Non-cognate hybridization system (NCHS)

• US 6,544,777 B1
• Filed: 06/02/2000
• Issued: 04/08/2003
• Est. Priority Date: 06/03/1999
• Status: Expired due to Fees

• Current Assignee: Jacques Schrenzel, Jonathan Hibbs
• Original Assignee: Jacques Schrenzel, Jonathan Hibbs
• Inventors: Schrenzel, Jacques, Hibbs, Jonathan
• Primary Examiner(s): Siew, Jeffrey
• Application Number:
  US09/586,101
• Time in Patent Office: 1,040 Days
• Field of Search: 435/6, 435/91.1, 435/5, 435/286.5, 435/287.2, 435/402, 536/25.3, 536/24.3, 536/24.32, 536/24.33, 536/22.1, 436/518
• US Class Current: 435/287.2
• CPC Class Codes: B01J 2219/00274 Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
• CPC Class Codes: B01J 2219/00585 Parallel 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 2219/00659 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 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/185 incorporating bases where the precise position of the bases in the nucleic acid string is important
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/30 Microarray design

Abstract

The present invention comprises a non-cognate hybridization system (NCHS). The NCHS generally includes a hybridization technology that is simply and economically used to probe for non-cognate nucleic acid sequences, i.e., for nucleic acid strands without known target sequences. NCHS causes nucleic acids, bound to a probe surface, to create a hybridization pattern that provides information about the presence and/or quantity of the nucleic acid sequences in a sample. The NCHS results normally orient the examiner towards a small number of specific diagnoses across a wide variety of diagnostic categories (including but not limited to infections, neoplasms and autoimmune diseases). The test will also identify final-common-pathway syndromes such as sepsis, anaphylaxis and tumor necrosis. While the test utilizes genetic information, it does not depend on prior knowledge of the genes involved in a particular disease or syndrome.

Claims

1. A device for assaying nucleic acids in a sample, the device comprising:

at least one surface and one or more arrays of a plurality of at least 100 different oligomer probes, each comprising an oligomer sequence, being attached to the surface,

wherein the length of every oligomer sequence in an array is fixed and each different oligomer sequence has a distinct address on the surface;

wherein the oligomer sequences in the arrays are chosen from the set of all possible combinations of sequences that can be generated from a number of different bases that does not include all four of the bases deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine, and does not include all four of the bases adenine, uracil, guanine, and cytosine.

2. The device of claim 1 wherein the array consists of every possible combination of sequences that can be generated for the length of the oligomer and the number of different bases that are used.

3. The device of claim 2 wherein the length of the oligomer is 8-35 bases and the number of different bases is two.

4. The device of claim 2 wherein the length of the oligomer is 8-35 bases and the number of different bases is three.

5. The device of claim 1 wherein the different bases are guanine and cytosine.

6. The device of claim 1 wherein the oligomers in the arrays have a length of 12 bases.

7. The device of claim 1 wherein the oligomers in the arrays have a length of 11 to 30 bases.

8. The device of claim 1 wherein the oligomers in the first array have a length of 15 to 20 bases.

9. The device of claim 1 wherein the oligomers in the first array have a length of 15 bases.

29. The device of claim 1 wherein at least one array is interspersed with at least one other array.

10. An array of oligonucleic acid probes immobilized on a solid support for assaying nucleic acids in a sample, said array comprising at least 100 different probes each of 9 to 30 bases in length occupying separate known sites in said array, said oligonucleic acid probes including probes that are chosen from a set of all possible combinations of sequences that may be generated by using a group of different bases;

wherein the number of different bases does not include all four of the bases deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine, and does not include all four of the bases adenine, uracil, guanine, and cytosine.

12. The array of oligonucleic acid probes in claim 10 wherein the nucleic acids are nucleosides.

30. The array of oligonucleic acid probes in claim 10 wherein the different bases are chosen from the group consisting of adenine, thymine, guanine, cytosine, deoxyadenosine, deoxythymidine, deoxyguanosine, deoxycytidine, and uracil.

14. An array of oligomers having nucleic acid sequences for assaying nucleic acids in a sample, the array comprising:

a plurality of at least 100 different oligomer probes, immobilized to distinct known sites on a surface, wherein the sequences are fixed in length and the oligomer probes are attached to the surface by a spacer;

wherein the oligomer sequences are chosen from the set of all possible combinations of sequences that can be generated for the total number of bases in the oligomer and the number of different bases that are used; and

wherein the number of different bases does not include all four of the bases deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine, and does not include all four of the bases adenine, uracil, guanine, and cytosine.

11. The array of oligonucleic acid probes in claim 15 wherein the number of different bases is two or three bases.

13. The array of oligonucleic acid probes in claim 11 wherein the number of different bases is two, and the different bases are adenine and thymine.

15. The array of claim 14 wherein the spacer is less than 100 nanometers in length.

16. The array of claim 14 wherein the spacer is a linear polymer with a molecular weight between 100 and 100,000.

17. The array of claim 16 wherein the linear polymer is poly(ethylene oxide).

18. The array of claim 14 wherein the spacer comprises nucleic acid bases.

19. The array of claim 18 wherein all of the bases are nucleotides.

20. An array for assaying nucleic acids in a sample comprising:

a plurality of at least 100 different nucleic acid oligomer probes comprising sequences immobilized to distinct known sites on a surface wherein the sequences comprise at least one variable portion and at least one fixed portion and the sequences are at least 4 bases in length;

wherein each variable portion comprises oligomer sequences chosen from the set of all possible combinations of sequences that can be generated for the length of the variable portion and the number of different bases in the variable portion, and

wherein the number of different bases in the variable portion does not include all four of the bases deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine, and does not include all four of the bases adenine, uracil, guanine, and cytosine.

21. The array of claim 20 having only one fixed portion and only one variable portion.

22. The array of claim 21 wherein the variable portion is six bases in length and a number of different bases in the variable portion is two or three.

23. The set of arrays of claim 21 wherein the sequences comprise two fixed portions and one variable portion.

24. The set of arrays of claim 23 wherein the variable portion is disposed between two fixed portions, whereby a first fixed portion is affixed to the surface, the variable portion is attached to the first fixed portion, and a second fixed portion is disposed at the unbound end of the sequence.

25. A device for diagnosis of disease in a living organism having oligomers having nucleic acid sequences, the device comprising:

an array of a plurality of at least 100 different nucleic acid oligomer probes having sequences immobilized to known distinct sites on a surface, wherein a fraction of the chemically distinct oligomers in the organism that reproducibly hybridize to the oligomer probes attached to the surface is at least one percent and the oligomers in the array are made from a number of different bases tat does not include all four of the bases deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine, and does not include all four of the bases adenine, uracil, guanine, and cytosine.

26. The device of claim 25 wherein the device immobilizes at least one percent of the total number of chemically distinct species of RNA oligomers that are present in the organism.

27. The device of claim 26 wherein the device immobilizes at least five percent of the total number of chemically distinct RNA oligomers that are present in the organism.

28. The device of claim 25 wherein the fraction of the chemically distinct nucleic acid oligomers in the organism that reproducibly hybridize to a unique position on the surface is at least 30 percent.