RANDOM ARRAY DNA ANALYSIS BY HYBRIDIZATION

• US 20160023180A1
• Filed: 10/07/2015
• Published: 01/28/2016
• Est. Priority Date: 12/20/2002
• Status: Abandoned Application

• Current Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Original Assignee: Callida Genomics, Inc. (SBH Genomics, Inc.)
• Inventors: Drmanac, Radoje
• Application Number:
  US14/877,814
• Publication Number:
  US 20160023180A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00479 Means for mixing reactants or products in the reaction vessels
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B82Y 10/00 Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: B82Y 20/00 Nanooptics, e.g. quantum optics or photonic crystals
• 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 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/101 Interaction between at least two labels
• CPC Class Codes: C12Q 2565/619 being a video camera
• CPC Class Codes: G01N 2021/6439 with indicators, stains, dyes, tags, labels, marks
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 2201/06113 Coherent sources; lasers
• CPC Class Codes: G01N 2223/413 sensor array [CCD]

Abstract

The invention relates to methods and devices for analyzing single molecules, i.e., nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.

Claims

1. An apparatus for determining sequence information for a target nucleic acid by probe hybridization, comprising:

a sample integration module configured for mixing, introducing, and/or removing reagents;

a disposable plug-in reaction cartridge configured for contacting an array of target nucleic acid fragments with probe pools, wherein the reaction cartridge comprises a slot for securing an array of single DNA molecules or amplicons, and quick connect ports for flow-through connection to the sample integration module;

a subsystem configured for illuminating fluorophores on an array in the reaction cartridge; and

a subsystem configured for detecting fluorophores on an array in the reaction cartridge.

2. The apparatus of claim 1, wherein the sample integration module is configured for arraying fragments of a target nucleic acid in a substrate.

3. The apparatus of claim 1, wherein the reaction cartridge comprises a mixing chamber connected to a plurality of probe pool reservoirs by means of a single microfluidic channel.

4. The apparatus of claim 1, wherein the illuminating subsystem is configured to create a 100 to 500 nm thick evanescent field at the interface of two optically different materials.

5. The apparatus of claim 1, wherein the detecting subsystem is a sensitive electron multiplying charge-coupled device (CCD) configured for detection of fluorophores on the array.

6. The apparatus of claim 1, further comprising probe modules that are configured for delivering fluorescently labeled probes to the apparatus.

7. A system for determining sequence information for a target nucleic acid comprising an apparatus according to claim 1, and a plurality of probe pools.

8. The system of claim 7, wherein the probes in the probe pools contain a label and a nucleotide sequence comprising the formula N_xB_yN_z, the formula N_xB_y or the formula B_yN_z, wherein:

(i) each N is independently a degenerate base wherein N represents any of the four nucleotide bases and varies between probes in each of said probe pools;

(ii) each B is independently an informative base, wherein B is the same base for probes in each of said probe pools;

(iii) x and z are each at least one.

9. The system of claim 8, further comprising a computer programmed for parallel processing of data from the subsystem configured for detecting fluorophores on an array in the reaction cartridge.

10. The system of claim 8, further comprising an array of fragments of a target nucleic acid configured for hybridizing with the probe pools.