IDENTIFICATION OF GENETIC TARGETS FOR MODULATION BY OLIGONUCLEOTIDES AND GENERATION OF OLIGONUCLEOTIDES FOR GENE MODULATION

• US 20020028923A1
• Filed: 04/28/1998
• Published: 03/07/2002
• Est. Priority Date: 04/13/1998
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: FREIER, SUSAN M., BAKER, BRENDA F., MCNEIL, JOHN, COWSERT, LEX M., SASMOR, HENRI M.
• Granted Patent: US 7,321,828 B2
• Time in Patent Office: Days
• US Class Current: 536/23.1
• CPC Class Codes: B01J 2219/007 Simulation or vitual synthesis
• CPC Class Codes: C12N 15/1048 SELEX
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 35/20 Screening of libraries
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry

Abstract

Interative, preferably computer based iterative processes for generating synthetic compounds with desired physical, chemical and/or bioactive properties, i.e., active compounds, are provided. During iterations of the processes, a target nucleic acid sequence is provided or selected, and a library of candidate nucleobase sequences is generated in silico according to defined criteria. A “virtual” oligonucleotide chemistry is chosen and a library of virtual oligonucleotide compounds having the selected nucleobase sequences is generated. These virtual compounds are reviewed and compounds predicted to have particular properties are selected. The selected compounds are robotically synthesized and are preferably robotically assayed for a desired physical, chemical or biological activity. Active compounds are thus generated and, at the same time, preferred sequences and regions of the target nucleic acid that are amenable to oligonucleotide or sequence-based modulation are identified.

Claims

1. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence comprising generating a library of nucleobase sequences in silico according to defined criteria.

19. The method of claim 1, wherein said target nucleic acid sequence is that of a genomic DNA, a cDNA, a product of a polymerase chain reaction, an expressed sequence tag, an mRNA or a structural RNA.

20. The method of claim 1, wherein said target nucleic acid sequence is a human nucleic acid.

42. A computer formatted medium comprising computer readable instructions for performing the method of any one of claims 1 to 20.

2. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence comprising evaluating in silico a plurality of virtual oligonucleotides according to defined criteria.

3. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence comprising robotically synthesizing a plurality of defined oligonucleotide compounds.

4. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence comprising robotically assaying a plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

18. The method of claim 4, wherein said step of robotically assaying said plurality of oligonucleotide compounds is performed by computer-controlled real-time polymerase chain reaction or by computer-controlled enzyme-linked immunosorbent assay.

5. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence comprising generating a library of nucleobase sequences in silico according to defined criteria and evaluating in silico a plurality of virtual oligonucleotides having said nucleobase sequences according to defined criteria.

6. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence comprising evaluating in silico a plurality of virtual oligonucleotides according to defined criteria and robotically synthesizing a plurality of oligonucleotide compounds corresponding to said plurality of virtual oligonucleodites.

7. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence comprising evaluating in silico a plurality of virtual oligonucleotides according to defined criteria and robotically assaying a plurality of oligonucleotide compounds corresponding to said virtual oligonucleotides for one or more desired physical, chemical or biological properties.

8. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence comprising generating a library of nucleobase sequences in silico according to defined criteria and robotically synthesizing a plurality of oligonucleotide compounds having said nucleobase sequences.

9. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence comprising robotically synthesizing a plurality of oligonucleotide compounds and robotically assaying said plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

10. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence comprising generating a library of nucleobase sequences in silico according to defined criteria and robotically assaying a plurality of oligonucleotide compounds having said nucleobase sequences for one or more desired physical, chemical or biological properties.

11. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence, comprising the steps of:

(a) generating a library of nucleobase sequences in silico according to defined criteria;

(b) evaluating in silico a plurality of virtual oligonucleotides having the nucleobase sequences of (a) according to defined criteria; and

(c) robotically synthesizing a plurality of oligonucleotide compounds.

12. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence, comprising the steps of:

(a) generating a library of nucleobase sequences in silico according to defined criteria;

(b) evaluating in silico a plurality of virtual oligonucleotides having the nucleobase sequences of (a) according to defined criteria; and

(c) robotically assaying a plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

13. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence, comprising the steps of:

(a) generating a library of nucleobase sequences in silico according to defined criteria;

(b) robotically synthesizing a plurality of oligonucleotide compounds; and

(c) robotically assaying a plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

14. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence, comprising the steps of:

(a) evaluating in silico a plurality of virtual oligonucleotides according to defined criteria;

(b) robotically synthesizing a plurality of oligonucleotide compounds; and

(c) robotically assaying a plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

15. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence, comprising the steps of:

(a) generating a library of nucleobase sequences in silico according to defined criteria;

(b) evaluating in silico a plurality of virtual oligonucleotides having the nucleobase sequences of (a) according to defined criteria;

(c) robotically synthesizing a plurality of oligonucleotide compounds; and

(d) robotically assaying a plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

16. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence, comprising the steps of:

(a) generating a library of nucleobase sequences in silico according to defined criteria;

(b) choosing an oligonucleotide chemistry;

(c) robotically synthesizing a set of oligonucleotide compounds having said nucleobase sequences of step (a) and said oligonucleotide chemistry of step (b);

(d) robotically assaying said set of oligonucleotide compounds of step (c) for a physical, chemical or biological activity; and

(e) selecting a subset of said set of oligonucleotide compounds of step (c) having a desired level of physical, chemical or biological activity in order to generate said set of compounds.

17. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence, comprising the steps of:

(a) generating a library of nucleobase sequences in silico according to defined criteria;

(b) choosing an oligonucleotide chemistry;

(c) evaluating in silico a plurality of virtual oligonucleotides having the nucleobase sequences of (a) and the oligonucleotide chemistry of (b) according to defined criteria, and selecting those having preferred characteristics, in order to generate a set of preferred nucleobase sequences;

(d) robotically synthesizing a set of oligonucleotide compounds having said preferred nucleobase sequences of step (c) and said oligonucleotide chemistry of step (b);

(e) robotically assaying said set of oligonucleotide compounds of step (d) for a physical, chemical or biological activity; and

(f) selecting a subset of said set of oligonucleotide compounds of step (d) having a desired level of physical, chemical or biological activity in order to generate said set of compounds.

21. A method of identifying one or more nucleic acid sequences amenable to antisense modulation comprising generating a library of antisense nucleobase sequences in silico according to defined criteria.

39. The method of claim 21, wherein said nucleic acid sequence is that of a genomic DNA, a cDNA, a product of a polymerase chain reaction, an expressed sequence tag, an mRNA or a structural RNA.

40. The method of claim 21, wherein said nucleic acid sequence is a human nucleic acid.

44. A computer formatted medium comprising computer readable instructions for performing the method of any one of claims 21 to 40.

46. A computer formatted medium comprising one or more nucleic acid sequences amenable to antisense modulation in computer readable form, wherein said one or more nucleic acid sequences is identified according to the method of any one of claims 21, 22 or 24-40.

22. A method of generating a set of compounds that modulate the expression of a target nucleic acid sequence comprising evaluating in silico a plurality of virtual oligonucleotides according to defined criteria.

38. The method of claim 24, wherein said step of robotically assaying said plurality of nucleic acid sequences is performed by computer-controlled real-time polymerase chain reaction or by computer-controlled enzyme-linked immunosorbent assay.

23. A method of identifying one or more nucleic acid sequences amenable to antisense modulation comprising robotically synthesizing a plurality of antisense compounds.

24. A method of identifying one or more nucleic acid sequences amenable to antisense modulation comprising robotically assaying a plurality of antisense compounds for one or more desired physical, chemical or biological properties.

25. A method of identifying one or more nucleic acid sequences amenable to antisense modulation comprising generating a library of nucleobase sequences in silico according to defined criteria and evaluating in silico a plurality of virtual oligonucleotides having said nucleobase sequences according to defined criteria.

26. A method of identifying one or more nucleic acid sequences amenable to antisense modulation comprising evaluating in silico a plurality of virtual oligonucleotides according to defined criteria and robotically synthesizing a plurality of oligonucleotide compounds.

27. A method of identifying one or more nucleic acid sequences amenable to antisense modulation comprising evaluating in silico a plurality of virtual oligonucleotides according to defined criteria and robotically assaying a plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

28. A method of identifying one or more nucleic acid sequences amenable to antisense modulation comprising generating a library of nucleobase sequences in silico according to defined criteria and robotically synthesizing a plurality of oligonucleotide compounds having said nucleobase sequences.

29. A method of identifying one or more nucleic acid sequences amenable to antisense modulation comprising robotically synthesizing a plurality of oligonucleotide compounds and robotically assaying said plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

30. A method of identifying one or more nucleic acid sequences amenable to antisense modulation comprising generating a library of nucleobase sequences in silico according to defined criteria and robotically assaying a plurality of oligonucleotide compounds having said nucleobase sequences for one or more desired physical, chemical or biological properties.

31. A method of identifying one or more nucleic acid sequences amenable to antisense modulation comprising the steps of:

(a) generating a library of nucleobase sequences in silico according to defined criteria;

(b) evaluating in silico a plurality of virtual oligonucleotides having the nucleobase sequences of (a) according to defined criteria; and

(c) robotically synthesizing a plurality of oligonucleotide compounds.

32. A method of identifying one or more nucleic acid sequences amenable to antisense modulation, comprising the steps of:

(a) generating a library of nucleobase sequences in silico according to defined criteria;

(b) evaluating in silica a plurality of virtual oligonucleotides having the nucleobase sequences of (a) according to defined criteria; and

(c) robotically assaying a plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

33. A method of identifying one or more nucleic acid sequences amenable to antisense modulation, comprising the steps of:

(a) generating a library of nucleobase sequences in silica according to defined criteria;

(b) robotically synthesizing a plurality of oligonucleotide compounds; and

(c) robotically assaying a plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

34. A method of identifying one or more nucleic acid sequences amenable to antisense modulation, comprising the steps of:

(a) evaluating in silico a plurality of virtual oligonucleotides according to defined criteria;

(b) robotically synthesizing a plurality of oligonucleotide compounds; and

(c) robotically assaying a plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

35. A method of identifying one or more nucleic acid sequences amenable to antisense modulation, comprising the steps of:

(a) generating a library of nucleobase sequences in silico according to defined criteria;

(b) evaluating in silico a plurality of virtual oligonucleotides having the nucleobase sequences of (a) according to defined criteria;

(c) robotically synthesizing a plurality of oligonucleotide compounds; and

(d) robotically assaying a plurality of oligonucleotide compounds for one or more desired physical, chemical or biological properties.

36. A method of identifying one or more nucleic acid sequences amenable to antisense modulation, comprising the steps of:

(a) generating a library of nucleobase sequences in silico according to defined criteria;

(b) choosing an oligonucleotide chemistry;

(c) robotically synthesizing a set of oligonucleotide compounds having said nucleobase sequences of step (a) and said oligonucleotide chemistry of step (b);

(d) robotically assaying said set of oligonucleotide compounds of step (c) for a physical, chemical or biological activity; and

(e) selecting a subset of said set of oligonucleotide compounds of step (c) having a desired level of physical, chemical or biological activity in order to generate said set of compounds.

37. A method of identifying one or more nucleic acid sequences amenable to antisense modulation, comprising the steps of:

(a) generating a library of nucleobase sequences in silico according to defined criteria;

(b) choosing an oligonucleotide chemistry;

(c) evaluating in silico a plurality of virtual oligonucleotides having the nucleobase sequences of (a) according to defined criteria, and selecting those having preferred characteristics, in order to generate a set of preferred nucleobase sequences;

(d) robotically synthesizing a set of oligonucleotide compounds having said preferred nucleobase sequences of step (b) and said oligonucleotide chemistry of step (c);

(e) robotically assaying said set of oligonucleotide compounds of step (d) for a physical, chemical or biological activity; and

(f) selecting a subset of said set of oligonucleotide compounds of step (d) having a desired level of physical, chemical or biological activity in order to generate said set of compounds.

41. A computer formatted medium comprising computer readable instructions for identifying active compounds.

43. A computer formatted medium comprising computer readable instructions for performing a method of identifying one or more nucleic acid sequences amenable to antisense modulation.

45. A computer formatted medium comprising one or more nucleic acid sequences amenable to antisense modulation in computer readable form.