Novel oligonucleotide arrays and their use for sorting, isolating, sequencing, and manipulating nucleic acids

• US 20050266441A1
• Filed: 03/24/2005
• Published: 12/01/2005
• Est. Priority Date: 02/19/1992
• Status: Abandoned Application

• Current Assignee: University of Medicine and Dentistry of New Jersey (State of New Jersey)
• Original Assignee: The Public Health Research Institute of the City of New York, Inc.
• Inventors: Kramer, Fred Russell, Chetverin, Alexander B.
• Application Number:
  US11/088,979
• Publication Number:
  US 20050266441A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2219/00283 Reactor vessels with top opening
• CPC Class Codes: B01J 2219/00313 the reactor vessels being formed by arrays of wells in blocks
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12N 15/10 : Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12Q 1/6806 : Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6811 : Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 1/6834 : Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6853 : using modified primers or templates
• CPC Class Codes: C12Q 1/686 : Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6874 : involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/131 : incorporating a restriction site
• CPC Class Codes: C12Q 2525/179 : incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2525/191 : incorporating an adaptor
• CPC Class Codes: C12Q 2531/107 : Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2563/179 : the label being a nucleic acid
• CPC Class Codes: C12Q 2565/519 : characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: C12Q 2565/537 : characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/14 : Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: Y10S 435/81 : Packaged device or kit
• CPC Class Codes: Y10S 436/808 : Automated or kit

Abstract

The invention provides hyperactive mutant recombinases and hybrid mutant recombinases, and methods for their identification. Also provided are nucleic acids encoding hyperactive mutant recombinases and hybrid recombinases, as well as vectors and host cells. Host cells include eukaryotic cells capable of expressing said recombinases and carrying out site-specific recombination in the cell. The mutant recombinases may be used, for example, in biotechnology, gene therapy or transgenic applications.

Claims

1-159. -159. (canceled)

160. A composition comprising at least two oligonucleotides complementary to unique sequences of interest in a DNA sample, and an amplified mixture of DNA isolated from a genome, wherein the amplified mixture of DNA is made by cleaving a genomic DNA sample with a restriction enzyme, thereby providing restriction fragments;

ligating linker nucleic acids to the DNA restriction fragments;

providing oligomers that are complementary to the linker nucleic acids; and

,

amplifying the linked DNA by the polymerase chain reaction using the oligomers as primers, thereby providing the amplified mixture of DNA.

161. The composition of claim 160, wherein the at least two oligonucleotides are immobilized on a solid substrate.

162. A method of characterizing a nucleic acid, comprising:

providing at least one oligonucleotide which is complementary to a unique sequence of interest in a genomic DNA sample;

amplifying a mixture of nucleic acids comprising a group of genome fragments, thereby providing an amplified nucleic acid mixture of genome fragments; and

hybridizing the at least one oligonucleotide to the amplified nucleic acid mixture, thereby detecting at least one nucleic acid of interest in said amplified mixture.

163. The method of claim 162, wherein the oligonucleotide is a member of an array of oligonucleotides, which array comprises additional oligonucleotides which hybridize to unique genomic sequences of interest.

164. The method of claim 162, wherein the amplified nucleic acid mixture is made by cleaving a genomic DNA sample with a restriction enzyme, thereby providing restriction fragments;

ligating linker nucleic acids to the DNA restriction fragments;

providing oligomers that are complementary to the linker nucleic acids; and

,

amplifying the linked DNA by the polymerase chain reaction using the oligomers as primers, thereby providing the amplified nucleic acid mixture.