System of components for preparing oligonucleotides

• US 7,321,828 B2
• Filed: 04/28/1998
• Issued: 01/22/2008
• Est. Priority Date: 04/13/1998
• Status: Expired due to Fees

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Cowsert, Lex M., Sasmor, Henri M., Ohashi, Cara, Brooks, Douglas G., Freier, Susan M., Baker, Brenda F., McNeil, John, Vickers, Timothy A., Wyatt, Jacqueline R., Borchers, Alexander H.
• Primary Examiner(s): Moran; Marjorie A.
• Application Number:
  US09/067,638
• Publication Number:
  US 20020028923A1
• Time in Patent Office: 3,556 Days
• Field of Search: 435/6, 435/69.1, 435/810, 435/283.1, 435/286.1, 435/286.2, 435/286.5, 435/286.7, 435/287.1, 435/257.2, 435/287.3, 435/287.7, 435/287.9, 435/288.3, 435/288.4, 435/288.5, 435/288.7, 435/289.1, 435/303.1, 435/305.1, 435/91.1, 435/7.92, 436/501, 536/25.3, 422/50, 422/68.1, 935/77, 935/78, 702/19
• US Class Current: 702/19
• 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 system of associated components for preparing a set of oligonucleotides that modulates expression of a selected nucleic acid comprising:

a computer system that

i) generates a list of oligonucleotide sequences according to a desired oligonucleotide length, thereby generating a series of oligonucleotide sequences;

ii) applies a virtual oligonucleotide chemistry to the oligonucleotide sequences generated in step i) to yield a set of virtual oligonucleotides;

iii) generates a subset of said set of virtual oligonucleotides, said subset being the result of a decision to target a functional region of said selected nucleic acid; and

iv) generates synthesis instructions in computer manipulable form for said oligonucleotide sequences in said subset of said set of virtual oligonucleotides;

an automated synthesizer that receives said synthesis instructions from said computer system and synthesizes only said oligonucleotide sequences in said subset of said set of virtual oligonucleotides, wherein the product of said synthesis is a set of synthesized oligonucleotides; and

an apparatus that accepts said set of synthesized oligonucleotides and performs at least one procedure for each of said synthesized oligonucleotides wherein said procedure identifies particular members of said set that modulate expression of said selected nucleic acid.

2. The system of claim 1 wherein said functional region is the transcription start site, 5′

cap, start codon, 5′

untranslated region, 3′

untranslated region, stop codon, 5′

splice site or polyadenylation site.

3. A system of associated components for preparing a set of oligonucleotides that modulates expression of a selected nucleic acid comprising:

a computer system that

i) generates a list of oligonucleotide sequences according to a desired oligonucleotide length, thereby generating a series of oligonucleotide sequences;

ii) applies a virtual oligonucleotide chemistry to the oligonucleotide sequences generated in step i) to yield a set of virtual oligonucleotides;

iii) generates a subset of said set of virtual oligonucleotides, said subset being the result of a decision to;

a) target a functional region of said selected nucleic acid, b) target an accessible site on said selected nucleic acid, and/or c) uniformly distribute oligonucleotide compounds across said selected nucleic acid; and

iv) generates synthesis instructions in computer manipulable form for said oligonucleotide sequences in said subset of said set of virtual oligonucleotides;

an automated synthesizer that receives said synthesis instructions from said computer system and synthesizes only said oligonucleotide sequences in said subset of said set of virtual oligonucleotides, wherein the product of said synthesis is a set of synthesized oligonucleotides;

a first apparatus that accepts said set of synthesized oligonucleotides and performs at least one procedure for each of said synthesized oligonucleotides wherein said procedure identifies particular members of said set that modulate expression of said selected nucleic acid; and

a second apparatus for analyzing said set of synthesized oligonucleotides by a method or technique, selected from the group consisting of liquid chromatography, optical densiometry, mass speetroscopy, gel fluorescence and scintillation imaging, and capillary gel electrophoresis.

4. A system of associated components for preparing a set of oligonucleotides that modulates expression of a selected nucleic acid comprising:

a computer system that

i) generates a list of oligonucleotide sequences according to a desired oligonucleotide length, thereby generating a series of oligonucleotide sequences;

ii) applies a virtual oligonucleotide chemistry to the oligonucleotide sequences generated in step i) to yield a set of virtual oligonucleotides;

iii) generates a subset of said set of virtual oligonucleotides, said subset being the result of a decision to;

a) target a functional region of said selected nucleic acid, b) target an accessible site on said selected nucleic acid, and/or c) uniformly distribute oligonucleotide compounds across said selected nucleic acid; and

iv) generates synthesis instructions in computer manipulable form for said oligonucleotide sequences in said subset of said set of virtual oligonucleotides;

an automated synthesizer that receives said synthesis instructions from said computer system and synthesizes only said oligonucleotide sequences in said subset of said set of virtual oligonucleotides, wherein the product of said synthesis is a set of synthesized oligonucleotides; and

an apparatus that accepts said set of synthesized oligonucleotides and performs at least one procedure for each of said synthesized oligonucleotides wherein said procedure identifies particular members of said set that modulate expression of said selected nucleic acid.