Nucleic acid probe libraries

Details Nucleic acid probe libraries Nucleic acid probe libraries

2002-10-22

2004-12-14

Ponnaluri, Padmashri (Department: 1639)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C435S007100, C435S091500, C435S091500, C435S091500, C435S091500, C436S518000, C536S023100, C536S025300, C536S024300

Reexamination Certificate

active

06830890

ABSTRACT:

BACKGROUND OF THE INVENTION
The present invention relates to the field of polymer synthesis and the use of polymer libraries for biological screening. More specifically, in one embodiment the invention provides arrays of diverse double-stranded oligonucleotide sequences. In another embodiment, the invention provides arrays of conformationally restricted probes, wherein the probes are held in position using double-stranded DNA sequences as scaffolding. Libraries of diverse unimolecular double-stranded nucleic acid sequences and probes may be used, for example, in screening studies for determination of binding affinity exhibited by binding proteins, drugs, or RNA.
Methods of synthesizing desired single stranded DNA sequences are well known to those of skill in the art. In particular, methods of synthesizing oligonucleotides are found in, for example,
Oligonucleotide Synthesis: A Practical Approach
, Gait, ed., IRL Press, Oxford (1984), incorporated herein by reference in its entirety for all purposes. Synthesizing unimolecular double-stranded DNA in solution has also been described. See, Durand, et al.
Nucleic Acids Res.
18:6353-6359 (1990) and Thomson, et al.
Nucleic Acids Res.
21:5600-5603 (1993), the disclosures of both being incorporated herein by reference.
Solid phase synthesis of biological polymers has been evolving since the early “Merrifield” solid phase peptide synthesis, described in Merrifield,
J. Am. Chem. Soc.
85:2149-2154 (1963), incorporated herein by reference for all purposes. Solid-phase synthesis techniques have been provided for the synthesis of several peptide sequences on, for example, a number of “pins.” See e.g., Geysen et al.,
J. Immun. Meth.
102:259-274 (1987), incorporated herein by reference for all purposes. Other solid-phase techniques involve, for example, synthesis of various peptide sequences on different cellulose disks supported in a column. See Frank and Doring,
Tetrahedron
44:6031-6040 (1988), incorporated herein by reference for all purposes. Still other solid-phase techniques are described in U.S. Pat. No. 4,728,502 issued to Hamill and WO 90/00626 (Beattie, inventor).
Each of the above techniques produces only a relatively low density array of polymers. For example, the technique described in Geysen et al. is limited to producing 96 different polymers on pins spaced in the dimensions of a standard microtiter plate.
Improved methods of forming large arrays of oligonucleotides, peptides and other polymer sequences in a short period of time have been devised. Of particular note, Pirrung et al., U.S. Pat. No. 5,143,854 (see also PCT Application No. WO 90/15070) and Fodor et al., PCT Publication No. WO 92/10092, all incorporated herein by reference, disclose methods of forming vast arrays of peptides, oligonucleotides and other polymer sequences using, for example, light-directed synthesis techniques. See also, Fodor et al.,
Science,
251:767-777 (1991), also incorporated herein by reference for all purposes. These procedures are now referred to as VLSIPS™ procedures.
In the above-referenced Fodor et al., PCT application, an elegant method is described for using a computer-controlled system to direct a VLSIPS™ procedure. Using this approach, one heterogenous array of polymers is converted, through simultaneous coupling at a number of reaction sites, into a different heterogenous array. See, U.S. application Ser. Nos. 07/796,243 and 07/980,523, the disclosures of which are incorporated herein for all purposes.
The development of VLSIPS™ technology as described in the above-noted U.S. Pat. No. 5,143,854 and PCT patent publication Nos. WO 90/15070 and 92/10092, is considered pioneering technology in the fields of combinatorial synthesis and screening of combinatorial libraries. More recently, patent application Ser. No. 08/082,937, filed Jun. 25, 1993, describes methods for making arrays of oligonucleotide probes that can be used to check or determine a partial or complete sequence of a target nucleic acid and to detect the presence of a nucleic acid containing a specific oligonucleotide sequence.
A number of biochemical processes of pharmaceutical interest involve the interaction of some species, e.g., a drug, a peptide or protein, or RNA, with double-stranded DNA. For example, protein/DNA binding interactions are involved with a number of transcription factors as well as tumor suppression associated with the p53 protein and the genes contributing to a number of cancer conditions.
SUMMARY OF THE INVENTION
High-density arrays of diverse unimolecular, double-stranded oligonucleotides, as well as arrays of conformationally restricted probes and methods for their use are provided by virtue of the present invention. In addition, methods and devices for detecting duplex formation of oligonucleotides on an array of diverse single-stranded oligonucleotides are also provided by this invention. Further, an adhesive based on the specific binding characteristics of two arrays of complementary oligonucleotides is provided in the present invention.
According to one aspect of the present invention, libraries of unimolecular, double-stranded oligonucleotides are provided. Each member of the library is comprised of a solid support, an optional spacer for attaching the double-stranded oligonucleotide to the support and for providing sufficient space between the double-stranded oligonucleotide and the solid support for subsequent binding studies and assays, an oligonucleotide attached to the spacer and further attached to a second complementary oligonucleotide by means of a flexible linker, such that the two oligonucleotide portions exist in a double-stranded configuration. More particularly, the members of the libraries of the present invention can be represented by the formula:
Y-L
1
-X
1
-L
2
-X
2
in which Y is a solid support, L
1
is a bond or a spacer, L
2
is a flexible linking group, and X
1
and X
2
are a pair of complementary oligonucleotides.
In a specific aspect of the invention, the library of different unimolecular, double-stranded oligonucleotides can be used for screening a sample for a species which binds to one or more members of the library.
In a related aspect of the invention, a library of different conformationally-restricted probes attached to a solid support is provided. The individual members each have the formula:
-X
11
-Z-X
12
in which X
11
and X
12
are complementary oligonucleotides and Z is a probe having sufficient length such that X
11
and X
12
form a double-stranded oligonucleotide portion of the member and thereby restrict the conformations available to the probe. In a specific aspect of the invention, the library of different conformationally-restricted probes can be used for screening a sample for a species which binds to one or more probes in the library.
According to vet another aspect of the present invention, methods and devices for the bioelectronic detection of duplex formation are provided.
According to still another aspect of the invention, an adhesive is provided which comprises two surfaces of complementary oligonucleotides.


REFERENCES:
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patent: 4562157 (1985-12-01), Lowe et al.
patent: 4728502 (1988-03-01), Hamill
patent: 5143854 (1992-09-01), Pirrung et al.
patent: 5288514 (1994-02-01), Ellman
patent: 5556752 (1996-09-01), Lockhart et al.
patent: 6482591 (2002-11-01), Lockhart et al.
patent: WO 90/10713 (1990-09-01), None
patent: WO 89/10977 (1989-11-01), None
patent: WO 89/11548 (1989-11-01), None
patent: WO 90/00626 (1990-01-01), None
patent: WO 90/15070 (1990-12-01), None
patent: WO 92/10092 (1992-06-01), None
patent: WO 92/00091 (1992-09-01), None
patent: WO 93/06122 (1993-04-01), None
Ma et al., “Design and Synthesis of RNA Miniduplexes via a Synthetic Linker Approach,” Biochemistry, 32, 1751-1758, 1993.*
Cuniberti et al., “Environment-Induced Changes in DNA Conformation as Probed by Ethidium Bromide Florescence,” Biophysical Chem., 38, 11-22, 1990.*
Cotton & Wilkinson, Advanced Inorganic Chemistry, Chapter 8, 5th Ed., John Wiley & Sons, p. 278, 1993.

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