Oligonucleotides

• US 20010053519A1
• Filed: 03/06/2000
• Published: 12/20/2001
• Est. Priority Date: 12/06/1990
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Fodor, Stephen P.A., Solas, Dennis W., Dower, William J., Huang, Xiaohua C.
• Granted Patent: US 6,582,908 B2
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00434 Liquid crystal masks
• CPC Class Codes: B01J 2219/00436 Maskless processes
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/00475 Sheets
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00531 essentially square
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 : Covalent
• CPC Class Codes: B01J 2219/0063 : Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 : by coating it with another layer
• CPC Class Codes: B01J 2219/00648 : by the use of solid beads
• CPC Class Codes: B01J 2219/00659 : Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 : using computers
• CPC Class Codes: B01J 2219/00695 : Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B82Y 10/00 : Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6827 : for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2535/131 : Allele specific probes
• CPC Class Codes: C12Q 2545/114 : involving a quantitation step
• CPC Class Codes: C12Q 2565/519 : characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: C12Q 3/00 : Condition responsive control processes apparatus therefor C12M1/36; controlling or regulating in general G05
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 15/1433 : using image recognition
• CPC Class Codes: G01N 15/1475 : using image analysis for extracting features of the particle
• CPC Class Codes: G03F 7/00 : Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printing surfaces; Materials therefor, e.g. comprising photoresists; Apparatus specially adapted therefor using photoresist structures for special production processes, see the relevant places, e.g. B44C, H01L, e.g. H01L21/00, H05K
• CPC Class Codes: G03F 7/265 : Selective reaction with inorganic or organometallic reagents after image-wise exposure, e.g. silylation
• CPC Class Codes: G11C 13/0014 : comprising cells based on organic memory material
• CPC Class Codes: G11C 13/0019 : comprising bio-molecules

Abstract

The present invention provides a number of oligonucleotide sequences which can be used for a wide variety of analyses applicable to the diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine, and medical diagnostics. In certain embodiments these oligonucleotides may be used as probes to be used in, for example, gene expression analysis.

Claims

1. A nucleic acid array comprising at least 75% of 4ⁿ unique oligonucleotide sequences of a given length n wherein n is a number from 10-25.

2. The array of

claim 1

wherein said array is used to analyze the expression level of at least one gene.

3. The array of

claim 1

wherein said array is used to analyze the expression level of at least two genes.

4. The array of

claim 1

wherein the array is used to compare gene expression levels from at least two different samples.

5. The array of

claim 1

wherein said array is used to detect at least one polymorphism in a target sequence.

6. The array of

claim 1

wherein said array is used to detect at least two different polymorphisms in a target sequence.

7. The nucleic acid array of

claim 1

comprising at least 90% of 4ⁿ unique oligonucleotide sequences of a given length n wherein n is a number from 10-25.

8. A method of analyzing a first target sequence comprising:

hybridizing said first target sequence to a first nucleic acid array comprising at least 75% of 4ⁿ unique oligonucleotide sequences of a given length n wherein n is a number from 10-25;

detecting a hybridization pattern created by the hybridization of said first target sequence to said first array.

9. The method of

claim 8

wherein said analysis comprises determining gene expression levels.

10. The method of

claim 8

wherein said analysis comprises polymorphism detection.

11. The method of

claim 8

wherein said step of detecting is performed by a computer system.

12. The method of

claim 8

wherein said hybridization pattern from said first target sequence is compared with a hybridization pattern created by hybridizing a second target sequence to a second nucleic acid array.

13. The method of

claim 12

wherein said second nucleic acid array is identical to said first array.

14. A not previously known nucleic acid consisting of the sequence:

X₁-X₂-X₃-X₄-X₅-X₆-X₇-X₈-X₉-X₁₀-X₁₁-X₁₂-X₁₃-X₁₄-X₁₅-X₁₆-X₁₇-X₁₈-X₁₉-X₂₀-X₂₁-X₂₂-X₂₃-X₂₄-X₂₅ wherein each X is selected from the group consisting of A, C, T(U), G and analogs thereof.

15. The nucleic acid of

claim 14

used as a probe for a gene known to have a sequence which is complementary to the sequence of said nucleic acid.

16. The nucleic acid of

claim 14

used as an antisense compound to specifically bind and disable a gene containing a sequence which is complementary to the sequence of said nucleic acid.

20. The array of

claim 16

wherein said array is used to detect at least one polymorphism.

17. A not previously known nucleic acid attached to a solid support wherein said not previously known nucleic acid consists of the sequence:

X₁-X₂-X₃-X₄-X₅-X₆-X₇-X₈-X₉-X₁₀-X₁₁-X₁₂-X₁₃-X₁₄-X₁₅-X₁₆-X₁₈-X₁₉-X₂₀-X₂₁-X₂₂-X₂₃-X₂₄-X₂₅ wherein each X is selected from the group consisting of A, C, T(U), G and analogs thereof.

18. The array of

claim 17

wherein said array is used to determine the expression level of at least one gene.

19. The array of

claim 17

wherein said array is used to determine the expression levels of at least two genes.

22. The compound of

claim 19

wherein thymine is replaced by uracil.

21. A compound of the formula:

X₁-X₂-X₃-X₄-X₅-X₆-X₇-x₈-X₉-X₁₀-X₁₁-X₁₂-X₁₃-X₁₄-X₁₅-X₁₆-X₁₇-X₁₈-X₁₉-x₂₀-X₂₁-X₂₂-X₂₃-X₂₄-X₂₅

in which;

X₁ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₂ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₃ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₄ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₅ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₆ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₇ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₈ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₉ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₁₀ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₁₁ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₁₂ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₁₃ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof,

X₁₄ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₁₅ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₁₆ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₁₇ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₁₈ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₁₉ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₂₀ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₂₁ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₂₂ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₂₃ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₂₄ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

X₂₅ is chosen from the group consisting of;

adenine, cytosine, guanine, thymine and analogs thereof;

wherein said compound is previously unknown.

23. A composition made by combining a first nucleotide, a second nucleotide, a third nucleotide, a fourth nucleotide, a fifth nucleotide, a sixth nucleotide, a seventh nucleotide, an eighth nucleotide, a ninth nucleotide, a tenth nucleotide, an eleventh nucleotide, a twelfth nucleotide, a thirteenth nucleotide, a fourteenth nucleotide, a fifteenth nucleotide, a sixteenth nucleotide, a seventeenth nucleotide, an eighteenth nucleotide, a nineteenth nucleotide, a twentieth nucleotide, a twenty-first nucleotide, a twenty-second nucleotide, a twenty third nucleotide, a twenty-fourth nucleotide and a twenty-fifth nucleotide wherein said composition is previously unknown.