Charge perturbation detection system for DNA and other molecules

• US 8,313,907 B2
• Filed: 06/28/2011
• Issued: 11/20/2012
• Est. Priority Date: 11/12/2004
• Status: Active Grant

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Inventors: Pourmand, Nader, Karhanek, Miloslav, Davis, Ronald W.
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US13/170,607
• Publication Number:
  US 20110281739A1
• Time in Patent Office: 511 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: B82Y 15/00 Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: B82Y 40/00 Manufacture or treatment of nanostructures
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: G01N 27/3275 Sensing specific biomolecules, e.g. nucleic acid strands, based on an electrode surface reaction
• CPC Class Codes: G01N 27/3276 being a hybridisation with immobilised receptors using a FET type sensor G01N27/4145; concerning the hybridisation C12Q1/68

Abstract

Methods and apparatus for direct detection of chemical reactions are provided. In a preferred embodiment, electric charge perturbations of the local environment during enzyme-catalyzed reactions are sensed by an electrode system with an immobilized target molecule. The target molecule is preferably DNA. The charge perturbation caused by the polymerase reaction can uniquely identify a DNA sequence. The polymerization process generates local perturbations of charge in the solution near the electrode surface and induces a charge in a polarazible gold electrode. This event is detected as a transient current by a voltage clamp amplifier. Detection of single nucleotides in a sequence can be determined by dispensing individual dNTPs to the electrode solution and detecting the charge perturbations. Alternatively, multiple bases can be determined at the same time using a mix of all dNTPs with subsequent analysis of the resulting signal. The initial enzyme attachment to the DNA molecule can be detected prior to polymerization, with electrode capacitance measurement using the same voltage-clamp amplifier. This technique and device may be adapted to other reaction determinations, such as enzymatic reactions, other electrode configurations, and other amplifying circuits.

Claims

1. A device for nucleic acid sequence detection, comprising:

(a) a vessel for containing a reaction medium including at least one template nucleic acid molecule with components for template polymerization by complimentary addition of one or more nucleotides to the at least one template nucleic acid molecule with a concomitant proton release;

(b) at least one polarizable electrode, connected to an amplifying circuit to amplify signals generated in response to polarity changes induced in the at least one polarizable electrode, so as to be sensitive to charge perturbations in the reaction medium whereby the polarity changes in the at least one electrode result in response to charge perturbations from the concomitant proton release as template polymerization of the at least one template nucleic acid molecule; and

(c) a detection component, comprising the amplifying circuit, that generates signals in response to the polarity changes induced in the electrode, the signals indicating whether one or more corresponding nucleotides are added to the at least one template nucleic acid to thereby discern at least a portion of the at least one template nucleic acid sequence.

2. The device of claim 1 further comprising an insulating layer formed on the at least one polarizable electrode.

3. The device of claim 2 wherein the insulating layer comprises a self-assembled monolayer.

4. The device of claim 2 wherein the at least one template nucleic acid is linked to the insulating layer.

5. The device of claim 1 wherein the at least one amplifying circuit comprises a differential feedback amplifier.

6. The device of claim 1 wherein the at least one polarizable electrode comprises a metallic composition.

7. The device of claim 1 wherein the at least one polarizable electrode comprises an addressable array of polarizable electrodes.

8. The device of claim 1 wherein the at least one polarizable electrode comprises an integrated circuit formed on a semiconductor substrate.