound to said first oligonucleotide bound thereto; wherein said third oligonucleotide is partially deprotected (i.e., has a number of protecting groups covalently bound thereto which is intermediate between that bound to the first and second oligonucleotide, e.g., at least one, two three or four more protecting groups than the first oligonucleotide, up to at least 10, 20 or more protecting groups than the first oligonucleotide); and wherein the nucleotide sequence of said first, second, and third oligonucleotides are the same. Of course, still more oligonucleotides carrying varying numbers of protecting groups may be included on the substrate in additional separate and discrete locations, if desired. The discrete regions to which the separate oligonucleotides are bound may be in any form, such as dots.
6. Affinity Purification Methods
In addition to immunoassays, the present invention also provides affinity purification techniques for the separation of fully deprotected oligonucleotides from partially deprotected (including fully protected) oligonucleotides (e.g., both oligonucleotides that have been subjected to a deprotection process to remove the protecting group, and oligonucleotides that have not). Such a procedure typically comprises (a) contacting a mixture of protected and fully deprotected synthetic oligonucleotides to antibodies as described above, wherein the protected synthetic oligonucleotides have the organic protecting group for which the antibody is selective covalently bound thereto, so that the protected synthetic oligonucleotides bind to the antibody; and then (b) separating said antibodies from said fully deprotected oligonucleotides. The antibody may be immobilized on a solid support to facilitate separation. The protected synthetic oligonucleotide may be a partially protected synthetic oligonucleotide, or a fully protected synthetic oligonucleotide that has not undergone deprotection. Any separation format may be used, including but not limited to affinity chromatography.
7. Production of Antibodies
A method of making an antibody that specifically binds to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to the said synthetic oligonucleotide when said organic protecting group is not covalently bound thereto, comprises the steps of: (a) synthesizing the synthetic oligonucleotide on a solid particulate support (and preferably covalently bound thereto, e.g., with a succinyl linker) with the organic protecting group covalently bound to said synthetic oligonucleotide; and then, without removing the oligonucleotide from said solid support; and (b) immunizing an animal with the synthetic oligonucleotide bound to the solid support in an amount sufficient to produce the antibody. In addition, a single nucleotide can be bound to the solid particulate support with the organic protecting group bound thereto, and used as described hereinabove.
The synthesis step may be carried out on the solid support in accordance with known techniques. The solid support may be in particulate form prior to synthesis, or may be fragmented into particles after synthesis. In general, the solid supports are beads, which may be completely solid throughout, porous, deformable or hard. The beads will generally be at least 10, 20 or 50 to 250, 500, or 2000 μm in diameter, and are most typically 50 to 250 μm in diameter. Any convenient composition can be used for the solid support, including cellulose, pore-glass, silica gel, polystyrene beads such as polystyrene beads cross-linked with divinylbenzene, grafted copolymer beads such as polyethyleneglycol/polystyrene, polyacrylamide beads, latex beads, dimethylacrylamide beads, composites such as glass particles coated with a hydrophobic polymer such as cross-linked polystyrene or a fluorinated ethylene polymer to which is grafted linear polystyrene, and the like. Where separate discrete solid supports such as particles or beads are employed, they generally comprise from about 1 to 99 percent by weight of the total reaction mixture.
In a preferred embodiment, the synthesizing step is followed by the step of fragmenting the solid support (e.g., by crushing) prior to the immunizing step. Polyclonal antibodies may be collected from the serum of the animal in accordance with known techniques, or spleen cells may be collected from the animal, a plurality of hybridoma cell lines produced from the spleen cells; and then a particular hybridoma cell line that produces the antibody isolated from the plurality of hybridoma cell lines.
A particular protocol for the production of antiserum/polyclonal antibodies and monoclonal antibodies against protecting groups used in nucleic acid and other synthesis typically involves the following steps: (a) preparation of oligonucleotides and others that contain or do not contain protecting groups; (b) immunization of animals with those preparations; (c) screening of animals to identify those that exhibit antibodies against protecting groups; (d) production of monoclonal antibody by classical fusion method; (e) optionally, production of scFab, Fab fragments and whole antibody molecules by antibody engineering; and (f) evaluation and characterization of monoclonal antibodies against the protecting groups. Each of these steps is discussed in greater detail below.
Synthetic oligonucleotides that contain protecting groups can be synthesized in a variety of ways known to those skilled in the art. For example, protecting groups can be attached to individual nucleotides that are linked to controlled pore glass (CPG) beads. An example is:

    
    
        CPG bead---dT (only with DMT group).
    
    


In the alternative, protecting groups may be attached to oligonucleotide chains that are linked to CPG beads. Examples include:
Pac-dA---Pac-dA---CPG beads with Bz-dC and Ibu-dG;
Ipr-Pac-dG---Ipr-Pac-dG---CPG beads with Bz-dC and Ibu-dG;
Ac-dC---Ac-dC---CPG beads with Bz-dC and Ibu-dG;
dmf-G---dmf-G---CPG beads with Bz-dC and Ibu-dG; and
mixtures of the four oligonucleotides described above.
In another alternative, protecting groups may be attached to oligonucleotide chains that are partially deprotected (the procedure for deprotection will be described below). Examples include:
Poly dT20mers (only with DMT group); (SEQ. ID No:1)
Poly dT20mers (only with cyanoethyl groups); (SEQ. ID No:1)
Poly Ibu-dG 20mers (partially deprotected); (SEQ. ID No: 2)
Poly Ipr-Pac-dG 20mers (partially deprotected); (SEQ. ID No: 2)
Poly Bz-dC 20mers (partially deprotected); (SEQ. ID No: 3)
Poly Pac-dA 20mers (partially deprotected); and (SEQ. ID No: 4)
Poly Ac-dC 20mers (partially deprotected). (SEQ. ID No: 3)
Synthetic oligonucleotides prepared as described herein may be partially deprotected as follows: (a) add 30% ammonium hydroxide solution to synthetic polynucleotides, then incubate at room temperature for different time periods (5, 10 and 30 min); (b) take the ammonium solution of treated oligomers and add into 1:1 diluted acetic acid pre-cooled at 4° C. and according to 1:4 ratio of ammonium to acetic acid; (c) keep samples in ice bath for 30 min; (d) dry samples with speed-Vac; (e) dissolve the dried pellets in water; (f) desalt samples with Sephadex G-25 column; (g) dry samples with speed-Vac; and (h) dissolve the desalted samples in water.
Synthetic oligonucleotides prepared as described herein may be completely deprotected by any suitable technique. One particular technique is as follows: (a) add 30% ammonium hydroxide solution to synthetic oligonucleotides, then incubate at 65° C. for 6 hrs; (b) dry samples with speed-Vac; (c) dissolve the dried pellets in water; (d) desalt samples with Sephadex G-25 column; and (e) dry samples with speed-Vac; (f) redissolve desalted samples in water.
Partially and completely deprotected oligonucleotides may be characterized for further use or to verify procedures by any suitable means, including but not limited to gel electrophoresis, urea-acrylamide gel electrophoresis, 5′end labeling with T4 polynucleotide kinase, HPLC analysis, mass spectrometry, etc.
Suitable animals can be immunized with the oligonucleotides described above by parenteral injection of the oligonucleotide in a suitable carrier, such as sterile saline solution. Injection may be by any suitable route, including but not limited to subcutaneous, intraperitoneal, intravenous, intraarterial, intramuscular, etc. Suitable animals are typically mammals, including mice, rabbits, rats, etc.
In a particular embodiment, for the production of monoclonal antibodies, young female BALB/c mice are used, and the time course of injection of the antigen material is:















first day
initial injection



14th day
first boosting



28th day
second boosting



4 day before fusion
final boosting









Additional injections may be employed if desired. The antigen amount may be 50 μg or 100 μg of oligonucleotides unprotected (for control antibody) or protected, for each mouse per time. When, as preferred, beads or other solid support used as the support for oligonucleotide synthesis are injected into the animal, the beads or particles are suspended in water, then injected into mice. If a nucleotide solution is used, then the solution is mixed with complete or incomplete Freund's adjuvant and injected into mice.

Polyclonal antibodies can be harvested from animals immunized or innoculated as described above in accordance with known techniques, or spleen cells harvested from the animals, hybridoma cell lines produced from the spleen cells, and the hybridoma cell lines screened for the production of desired antibodies, also in accordance with known techniques.
Oligonucleotides that contain or do not contain biotin molecules at 3′ or 5′ ends (for ELISA assay as described below) may be synthesized in accordance with standard techniques. Examples are:

    
    
        Poly Ibu-dG 20 mers (with or without biotin);
        Poly Ibu-dA 20 mers (with or without biotin);
        Poly Ibu-dC 20 mers (with or without biotin);
        Poly Ipr-Pac-dG 20 mers (with or without biotin);
        Poly Bz-dC 20 mers (with or without biotin);
        Poly Bz-dA 20 mers (with or without biotin);
        Poly dT 20 mers (with or without biotin);
        Poly Pac-dA 20 mers (with or without biotin);
        Poly Ac-dC 20 mers (with or without biotin); and
        Poly dmf-G 20 mers (with or without biotin).
    
    


Antibodies produced as described above may be characterized by any suitable technique to determine the binding properties thereof, including but not limited to Western blot and immunodot-blot.
In addition to the use of polyclonal and monoclonal antibodies, the present invention contemplates the production of antibodies by recombinant DNA, or “antibody engineering” techniques. For example, mRNA isolated from hybridoma cells may be used to construct a cDNA library and the sequence encoding whole antibody or antibody fragments (e.g., scFab or Fab fragments) isolated and inserted into suitable expression vector, and the expression vector inserted into a host cell in which the isolated cDNA encoding the antibody is expressed.
Monoclonal Fab fragments may be produced in Escherichia coli by recombinant techniques known to those skilled in the art. See, e.g., W. Huse, Science 246, 1275-81 (1989).
8. Screening of Antibodies
Screening sera and hybridoma cell culture media for protecting group specific antibodies may be carried out as follows:
A. Sera
1. Pre-immune (prior to immunization) sera are collected by standard means from the mice to be inoculated with protecting group conjugated to a solid support (directly or through an oligomer).
2. Post-innoculation sera are also collected.
3. An ELISA assay is performed in which the specific protecting group remains on a biotinylated oligonucleotide conjugated to the microtiter plate. Other microtiter plate wells contain control oligomers that have no protecting groups, or oligonucleotides with other protecting groups. The secondary antibody is a goat anti-mouse IgG with a conjugated phosphotase for visualization of antibody.
4. Those mice that have positive activity against the specific protecting group are boosted and sacrificed for the production of hybridomas.
B. Hybridoma Cell Culture Media
1. Approximately 1000 cultures are generated from each spleen hybrid cell production.
2. Cultures are grown in microtiter plate wells, 96 well plates.
3. Culture medium is removed from each well and used in ELISA assays as described above in which each of the  ̃1000 microtiter plate wells contain the protected oligonucleotide conjugated to the plate.
4. Those cultures producing antibody that has positive activity are transferred to larger culture wells, 24 well microtiter plates.
5. Culture media from the larger cultures are re-tested for activity against the protecting group and are also assayed for specificity; i.e. controls of no protecting group and of other protecting groups.
6. Those cultures that are positive are cloned out (diluted), re-tested and cloned out again to the point that each final culture must be the result of one cell; i.e., mono-culture. Media from these final cultures are thoroughly assessed for specificity and affinity. Specificity and affinity are assessed using a dot-blot assay.
C. Dot-Blot Assays in Lieu of ELISA Assays
1. Antibodies against some protecting groups are not tractable to being tested in the microtiter plate well environment and must be tested using a dot-blot assay. One example is the 5′-terminal protecting group, dimethyl-trityl (DMT).
2. The Dot-blot assay on a nitrocellulose membrane is accomplished as described elsewhere in the application for most purposes. However, this is not possible in assessing antibody production by  ̃1000 microtiter well cultures with little media available. Thus, a novel adaptation has been developed.
a) The protected oligonucleotide is attached in dots to the nitrocellulose using UV-crosslinking. With DMT, the presence of the 5′-DMT on the membrane is confirmed by treatment of a dot with mild acid—the dot turns yellow-orange. The presence of the 3′-biotin can be confirmed with a commercial avidin stain.
b) The membrane is blocked (see dot-blot assay).
c) The dry membrane dots are carefully marked (pencil) and “punched” out of the membrane.
d) Individual dots are added to the cell culture media in individual microtiter plate wells and incubated.
e) The individual dots are removed and passed on through the washing, secondary antibody, phosphotase reaction and color development using microtiter plate wells with the appropriate reagents.
f) Those dots that are positive are related back to the original microtiter plate well cultures from which the small amount of culture media was obtained.
g) Further culturing and cloning is accomplished as described in B.
9. Testing of Microarrays
The present invention may be used to test or screen oligonucleotides that are immobilized on a solid support such as a microarray for insufficient deprotection or elongation of the oligonucleotides synthesized thereon.
Solid supports used to carry out the present invention are typically discrete solid supports. Discrete solid supports may be physically separate from one another, or may be discrete regions on a surface portion of a unitary substrate. Such “chip-type” or “pin-type” solid supports are known. See, e.g., U.S. Pat. No. 5,143,854 to Pirrung; U.S. Pat. No. 5,288,514 to Ellman (pin-based support); U.S. Pat. No. 5,510,270 to Fodor et al. (chip-based support). Additional non-limiting examples of oligonucleotide arrays which may be used to carry out the present invention, and methods of making the same, include but are not limited to those described in U.S. Pat. Nos. 5,631,734; 5,599,695; 5,593,839; 5,578,832; 5,510,270; 5,571,639; 6,056,926; 5,445,934; and 5,703,223. Such devices maybe used as described therein to carry out the instant invention.
The solid support or substrate from which the array is formed may be comprised of any suitable material, including silicon. The oligonucleotides may be polymerized or grown in situ from monomers (or individual nucleotides) in situ on the microarray (in which case none of the currently available techniques for detecting protecting groups would be useful for detecting incomplete deprotection or elongation of the oligonucleotides on the array, as one cannot pass the solid support through an analytical device) or the oligonucleotides may be polymerized separately and then linked to the appropriate regions of the solid support. The array may include any number of different oligonucleotides in different separate and discrete regions thereon, examples including arrays of at least 1,000, at least 2,000, at least 10,000, or at least 20,000 different oligonucleotides in different separate and discrete regions.
In general, a method of screening an oligonucleotide array for insufficient deprotection or insufficient elongation of oligonucleotides therein comprises the steps of:
(a) providing an oligonucleotide array as described above;
(b) providing an antibody as described above (that is, an antibody that specifically binds to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to said synthetic oligonucleotide when said organic protecting group is not covalently bound thereto). Preferably the antibody is one that specifically binds to an oligonucleotide having a protecting group, where the protecting group was employed in the course of the organic synthesis of oligonucleotides carried by that array. Then;
(c) contacting said oligonucleotide array to said antibody to thereby detect the presence of insufficient deprotection or insufficient elongation of oligonucleotides therein. Such detection, which may be qualitative or quantitative, may be carried out by any suitable immunoassay technique as described above.
In the method, steps (b) to (c) may be repeated at least once, with a different antibody on each repetition, so that a plurality of different protecting groups which may be present on oligonucleotides in the array may be detected.
Preferably, once insufficient deprotection (the presence of protecting groups) in oligonucleotides in one or more (e.g., plurality) of the separate and discrete regions is detected, the method further comprises generating a record or indicia recording the presence of insufficient deprotection or insufficient elongation of oligonucleotides in the least one separate and discrete location (or plurality of separate and discrete locations) on the array. The indicia may be a qualitative or quantitative indicia of insufficient deprotection (including insufficient elongation).
The foregoing methods provide a correctable oligonucleotide array as illustrated in FIG. 11. The array comprises, in combination:
(a) a substrate 30 having a plurality of different oligonucleotides immobilized thereon, with the different oligonucleotides immobilized in different separate and discrete locations 31 on said substrate; and
(b) a plurality of indicia associated with said array, these indicia recording the presence of insufficient deprotection or insufficient elongation of a plurality of different oligonucleotides, said different oligonucleotides located in separate and discrete locations on said array. These indicia may be printed in a region of the array 32 by a technique such a microlithography, printed on conventional medium such as paper and shipped with the array, stored in a memory or memory device connected to or formed on the array chip (which may be incorporated at location 32), provided in a separate data or computer file which may be provided on a computer-readable medium such as a floppy diskette or CD-ROM, stored on a web site on the world wide web for downloading by the end user of the array, etc. When the indicia are provided in a separate data file, the array preferably further includes an identifier such as a code number formed on, connected to or associated with the array (e.g., printed on a package containing the array, or on an information sheet packaged with the array, and/or printed directly on the array). The identifier may then be associated with the separate indicia (e.g., printed on a data sheet, used as a pass-word, file identifier and/or access code for the computer file, etc.) to insure the correct indicia containing the record of insufficient deprotection and/or elongation are ultimately associated with the array by the ultimate end user of the array.
A data device or memory device connected to the array may be carried out in accordance with known techniques, as described in U.S. Pat. Nos. 5,925,562; 6,017,496; 5,751,629; and 5,741,462, and such devices used as described therein to carry out the instant invention.
The end user of the array may utilize the indicia described above to compensate for insufficient deprotection or insufficient elongation of oligonucleotides on said array in a method comprising:
(a) providing a substrate as described above.
(b) providing at least one, or a plurality of, indicia associated with said array as described above.
(c) providing a test compound. The test compound may be a member of a library of test compounds, and may be any suitable compound such as a protein, peptide or oligonucleotide (e.g., a DNA or RNA, such as mRNA); and then
(d) detecting the binding of said test compound to at least one of said plurality of different oligonucleotides (e.g., by contacting the test compound to the array); and then
(e) detecting determining the degree of binding (including simply the presence or absence of binding) of the test compound to one or more oligonucleotides on the array from (i) said detected binding and (ii) said indicia recording the presence of insufficient deprotection or insufficient elongation. Thus, insufficient deprotection or insufficient elongation of oligonucleotides in one or more locations in the array may be compensated for during the determining step. Such compensation may be achieved by any means, including ignoring particular separate and discrete regions on the array (e.g., in favor of other separate and discrete regions of the array that contain the same oligonucleotide). In another example, if one or more locations contain insufficient deprotection or elongation such that binding to those locations is reduced, the binding data derived from an experiment with that array can be adjusted upwards for those locations to indicate greater binding than that which would otherwise be indicated without the control made possible by the recorded indicia. The detecting or determining step may be carried out by any suitable means, such as generating a color indication of degree of binding, generating a numeric indication of degree of binding, generating a graphic or other symbolic indication of degree of binding, etc. The degree of binding may be an indication of binding is binding affinity, binding amount, or both binding affinity and binding amount, but is typically an indication of the amount of test compound that binds to a particular separate and discrete region of the array.
10. Antibody Microarrays
The present invention includes antibody microarrays or “antibody chips” formed with a plurality or an array of antibodies immobilized on a substrate. Each of the antibodies used on the antibody microarray specifically binds to a synthetic oligomer (such as a synthetic oligonucleotide) having an organic protecting group bound thereto, as described above. Such an antibody chip may be used to detect incomplete deprotection of synthetic oligomers and/or separate protected synthetic oligomers from deprotected synthetic oligomers. Such an antibody chip may also be used to detect incomplete elongation of synthetic oligomers and/or separate full-length synthetic oligomers from incomplete synthetic oligomers (e.g., when the protecting group is chain terminating). The antibody chips according to the present invention and the methods of using them described below may be useful in high throughput assays of unbound oligomers or oligomers bound to a substrate (such as, for example, an oligonucleotide microarray).
The substrate from which the antibody microarray is formed may be comprised of any suitable material, including, for example, silicon, aluminum, glass, plastic, polycarbonate, polystyrene, polypropylene, polyethylene, agarose beads, or membranes made of nitrocellulose, nylon, or polyvinylidene difluoride (PVDF). The substrate is typically in the form of a “chip” having a flat surface, but may also comprise other alternative configurations such as, for example, beads, membranes, microparticles, and the interior surface of reaction vessels.
Suitable methods of immobilizing (i.e., attaching directly or indirectly by covalent bonds, non-covalent bonds, or other means) antibodies on suitable substrates are known to those skilled in the art. The antibody microarrays may have any desirable density (i.e., spots of antibodies/area), including a high-density of antibodies. Antibodies may be directly immobilized on a substrate, for instance, by covalently attaching the antibodies to a glass microscope slide. Antibodies may be indirectly immobilized on a substrate, for example, by immobilizing protein A or G on the substrate and then immobilizing the antibodies on the substrate through the antibodies' interactions with protein A or G. Another example of a suitable method comprises immobilizing an antibody within a three-dimensional hydrophilic polymer matrix on a glass microscope slide. A coupling reagent in the matrix may react with the antibody to covalently attach and immobilize the antibody within the matrix. Yet another suitable method for immobilizing antibodies on a substrate involves printing or spotting the antibodies onto a substrate by jet droplet printing methods such as, for example, the method described in U.S. Pat. No. 5,958,342, incorporated herein by reference in its entirety.
The following references, each of which is incorporated herein by reference in its entirety, also describe examples of suitable methods for immobilizing antibodies on suitable substrates: MacBeath and Schreiber, “Printing Proteins as Microarrays For High-Throughput Function Determination,” Science 289: 1760, 8 September 2000; Haab, B. B.; Dunham, M. J.; Brown, P. O., “Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions,” Genome Biology, 2001, 2(2): research0004.1-0004.12; and U.S. Pat. No. 6,197,599. In addition, other methods known to those skilled in the art may also be used to immobilize the antibodies described herein to a suitable substrate to form an antibody microarray in accordance with the present invention.
The antibodies may be immobilized at predetermined positions on the substrate so that, if desired, the antibodies can be identified by their specific position. Once immobilized, the antibodies retain their binding capability and specificity, and the variable regions of the antibodies will be fully exposed to interact with antigens (such as oligonucleotides having one or more organic protecting groups covalently bound thereto). Separate discrete regions (e.g., spots or other geometric or non-geometric shapes) of the antibody chip may include antibodies with the same or different binding specificity. In such an embodiment, each discrete region is preferably separated by areas not containing antibodies. Typically, each discrete region will only have antibodies with the same binding specificity in order to determine which protecting group or groups was not deprotected by detecting the presence of binding in each discrete region.
The antibodies on the antibody microarrays of the present invention may also be integrated into flow channels, flow chambers, or wells on or in the substrate so that the antibodies are always in aqueous solution or other suitable solution, thus ensuring the antibodies will not be denatured.
An antibody microarray according to the present invention may be used to detect incomplete deprotection of synthetic oligonucleotides and/or separate protected from deprotected synthetic oligonucleotides. An antibody microarray according to the present invention may also be used to detect incomplete elongation of synthetic oligonucleotides and/or separate full-length from incomplete synthetic oligonucleotides. Various embodiments are possible for such uses of an antibody microarray.
For example, free oligonucleotides that are synthesized for use on an oligonucleotide microarray may be contacted with an antibody chip that contains an array of antibodies designed to bind to oligonucleotides having some or all of the protecting groups used in the synthesis of the oligonucleotides. That is, the antibody microarray contains antibodies specific for at least one, preferably more than one, more preferably all of the protecting groups used in the synthesis of the oligonucleotides. The oligonucleotides that are not fully deprotected will be bound to one of the antibodies having binding specificity to the protecting group remaining on the oligonucleotide. Such a method would increase the purity of the unbound synthetic oligonucleotides that are to be immobilized (e.g., by printing, spotting, or other known methods) on the substrate of an oligonucleotide array. Using an antibody microarray having antibodies specific for all the protecting groups employed in the synthesis of the synthetic oligonucleotides, the method could be used to ensure that the oligonucleotides are fully deprotected and are full-length before being added to an oligonucleotide array. The antibodies of such an embodiment could be immobilized on a surface (flat or otherwise) of the substrate or could be immobilized in flow channels or flow chambers that the synthetic oligonucleotides could be passed through. Such flow channels or chambers may be used to ensure that the antibodies would remain in an appropriate solution or buffer to prevent denaturation and may possibly increase the throughput of detection or separation methods. Such an antibody chip could also be used to determine the specific protecting groups that were present in the synthetic oligonucleotide or oligonucleotides by correlating known locations of the specific antibodies on the antibody microarray with the detection of the presence of binding at specific locations.
It may also be possible to contact an antibody chip of the present invention with a fully or partially complete oligonucleotide microarray in order to detect insufficient deprotection and/or elongation of the oligonucleotides thereon. The antibody microarray may be formulated such that each oligonucleotide in the oligonucleotide array is subjected to the appropriate antibody or antibodies. After contacting the antibody chip with the fully or partially complete oligonucleotide microarray, a suitable detection method could be used to determine the location and identity of any protecting groups remaining on the oligonucleotide microarray. As described above, an indicia of the location of any incomplete deprotection/elongation could also be generated.
One aspect of the invention includes a method of detecting incomplete deprotection of a synthetic test oligonucleotide using an antibody microarray. The method comprises the following steps:
(a) providing an antibody microarray comprising a plurality of antibodies immobilized on a substrate, each antibody specifically binding to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to the synthetic oligonucleotide when the organic protecting group is not covalently bound thereto;
(b) contacting the synthetic test oligonucleotide with the antibodies immobilized on the antibody microarray; and
(c) detecting binding of the synthetic test oligonucleotide to the antibodies immobilized on the antibody microarray, the presence of binding indicating incomplete deprotection of the synthetic test oligonucleotide. Such a method may optionally include a separation step before step (c) in order to remove any unbound synthetic oligonucleotides from the antibody microarray, thus avoiding the detection of the unbound synthetic oligonucleotides in step (c).
Another aspect of the invention includes a method of purifying a synthetic oligonucleotide mixture prepared using organic protecting groups. The method uses an antibody microarray and comprises the following steps:
(a) providing a synthetic oligonucleotide mixture comprising fully deprotected synthetic oligonucleotides, partially deprotected synthetic oligonucleotides, and/or fully protected synthetic oligonucleotides, the mixture having at least one partially or fully protected synthetic oligonucleotide with a protecting group covalently bound thereto;
(b) providing an antibody microarray comprising a plurality of antibodies immobilized on a substrate, each antibody specifically binding to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to the synthetic oligonucleotide when the organic protecting group is not covalently bound thereto, the plurality of antibodies including at least one antibody that is capable of binding at least one of the partially or fully protected synthetic oligonucleotides;
(c) contacting the synthetic oligonucleotide mixture with the antibodies immobilized on the antibody microarray such that at least one of the protected synthetic oligonucleotides from the mixture is bound to at least one of the antibodies immobilized on the antibody microarray, wherein at least a portion of the oligonucleotides in the synthetic oligonucleotide mixture do not bind to the plurality of antibodies; and
(d) separating the antibody microarray and the unbound synthetic oligonucleotides, thus separating the unbound synthetic oligonucleotides from any partially and/or fully protected synthetic oligonucleotide or oligonucleotides bound to the antibodies immobilized on the antibody microarray.
Yet another aspect of the present invention includes a method of preparing an oligonucleotide microarray using an antibody microarray. The method comprises the following steps:
(a) providing a synthetic oligonucleotide mixture prepared using organic protecting groups, the mixture comprising fully deprotected synthetic oligonucleotides, partially deprotected synthetic oligonucleotides, and/or fully protected synthetic oligonucleotides, the mixture having at least one partially or fully protected synthetic oligonucleotide with a protecting group covalently bound thereto;
(b) providing an antibody microarray comprising a plurality of antibodies immobilized on a first substrate, each antibody specifically binding to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to the synthetic oligonucleotide when the organic protecting group is not covalently bound thereto, the plurality of antibodies including at least one antibody that is capable of binding at least one of the partially or fully protected synthetic oligonucleotides;
(c) contacting the synthetic oligonucleotide mixture with the antibodies immobilized on the antibody microarray such that at least one of the protected synthetic oligonucleotides from the mixture is bound to at least one of the antibodies immobilized on the antibody microarray, wherein at least a portion of the oligonucleotides in the synthetic oligonucleotide mixture do not bind to the plurality of antibodies;
(d) separating the antibody microarray and the unbound synthetic oligonucleotides, thus separating the unbound synthetic oligonucleotides from any partially and/or fully protected synthetic oligonucleotide or oligonucleotides bound to the antibodies immobilized on the antibody microarray; and
(e) immobilizing the unbound synthetic oligonucleotides on a second substrate to form an oligonucleotide microarray.
In any of the above aspects of the invention, the plurality of antibodies immobilized on the substrate may include one or more (e.g., at least two) sets of antibodies, with each set of antibodies having a different binding specificity from the other sets. In some embodiments, each set of antibodies is localized to a separate discrete region on the substrate, with each discrete region being separated by a region on the substrate to which no antibodies are immobilized. In addition, the antibodies of the antibody microarray may be immobilized in flow channels or flow chambers formed in or on the substrate of the antibody microarray.
As discussed above, each antibody immobilized on the antibody microarray specifically binds to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to the synthetic oligonucleotide when the organic protecting group is not covalently bound thereto. It is again noted that antibodies of the invention may be characterized by their selective binding to particular “reagent” or “benchmark” oligonucleotides, but the same antibodies may also bind to a variety of other oligonucleotides (e.g., longer or shorter nucleotides) or other compounds that contain the same protecting group. In some embodiments, each antibody may be characterized in that the synthetic oligonucleotide to which the antibody specifically binds includes a protected nucleotide according to Formula (I)




wherein:

    
    
        R is H or a protecting group; subject to the proviso that R is a covalent bond to an adjacent nucleotide when the protected nucleotide is not a 5′ terminal nucleotide in the oligonucleotide;
        R1 is H or a protecting group; subject to the proviso that R1 is a covalent bond to an adjacent nucleotide when the protected nucleotide is not a 3′ terminal nucleotide in the oligonucleotide;
        R2 is H or —OR3;
        R3 is H or a protecting group;
        Base is a purine or pyrimidine base;
        R4 is a protecting group substituted for a hydrogen on an amino group of the base, subject to the proviso that R4 is not present in Formula (I) when R, R1, or R3 is a protecting group or when the base does not include an amino group; and
        further subject to the proviso that only one of R, R1, R3, and R4 is a protecting group and the others of R, R1, R3, and R4 are not protecting groups.

In particular embodiments, R is a protecting group comprising dimethoxytrityl; R1 is a protecting group comprising β-cyanoethyl; R2 is —OR3 and R3 is a protecting group comprising tert-butyldimethylsilyl; and R4 is a protecting group selected from the group consisting of acetyl, benzoyl, dimethylformamidine, isobutyrl, phenoxyacetyl, and isopropyl-phenoxyacetyl. In other particular embodiments, the oligonucleotide to which the antibody selectively binds consists of from 3 to 20 nucleotides.

    
    


The synthetic oligonucleotides (or synthetic test oligonucleotides) used in the above methods may include a detectable marker. Such a detectable marker may be a radio label, a member of a binding pair such as biotin or avidin, a fluorophore such as green fluorescent protein, a detectable enzyme, and/or a dye. Other possible examples of detectable markers include rhodamine, fluorescein, digoxin, Cy3 dye, Cy5 dye, and dinitrophenol (DNP). In addition, any other detectable marker suitable for the specific method could also be used. In the method of detecting incomplete deprotection of a synthetic test oligonucleotide (or any of the other methods where detection of binding is desirable), the binding of the synthetic test oligonucleotide to the antibodies immobilized on the antibody microarray may be detected by detecting the detectable marker of the synthetic test oligonucleotide.
11. Pre-Impregnation of Oligonucleotide Microarrays with Antibodies
The present invention also includes an oligonucleotide array impregnated with antibodies. Each of the antibodies specifically binds to a synthetic oligomer having an organic protecting group covalently bound thereto, as described above. As used herein, “impregnated” means that antibodies are immobilized on an oligonucleotide array and “pre-impregnation” means that antibodies are immobilized of on a substrate that will eventually include an array of oligonucleotides.
According to this aspect of the present invention, the antibodies are pre-impregnated (i.e., immobilized) on a substrate that will eventually contain an oligonucleotide microarray. The antibodies may be immobilized on a substrate by any method known in the art, such as, for example, the methods described above in connection with antibody chips of the present invention.
After the antibodies have been immobilized on the substrate, the oligonucleotide array is formed on the microarray, either by synthesis in situ on the substrate or by polymerizing the oligonucleotides separately and then linking them to the appropriate regions of the substrate.
In some applications, it may be necessary to encapsulate the antibodies or block the binding sites on the antibodies with one or more blocking groups until such time as detection of incomplete deprotection and/or insufficient elongation is desired. In such embodiments, the antibodies may be contacted with the oligonucleotides when desired by releasing the antibodies from the capsules or removing the blocking groups from the antibodies. A suitable assay may then be performed to determine incomplete deprotection and/or elongation.
The present invention is explained in greater detail in the following non-limiting examples.
Example 1
Synthesis of Oligonucleotides
Synthesis was performed on an ABI DNA/RNA Synthesizer, Model 394 (PE Biosystems, 850 Lincoln Centre Drive, Foster City, Calif. 94404) according to manufacturer's protocol. Slightly modified 1 micromolar scale cycle was used during synthesis (see manufacturer's instructions). The primary starting materials (and suppliers/manufacturers in parentheses) were as follows:
Activator (0.45 M tetrazole in acetonitrile), CAP A (acetic anhydride/tetrahydrofuran/2,6 lutidine), CAP B (N-methyl imidazole/tetrahydrofuran) and oxidizer (0.02 M iodine/pyridine/THF/H2O) (Prime Synthesis)
Pac-dA (5′-dimethoxytrityl-N-phenoxyacetyl-2′-deoxyAdenosine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite (Glen Research)
Ipr-Pac-dG (5′-dimethoxytrityl-N-p-isopropyl-phenoxyacetyl-2′-Guanosine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite (Glen Research)
Ac-dC (5′-dimethoxytrityl-acetyl-2′-deoxycytidine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite (Glen Research)
dmf-G (5′-dimethoxytrityl-dimethylformamidine-Guanosine,2′-O-TBDMS-3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite (Glen Research)
Bz-dC---CPG beads (5′-dimethoxytrityl-N-benzoyl-2′-deoxycytidine, 3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite-succinyl linker-beads (3000 Ang) (CPG Inc.)
Ibu-dG---CPG beads (5′-dimethoxytrityl-N-isobutyl-2′-deoxycytidine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite-succinyl linker-beads (3000 Ang) (CPG Inc.)
The following compounds were synthesized, the compounds being linked to beads as shown:

    
    
        Pac-dA---Pac-dA---Bz-dC---succinyl linker---Beads
        Pac-dA---Pac-dA---Ibu-dG---succinyl linker---Beads
        Ipr-Pac-dG---Ipr-Pac-dG---Bz-dC---succinyl linker---Beads
        Ipr-Pac-dG---Ipr-Pac-dG---Ibu-dG---succinyl linker---Beads
        Ac-dC---Ac-dC---Bz-dC---succinyl linker---Beads
        Ac-dC---Ac-dC---Ibu-dG---succinyl linker---Beads
        dmf-G---dmf-G---Bz-dC---succinyl linker---Beads
        dmf-G---dmf-G---Ibu-dG---succinyl linker---Beads
    
    


The foregoing compounds were administered directly to animals as an immunogen, without separating the oligonucleotide from the solid support, for the production of antibodies, as further described in Example 2 below.
Example 2
Innoculation of Animals
Female BALB/c mice of eight to twelve weeks old were purchased from Charles River, Raleigh, N.C., USA. The mice were housed in cases with filter caps.
After oligonucleotide chain synthesis was completed as described in Example 1, the beads with nucleotides were gently crushed by hand-pressuring the glass plates, between which beads were positioned.
5 μM of each eight oligonucleotides mentioned above were mixed in 4 ml PBS (150 mM sodium chloride in 100 mM phosphate buffer, pH 7.2).
The mixture was thoroughly vortexed suspending the crushed beads. 150 μL of the vortexed mixture was taken and added into 300 μL of PBS in a syringe. Just before injection, the solution containing beads was mixed again by shaking the syringe to suspend the broken beads. Then 150 μL or 300 μL of well-mixed solution was injected into mouse peritoneal cavity. This procedure was used for the first injection and the following boosts.










Injection time schedule:










Injection
Date (day)






first
0



second
14th



third
28th



4th
42nd



5th
56th



6th
70th



7th
84th



8th
98th



9th
112th



10th
138th



11th (final, 4 day before fusion)
142nd









Four days after the final injection, spleen cells are harvested from the animals and fused with myeloma cells (P3x.63.Ag8.653) in accordance with known techniques to produce hybridoma cell lines, which are then screened to determine the binding characteristics as described below to isolate particular cell lines that produce the desired antibody of the invention.
Example 3
Immunodot-Blot Assay for Antibody Characterization
The Immunodot-blot assay involves UV cross linking of oligonucleotides onto membrane paper, and is directly applicable to a test kit for detection, identification and quantifying the protecting groups on product oligomers. This procedure may be carried out as follows: (a) wet membrane paper with TBS (10 mM Tris, pH 7.2; 150 mM NaCl); (b) blot oligonucleotides to be tested onto membrane paper under vacuum; (c) UV cross link nucleotide onto membrane paper; (d) block membrane paper with 1% casein-TBST (TBS plus Tween 20, 0.1% by volume) at room temperature for 2 hr or 4° C. overnight; (e) wash membrane with TBST 3 times, each for 15 min; (f) form antigen-antibody complex by incubation of plate with sample be tested (diluted in 1% casein-TBST) at room temperature for 1 hr; (g) wash as above; (h) react with second antibody conjugate (diluted in 1% casein-TBST) at room temperature for 1 hr; (i) wash as above; (j) develop color reaction by incubation of membrane with substrate solution.
Example 4
Dot-Blot Assay of Monoclonal Antibody 1H11
Monoclonal antibody 1 H11, produced as described in Example 2 above, was characterized by a dot-blot assay as described in Example 3 above. Results are shown as a bar graph in FIG. 1. In FIG. 1, lanes (or columns) 1 and 2 represent oligoPac-dA20mers treated with NH4OH for 6 hours at 65° C. and 15 minutes at 4° C., respectively. Columns 3 and 4 represent oligoBz-dC20mers treated with NH4OH for 6 hours at 65° C. and 15 minutes at 4° C., respectively. Columns 5 and 6 represent oligoAc-dC20mers treated with NH4OH for 6 hours at 65° C. and 15 minutes at 4° C., respectively. Columns 7 and 8 represent oligoIpr-Pac-dG20mers treated with NH4OH for 6 hours at 65° C. and 15 minutes at 4° C., respectively. Columns 9 and 10 represent oligoIbu-dG20mers treated with NH4OH for 6 hours at 65° C. and 15 minutes at 4° C., respectively. Columns 11, 12 and 13 represent oligodT20mers, completely deprotected, with DMT group only, and with cyanoethyl group only, respectively. Antibody activity is given as optical density (479 nm) from ELISA (Example 7 below), and the positive or negative result of the dot blot assay is given in the open or filled circle appearing over each column in the bar graph. Note the activity of monoclonal antibody 1 H11 in selectively binding to the oligoIbu-dG20mer in column 10.
Example 5
Dot-Blot Assay of Monoclonal Antibody 7H3
Monoclonal antibody 7H3, produced as described in Example 2 above, was characterized by a dot-blot assay as described in Example 3 above. Results are shown as a bar graph in FIG. 2. In FIG. 2, lanes (or columns) 1 and 2 represent oligoPac-dA20mers treated with NH4OH for 6 hours at 65° C. and 15 minutes at 4° C., respectively. Columns 3 and 4 represent oligoBz-dC20mers treated with NH4OH for 6 hours at 65° C. and 15 minutes at 4° C., respectively. Columns 5 and 6 represent oligoAc-dC20mers treated with NH4OH for 6 hours at 65° C. and 15 minutes at 4° C., respectively. Columns 7 and 8 represent oligoIpr-Pac-dG20mers treated with NH4OH for 6 hours at 65° C. and 15 minutes at 4° C., respectively. Columns 9 and 10 represent oligoIbu-dC20mers treated with NH4OH for 6 hours at 65° C. and 15 minutes at 4° C., respectively. Columns 11, 12 and 13 represent oligodT20mers, completely deprotected, with DMT group only, and with cyanoethyl group only, respectively. Antibody activity is given as optical density as described above, and the positive or negative result of the dot blot assay is given in the open or filled circle appearing over each column in the bar graph. Note the activity of monoclonal antibody 7H3 in selectively binding to the oligoBz-dC20mer in column 4.
Example 6
Western Blot Assay for Antibody Characterization
The Western blot assay involves low voltage transfer of oligonucleotides from gel to membrane paper and UV cross linking of oligonucleotides onto the membrane. This assay may be carried out as follows: (a) cast 15% non-denaturing gel containing 10 mM MgCl; (b) load oligonucleotides (oligomers) into the wells of the gel; (c) run gel at 200 voltage in ice bath; (d) transfer oligonucleotides from gel to membrane paper at 25 voltage for 25 min in ice bath; (e) UV cross link polynucleotides on membrane; (f) block membrane paper with 1% casein-TBST at room temperature for 2 hr or 4° C. overnight; (g) wash membrane with TBST 3 times, each for 15 min; (h) incubate samples be tested (diluted in 1% casein-TBST) at room temperature for 1 hr; (i) wash as above; (j) incubate membrane with second antibody conjugate (diluted in 1% casein-TBST) at room temperature for 1 hr; (k) wash as above; and (l) color-develop by incubation of membrane with substrate solution.
Example 7
Detection of Antibody Using Biotinylated Polynucleotides as Antigen and an ELISA involving Streptavidin-Biotin System
An enzyme-linked immunosorbent assay (ELISA) for the detection of the antibody is carried out as follows: (a) pre-screen microtiter plate that is pre-coated with streptavidin; (b) coat the plate with a preparation of biotinylated oligonucleotide or other materials to be tested (at 5 μg/ml in PBS)(PBS: 150 mM NaCl, 10 mM Phosphate buffer, pH 7.4), then incubate at room temperature for 2 hrs; (c) wash 3 times with 0.1% Tween in PBS (PBST), each for 15 min; (d) block with 1% casein in PBST at room temperature for hrs or 4° C. overnight; (e) wash as above; 69 form antigen-antibody complex by incubation of plate with antibody (or antibodies) at room temperature for 1 hr; (g) wash as above; (h) react with second antibody-peroxidase conjugate (in 1% casein-PBST) at room temperature for 1 hr; (i) wash as above; (j) develop color reaction by adding tetramethylbenzidine (TMB) solution (TMB solution: 42 mM TMB, 0.004% H2O2, 0.1 M acetate buffer, pH 5.6) and incubating at room temperature for 15 min, then stop the reaction with 2 M H2SO4; and (k) read absorption value at 469 nm.
Example 8
ELISA and Dot-Blot Assay of Monoclonal Antibody Against Benzoyl, Isobutryl, and Isopropyl-Phenoxyacetyl
Monoclonal antibodies (mAb) against protecting groups benzoyl (Bz), isobutryl (ibu), and isopropyl-phenoxyacetyl (ipr-Pac), produced as described in Example 2 above, were characterized by a standard ELISA assay and a dot-blot assay as described in Example 3 above. An ELISA assay developed with biotinylated nucleic acids of 20 residues each attached to a 96-well microtiter plate demonstrated the specificity of the antibodies for their respective antigens. FIG. 3A, FIG. 4A, and FIG. 5A show results for monoclonal antibodies against Bz, ibu, and ipr-Pac, respectively. The figures show completely deprotected (<1% Bz remaining) homopolymers of dC residues, designated oligo dC(Bz), ie. originally protected with Bz (lane 1, open bar), protected (>97% Bz remaining) oligo Bz-dC (lane 2, shaded bar), completely (<1% ipr-Pac remaining) deprotected oligo dG(ipr-Pac) (lane 3), protected (>76% ipr-Pac) oligo ipr-PacdG (lane 4), completely (<1% ibu remaining) deprotected oligo dG(ibu) (lane 5), protected (>91% ibu remaining) oligo ibu-dG (lane 6), and completely deprotected oligo dT (lane 7). The dT polymer had but one protecting group, dimethyltrityl (DMT) that was removed from the 5′OH of the 5′-terminal residue with mild acid. Finally, lane 8 shows oligo dT with DMT remaining.
Dot-Blot assays of anti-Bz mAb, anti-ibu mAb, and anti-ipr-Pac mAb activities were performed in which the 20mer DNAs were linked to nitrocellulose membrane by UV. The amounts of 20mer DNA applied to the membrane are shown on the left of FIG. 3B, FIG. 4B, and FIG. 5B and demonstrate the level of sensitivity of the assay. The DNAs used to test anti-Bz mAb were those described for the ELISA plus deprotected oligo dA(Bz), protected oligo Bz-dA, oligo dC(ibu), oligo ibu-dC, oligo dA(ibu) and oligo ibu-dA. FIG. 3B shows that the anti-Bz mAb recognized the protecting group on dA and dC. The DNAs used to test anti-ibu mAB were those described for the ELISA plus protected oligo ibu-dA, deprotected oligo dA(ibu), oligo ibu-dC, oligo dC(ibu) and all are noted at the top of the dot-blot. FIG. 4B shows that the anti-ibu mAb recognized ibu on dG, the most common use of the protecting group, but also on dA. The DNAs used to test anti-ipr-Pac mAb were those described for the ELISA plus protected oligo ibu-dA, deprotected oligo dA(ibu), oligo ibu-dC, oligo dC(ibu), oligo Bz-dA, oligo dA(Bz) and all are noted at the top of the dot-blot. FIG. 5B shows that the anti-ipr-Pac mAb recognized ipr-Pac on dG, the most common use of the protecting group, but also on dA and dC. The mAb also recognized the ibu protecting group (ibu-dG, ibu-dA and ibu-dC). This cross-reactivity indicates that the antibody was highly selective in its identification of a chemistry common to both ipr-Pac and ibu, possibly CH(CH3)2. Thus the anti-ibu and anti-iprPac mAbs could be used in combination to identify the protecting group remaining on an oligo.
Greater amounts of DNA were tested in a dot blot assay of anti-ibu mAb (FIG. 4C). The results of this experiment demonstrated that the ibu protecting group was recognized by the mAb no matter which nucleobase was protected.
FIG. 3C, FIG. 4D, and FIG. 5C demonstrate that partially deprotected oligomers can be re-treated to remove the remaining protecting groups, and re-tested with mAb. FIG. 3C shows that anti-Bz mAb recognized re-deprotected oligomer oligo Bz-dC (center column). Likewise, FIG. 4D shows that anti-ibu mAb recognized re-deprotected oligomer oligo ibu-dG (center column) and FIG. 5C shows that anti-ipr-Pac mAb recognized re-deprotected oligomers oligo ipr-Pac-dG and oligo ibu-dG (columns second from left and forth from left, respectively). Thus, this approach is applicable to quality control without having to discard expensive nucleic acid samples.
An RNA standard with protecting groups Bz, ibu and ipr-Pac was synthesized and assayed for identification of the protecting groups with the mAb against Bz (FIG. 3D), ibu (FIG. 4E), and ipr-Pac (FIG. 5D). Dot-blot assays clearly show that the monoclonal antibodies do not differentiate RNA from DNA. Although there was a higher background signal with RNA than with DNA, there was a significant distinction between RNA with and without protecting groups, especially at the lower amounts of RNA. The amount of RNA on the membrane was estimated from the optical absorbance of the sample.
Example 9
mAb Dot-Blot Assay of Protecting Groups Vs HPLC
Dot-blot detection of Bz groups remaining on a standardized 20mer oligo dC molecule were performed as described in Example 3. Completely deprotected and the untreated oligo dC 20mers were analyzed for the Bz protecting group using a totally independent and different quantification method. The two oligomers were hydrolyzed to the constituent nucleosides and then their nucleoside composition identified and quantified using a recognized high performance liquid chromatography (HPLC) method with concentrated samples. Because of the lack of sensitivity, HPLC detection required 50-100 fold the amounts of Bz-dC used in the mAb assays (see FIG. 7). FIG. 6A shows the result of anti-Bz mAb tested against nmole amounts of Bz groups on protected oligo Bz-dC (right column) and the same nmole amounts of Bz- on Bz-dC (left column). Each amount of Bz-dC oligo was diluted with completely deprotected dC oligo of the same length (20mer) to demonstrate the sensitivity of the mAb detection even in the presence of 2500-fold dC (ie. 0.04%). The mAb assay demonstrated that the mAb could detect the Bz group on DNA even in the presence of a 2500-fold excess of dC in DNA.
The dot-blot shown in FIG. 6A was subjected to densitometry to quantitate the mAb response. After background subtraction, the remaining density was plotted as a function of Bz groups in oligo Bz-dC determined by HPLC (FIG. 6B). The data indicated that the high sensitivity of the anti Bz mAb detection was linear in 0.1-1.0 nmol range.
Next, it was determined whether the mAb response could be enhanced with an increase in the amount of DNA on the dot-blot membrane. The amount of Bz was determined by standard HPLC methods. This experiment showed that detection of the Bz protecting group in a mixture of the protected sample with the deprotected sample at a ratio of 1/2500 could be enhanced by increasing the amount of DNA on the membrane, though the ratio was maintained (FIG. 6C).
Finally, experiments were conducted to show a direct comparison of the mAb and HPLC detection of Bz. Anti-Bz mAb was utilized in a dot-blot assay to detect Bz on dC in the oligo Bz-dC (20mer). The density response of the Bz group detected Bz by the mAb assay and quantified by densitometry was plotted against the amount of Bz in the DNA on each dot (FIG. 7A). The amount of Bz in the DNA was calibrated by digestion of a large amount of DNA and analysis by HPLC identification and quantification of the Bz-dC mononucleoside. For HPLC experiments, three samples of Bz-dC oligo were hydrolyzed and analyzed for composition by HPLC. The response of the UV-diode array detector was plotted against the amount of Bz in the samples (FIG. 7B). The sample amounts were determined by comparison to samples “spiked” with known amounts of Bz-dC. The amounts of Bz-dC added to samples as spikes were from a weighed stock of Bz-dC. Thus, the HPLC response was calibrated with known amounts of Bz-dC. The results of these experiments show that the detection of Bz by anti-Bz mAb was within the pmole range whereas HPLC detection of Bz was limited to the nmole range.
Example 10
Detection of Remaining Protecting Groups in Commercial Samples
A blind study was conducted to demonstrate the detection of remaining protecting groups in commercial samples by mAb. The purpose of the this experiment was to determine if protecting groups could be detected and identified with mAb technology in presumably completely deprotected samples that had been treated as commonly accomplished in the oligo synthesis industry. The nature of the protecting groups used by eight selected companies was not known, thus the experiment was a blind study. Two 20mer oligos (oligo dA-dC and oligo dG-dT) from each of the eight companies were ordered to be synthesized and deprotected, and salt removed under as identical conditions as possible. The oligos were shipped by express mail, as is often the case, and then subjected to mAb analysis by dot blot. The dA-dC oligo from one company (#6), and possibly a second (#2), had remaining Bz protecting groups as determined by anti-Bz mAb testing (FIG. 8A). The dG-dT oligos from two companies (#2 and #6) had ipr-Pac protecting groups remaining as determined by anti-ipr-Pac mAb (FIG. 8B). The remaining protecting groups in the commercial samples were confirmed by increasing amounts of sample and further deprotection and re-analyses. The oligo dA-dC samples from companies #2 and #6 were tested in higher amounts to confirm the presence of the Bz protecting group. In addition, the samples were treated to remove the remaining protecting groups using a standard protocol. The re-analysis after further deprotection indicated that the groups were now removed (FIG. 8C). This also demonstrates that expensive nucleic acid samples can be re-treated to remove protecting groups and that they need not be discarded. The oligo dG-dT samples were re-treated to remove remaining protecting groups and re-analyzed with anti-ipr-Pac mAb with the result that the ipr-Pac group could be removed without sacrificing the DNA (FIG. 8D).
Example 11
Polyclonal Antibody Against Dimethyltrityl
Production and analyses of polyclonal antibody against the 5′ terminal protecting group, dimethyltrityl (DMT) were as described in Example 2. Four mice were inoculated with DMT and sera were drawn from the mice after some weeks of boosting with antigen. DMT [DMT-OH], three DMT at the 5′-end of the deoxynucleotide trimer d(T)3 [(DMT)3-d(T)3], three DMT at the 5′-end of the deoxynucleotide 20mer d(T)3 with 3′-biotin [(DMT)3-d(T)20-biotin], one DMT at the 5′-end of the deoxynucleotide 20mer d(T)20 with 3′-biotin [DMT-d(T)20-biotin], the dT 20mer with 3′-biotin [d(T)20-biotin], one DMT with biotin [DMT-biotin] and tris-borate saline control were applied to a nitrocellulose membrane that was then assayed with mouse sera (inoculated mice #1-4 and a control serum, normal) to assess anti-DMT antibody, mild acid to reveal presence of the DMT (TBS), and avidin to reveal the presence of biotin (FIG. 9). Sera from mice #2 and #4 recognized DMT [as (DMT)3-d(T)3], whereas mice #1, #3, and the normal mouse did not. Mild acid revealed the presence of DMT as a yellow color (not visible in figure) and avidin revealed the presence of biotin.
The foregoing is illustrative of the present invention, and is not to be construed as limiting thereof. The invention is defined by the following claims, with equivalents of the claims to be included therein.

## Claims

1. A method of preparing an oligonucleotide microarray comprising the steps of:
(a) providing, for each oligonucleotide sequence in the oligonucleotide microarray, a synthetic oligonucleotide mixture prepared using organic protecting groups, the mixture comprising fully deprotected synthetic oligonucleotides, partially deprotected synthetic oligonucleotides, and/or fully protected synthetic oligonucleotides, the mixture having at least one partially or fully protected synthetic oligonucleotide with a protecting group covalently bound thereto;
(b) providing an antibody microarray comprising, for each oligonucleotide in the oligonucleotide microarray, a plurality of antibodies immobilized at a separate discrete location on a first substrate, each antibody specifically binding to a synthetic oligonucleotide having an organic protecting group covalently bound thereto, which antibody does not bind to the synthetic oligonucleotide when the organic protecting group is not covalently bound thereto, the plurality of antibodies including at least one antibody that is capable of binding at least one of the partially or fully protected synthetic oligonucleotides;
(c) separately contacting each synthetic oligonucleotide mixture with the antibodies immobilized at a separate discrete location on the antibody microarray such that at least one of the protected synthetic oligonucleotides from the mixture is bound to at least one of the antibodies immobilized on the antibody microarray, wherein at least a portion of the oligonucleotides in the synthetic oligonucleotide mixture do not bind to the plurality of antibodies;
(d) separating the unbound synthetic oligonucleotides of each synthetic oligonucleotide mixture from the antibody microarray, thus separating the unbound synthetic oligonucleotides from any partially and/or fully protected synthetic oligonucleotide or oligonucleotides bound to the antibodies immobilized on the antibody microarray; and
(e) immobilizing the unbound synthetic oligonucleotides from each synthetic oligonucleotide mixture at a separate discrete location on a second substrate to form an oligonucleotide microarray.

2. The method of claim 1, wherein the plurality of antibodies immobilized on the first substrate includes at least two sets of antibodies, each set of antibodies having a different binding specificity from the other sets.

3. The method of claim 1, wherein the synthetic oligonucleotide to which the antibodies specifically bind includes a protected nucleotide according to Formula (I)



wherein:
R is H or a protecting group; subject to the proviso that R is a covalent bond to an adjacent nucleotide when the protected nucleotide is not a 5′ terminal nucleotide in the oligonucleotide;
R1 is H or a protecting group; subject to the proviso that R1 is a covalent bond to an adjacent nucleotide when the protected nucleotide is not a 3′ terminal nucleotide in the oligonucleotide;
R2 is H or —OR3;
R3 is H or a protecting group;
Base is a purine or pyrimidine base;
R4 is a protecting group substituted for a hydrogen on an amino group of the base, subject to the proviso that R4 is not present in Formula (I) when R, R1, or R3 is a protecting group or when the base does not include an amino group; and
further subject to the proviso that only one of R, R1, R3, and R4 is a protecting group and the others of R, R1, R3, and R4 are not protecting groups.

4. The method of claim 3, wherein R4 is a protecting group selected from the group consisting of acetyl, benzoyl, dimethylformamidine, isobutyrl, phenoxyacetyl, and isopropyl-phenoxyacetyl.

5. The method of claim 3, wherein R is a protecting group comprising dimethoxytrityl.

6. The method of claim 3, wherein R1 is a protecting group comprising β-cyanoethyl.

7. The method of claim 3, wherein R2 is —OR3 and R3 is a protecting group comprising tert-butyldimethylsilyl.

8. The method of claim 3, wherein the plurality of antibodies immobilized on the first substrate includes at least two sets of antibodies, each set of antibodies having a different binding specificity from the other sets.

9. The method of claim 1, wherein the antibodies are immobilized in flow channels or flow chambers formed in or on the substrate of the antibody microarray.

10. The method of claim 9, wherein step (c) comprises flowing the synthetic oligonucleotide mixture through the flow channels or flow chambers and step (d) comprises flowing the unbound synthetic oligonucleotides out the flow channels or flow chambers to separate the unbound synthetic oligonucleotides from the antibody microarray.

11. The method of claim 1, wherein:
(1) the synthetic oligonucleotide to which the antibodies specifically bind includes a protected nucleotide according to Formula (I)




wherein:
R is H or a protecting group; subject to the proviso that R is a covalent bond to an adjacent nucleotide when the protected nucleotide is not a 5′ terminal nucleotide in the oligonucleotide;
R1 is H or a protecting group; subject to the proviso that R1 is a covalent bond to an adjacent nucleotide when the protected nucleotide is not a 3′ terminal nucleotide in the oligonucleotide;
R2 is H or —OR3;
R3 is H or a protecting group;
Base is a purine or pyrimidine base;
R4 is a protecting group substituted for a hydrogen on an amino group of the base, subject to the proviso that R4 is not present in Formula (I) when R, R1, or R3 is a protecting group or when the base does not include an amino group; and
further subject to the proviso that only one of R, R1, R3, and R4 is a protecting group and the others of R, R1, R3, and R4 are not protecting groups;

(2) the plurality of antibodies immobilized on the first substrate includes at least two sets of antibodies, each set of antibodies having a different binding specificity from the other sets;
(3) the antibodies are immobilized in flow channels or flow chambers formed in or on the substrate of the antibody microarray; and
(4) step (c) comprises flowing the synthetic oligonucleotide mixture through the flow channels or flow chambers; and
(5) step (d) comprises flowing the unbound synthetic oligonucleotides out the flow channels or flow chambers to separate the unbound synthetic oligonucleotides from the antibody microarray.