US6287765B1
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US
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Methods for detecting and identifying single molecules
Assignee: Molecular Machines Inc
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Filing: 1998-05-20
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Granted: 2001-09-11
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Expires: 2018-05-20
Abstract
Abstract Multimolecular devices and drug delivery systems prepared from synthetic heteropolymers, heteropolymeric discrete structures, multivalent heteropolymeric hybrid structures, aptameric multimolecular devices, multivalent imprints, tethered specific recognition devices, paired specific recognition devices, nonaptameric multimolecular devices and immobilized multimolecular structures are provided, including molecular adsorbents and multimolecular adherents, adhesives, transducers, switches, sensors and delivery systems. Methods for selecting single synthetic nucleotides, shape-specific probes and specifically attractive surfaces for use in these multimolecular devices are also provided. In addition, paired nucleotide-nonnucleotide mapping libraries for transposition of selected populations of selected nonoligonucleotide molecules into selected populations of replicatable nucleotide sequences are described.
Inventors
- 👤 Roger S. Cubicciotti
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-10-28 12:49
CPC Classifications
C; C07; C07H; C07H21/00; Y; Y10; Y10S; Y10S977/00; Y10S977/84; Y10S977/849; Y10S977/852; Y10S977/853
Claims Analysis
Total Claims: 32
Claim 1
Independent Claim
65 words
A method of detecting a single nonnaturally occurring oligonucleotide molecule capable of specifically binding to a selected nonoligonucleotide molecule comprising: (a) contacting a mixture comprising an assortment of nonnaturally occurring oligonucleotides with a selected nonoligonucleotide molecule; and (b) detecting a single nonnaturally occurring oligonucleotide molecule specifically bound to said selected nonoligonucleotide molecule by at least one of scanning probe microscopy, optical trapping or flow cytometry.
Claim 2
Independent Claim
65 words
A method of detecting a single nonnaturally occurring oligonucleotide molecule capable of specifically binding to a selected nonoligonucleotide molecule comprising: (a) contacting a mixture comprising an assortment of nonnaturally occurring oligonucleotides with a selected nonoligonucleotide molecule; and (b) detecting a single nonnaturally occurring oligonucleotide molecule specifically bound to said selected nonoligonucleotide molecule by at least one of scanning probe microscopy, optical trapping or flow cytometry.
Claim 3
Dependent Claim
15 words
The method of claim 1 wherein said selected nonoligonucleotide molecule is not a DNA-binding protein.
Claim 4
Dependent Claim
14 words
The method of claim 1 wherein said mixture comprises a random-sequence assortment of oligonucleotides.
Claim 5
Dependent Claim
29 words
The method of claim 1 wherein said mixture comprises at least one of a nonrandom assortment of oligonucleotides, a nucleic acid library, a combinatorial library, or a nucleotide-encoded library.
Claim 6
Dependent Claim
24 words
The method of claim 1 wherein said mixture comprises an oligonucleotide produced by at least one of amplification, replication, transcription, or in vitro evolution.
Claim 7
Dependent Claim
17 words
The method of claim 1 wherein said single nonnaturally occurring oligonucleotide molecule further comprises a nonnucleotide molecule.
Claim 8
Dependent Claim
25 words
The method of claim 6 wherein the identity of said nonnucleotide molecule is encoded by a nucleotide sequence comprising said single nonnaturally occurring oligonucleotide molecule.
Claim 9
Dependent Claim
16 words
The method of claim 1 wherein said selected nonoligonucleotide molecule is immobilized on a solid support.
Claim 10
Dependent Claim
64 words
The method of claim 1 further comprising isolating said single nonnaturally occurring oligonucleotide molecule by at least one of removing said single nonnaturally occurring oligonucleotide molecule from said mixture, removing said single nonnaturally occurring oligonucleotide molecule from said selected nonoligonucleotide molecule, transporting said single nonnaturally occurring oligonucleotide molecule to a sequencing apparatus, or transporting said single nonnaturally occurring oligonucleotide molecule to an amplification vessel.
Claim 11
Dependent Claim
26 words
The method of claim 1 further comprising at least one of determining, amplifying, replicating, or transcribing a nucleotide sequence comprising said single nonnaturally occurring oligonucleotide molecule.
Claim 12
Dependent Claim
14 words
The method of claim 1 further comprising identifying said single nonnaturally occurring oligonucleotide molecule.
Claim 13
Independent Claim
69 words
A method of detecting a single nonnaturally occurring oligonucleotide molecule capable of specifically binding to a selected nonoligonucleotide molecule comprising: (a) preparing a reaction mixture comprising a selected nonoligonucleotide molecule and a nonnaturally occurring oligonucleotide comprising an unknown nucleotide sequence; and (b) detecting a single nonnaturally occurring oligonucleotide molecule specifically bound to said selected nonoligonucleotide molecule by at least one of scanning probe microscopy, optical trapping or flow cytometry.
Claim 14
Independent Claim
69 words
A method of detecting a single nonnaturally occurring oligonucleotide molecule capable of specifically binding to a selected nonoligonucleotide molecule comprising: (a) preparing a reaction mixture comprising a selected nonoligonucleotide molecule and a nonnaturally occurring oligonucleotide comprising an unknown nucleotide sequence; and (b) detecting a single nonnaturally occurring oligonucleotide molecule specifically bound to said selected nonoligonucleotide molecule by at least one of scanning probe microscopy, optical trapping or flow cytometry.
Claim 15
Dependent Claim
15 words
The method of claim 12 wherein said selected nonoligonucleotide molecule is not a DNA-binding protein.
Claim 16
Dependent Claim
64 words
The method of claim 12 further comprising isolating said single nonnaturally occurring oligonucleotide molecule by at least one of removing said single nonnaturally occurring oligonucleotide molecule from said mixture, removing said single nonnaturally occurring oligonucleotide molecule from said selected nonoligonucleotide molecule, transporting said single nonnaturally occurring oligonucleotide molecule to a sequencing apparatus, or transporting said single nonnaturally occurring oligonucleotide molecule to an amplification vessel.
Claim 17
Dependent Claim
26 words
The method of claim 12 further comprising at least one of determining, amplifying, replicating, or transcribing a nucleotide sequence comprising said single nonnaturally occurring oligonucleotide molecule.
Claim 18
Independent Claim
78 words
A method of detecting a single nonnaturally occurring oligonucleotide molecule capable of specifically binding to a selected target that is not a DNA-binding protein comprising: (a) selecting a target that is not a DNA-binding protein; (b) contacting the selected target with a mixture comprising an assortment of nonnaturally occurring oligonucleotides; and (c) detecting a single nonnaturally occurring oligonucleotide molecule specifically bound to said selected target by at least one of scanning probe microscopy, optical trapping or flow cytometry.
Claim 19
Independent Claim
78 words
A method of detecting a single nonnaturally occurring oligonucleotide molecule capable of specifically binding to a selected target that is not a DNA-binding protein comprising: (a) selecting a target that is not a DNA-binding protein; (b) contacting the selected target with a mixture comprising an assortment of nonnaturally occurring oligonucleotides; and (c) detecting a single nonnaturally occurring oligonucleotide molecule specifically bound to said selected target by at least one of scanning probe microscopy, optical trapping or flow cytometry.
Claim 20
Dependent Claim
16 words
The method of claim 16 wherein said mixture contains an oligonucleotide comprising an unknown nucleotide sequence.
Claim 21
Dependent Claim
63 words
The method of claim 16 further comprising isolating said single nonnaturally occurring oligonucleotide molecule by at least one of removing said single nonnaturally occurring oligonucleotide molecule from said mixture, removing said single nonnaturally occurring oligonucleotide molecule from said selected target, transporting said single nonnaturally occurring oligonucleotide molecule to a sequencing apparatus, or transporting said single nonnaturally occurring oligonucleotide molecule to an amplification vessel.
Claim 22
Dependent Claim
26 words
The method of claim 16 further comprising at least one of determining, amplifying, replicating, or transcribing a nucleotide sequence comprising said single nonnaturally occurring oligonucleotide molecule.
Claim 23
Independent Claim
87 words
A method of detecting a single nonnaturally occurring oligonucleotide conjugate molecule capable of specifically binding to a selected nonoligonucleotide molecule, said method comprising: (a) preparing a reaction mixture comprising a selected nonoligonucleotide molecule and a plurality of different nonnaturally occurring oligonucleotide conjugates, each different nonnaturally occurring oligonucleotide conjugate comprising a different nonnucleotide moiety attached to an oligonucleotide; and (b) detecting a single nonnaturally occurring oligonucleotide conjugate molecule specifically bound to said selected nonoligonucleotide molecule by at least one of scanning probe microscopy, optical trapping or flow cytometry.
Claim 24
Independent Claim
87 words
A method of detecting a single nonnaturally occurring oligonucleotide conjugate molecule capable of specifically binding to a selected nonoligonucleotide molecule, said method comprising: (a) preparing a reaction mixture comprising a selected nonoligonucleotide molecule and a plurality of different nonnaturally occurring oligonucleotide conjugates, each different nonnaturally occurring oligonucleotide conjugate comprising a different nonnucleotide moiety attached to an oligonucleotide; and (b) detecting a single nonnaturally occurring oligonucleotide conjugate molecule specifically bound to said selected nonoligonucleotide molecule by at least one of scanning probe microscopy, optical trapping or flow cytometry.
Claim 25
Dependent Claim
15 words
The method of claim 20 wherein said selected nonoligonucleotide molecule is not a DNA-binding protein.
Claim 26
Dependent Claim
23 words
The method of claim 20 wherein the identity of said nonnucleotide moiety is encoded by a nucleotide sequence comprising said single oligonucleotide conjugate.
Claim 27
Dependent Claim
64 words
The method of claim 20 further comprising isolating said single nonnaturally occurring oligonucleotide conjugate by at least one of removing said single nonnaturally occurring oligonucleotide conjugate from said mixture, removing said single nonnaturally occurring oligonucleotide conjugate from said selected nonoligonucleotide molecule, transporting said single nonnaturally occurring oligonucleotide conjugate to a sequencing apparatus, or transporting said single nonnaturally occurring oligonucleotide conjugate to an amplification vessel.
Claim 28
Dependent Claim
26 words
The method of claim 20 further comprising at least one of determining, amplifying, replicating, or transcribing a nucleotide sequence comprising said single nonnaturally occurring oligonucleotide conjugate.
Claim 29
Independent Claim
70 words
A method of detecting a single nonoligonucleotide molecule comprising: (a) selecting a nonnaturally occurring oligonucleotide capable of specifically binding to a selected nonoligonucleotide molecule; (b) preparing a reaction mixture comprising said nonnaturally occurring oligonucleotide and said selected nonoligonucleotide molecule; and (c) detecting a single complex comprising said nonnaturally occurring oligonucleotide specifically bound to said selected nonoligonucleotide molecule by at least one of scanning probe microscopy, optical trapping or flow cytometry.
Claim 30
Independent Claim
70 words
A method of detecting a single nonoligonucleotide molecule comprising: (a) selecting a nonnaturally occurring oligonucleotide capable of specifically binding to a selected nonoligonucleotide molecule; (b) preparing a reaction mixture comprising said nonnaturally occurring oligonucleotide and said selected nonoligonucleotide molecule; and (c) detecting a single complex comprising said nonnaturally occurring oligonucleotide specifically bound to said selected nonoligonucleotide molecule by at least one of scanning probe microscopy, optical trapping or flow cytometry.
Claim 31
Dependent Claim
15 words
The method of claim 25 wherein said selected nonoligonucleotide molecule is not a DNA-binding protein.
Claim 32
Dependent Claim
15 words
The method of claim 25 wherein said nonnaturally occurring oligonucleotide further comprises a nonnucleotide molecule.
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USPTO Annuity & Maintenance Windows
| Annuity Stage | Window Opens | Payment Deadline | Surcharge Period Until | Estimated Fee | Status |
|---|---|---|---|---|---|
| 3.5 Years (Year 4) | 2004-09-10 | 2005-03-12 | 2005-09-11 | $2000.00 | Window Closed / Lapsed |
| 7.5 Years (Year 8) | 2008-09-10 | 2009-03-12 | 2009-09-11 | $3760.00 | Window Closed / Lapsed |
| 11.5 Years (Year 12) | 2012-09-10 | 2013-03-12 | 2013-09-11 | $7700.00 | Window Closed / Lapsed |