Methods and apparatus for characterizing polynucleotides

• US 7,238,485 B2
• Filed: 03/23/2005
• Issued: 07/03/2007
• Est. Priority Date: 03/23/2004
• Status: Active Grant

• Current Assignee: Agilent Technologies, Inc., President and Fellows of Harvard College (Harvard Corporation), Regents of the University of California (University of California)
• Original Assignee: Agilent Technologies, Inc., President and Fellows of Harvard College (Harvard Corporation), Regents of the University of California (University of California)
• Inventors: Deamer, David W., Sampson, Jeffrey R., Branton, Daniel, Akeson, Mark
• Primary Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US11/088,140
• Publication Number:
  US 20060063171A1
• Time in Patent Office: 832 Days
• Field of Search: 435/6, 435/283.1, 536/23.1, 536/24.3
• US Class Current: 435/6.11
• CPC Class Codes: B01L 2300/0896 Nanoscaled
• CPC Class Codes: B01L 2400/0475 specific mechanical means and fluid pressure
• CPC Class Codes: B01L 3/502707 characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: B82Y 5/00 Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/543 Immobilised enzyme(s)
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore
• CPC Class Codes: G01N 33/48721 Investigating individual macromolecules, e.g. by translocation through nanopores Coulter counters in general G01N15/12; fabrication methods for nanoscale apertures B81B1/00; sequencing of nucleic acids C12Q1/68

Abstract

Systems and methods for analysis of polymers, e.g., polynucleotides, are provided. The systems are capable of analyzing a polymer at a specified rate. One such analysis system includes a structure having a nanopore aperture and a molecular motor, e.g., a polymerase, adjacent the nanopore aperture.

Claims

1. A nanopore analysis system, comprising:

(a) a structure having a nanopore aperture; and

(b) a molecular motor adjacent the nanopore aperture, wherein the molecular motor is capable of moving a polynucleotide with respect to the nanopore aperture at a rate of 350–

2000 Hz.

2. The nanopore analysis system of claim 1, wherein the molecular motor is substantially immobilized inline with the nanopore aperture by a gel matrix.

3. The nanopore analysis system of claim 2, wherein the molecular motor is covalently bonded to the gel matrix.

4. The nanopore analysis system of claim 1, wherein the molecular motor comprises a DNA polymerase, a RNA polymerase, a ribosome, an exonuclease, or a helicase.

5. A nanopore analysis system, comprising:

(c) a structure having a nanopore aperture; and

(d) a molecular motor (i) comprising a DNA polymerase, a ribosome, an exonuclease, or a helicase and (ii) disposed adjacent the nanopore aperture, wherein the molecular motor is capable of moving a polynucleotide with respect to the nanopore aperture at a rate of 75–

2000 Hz.