Title: Solid phase sequencing of double-stranded nucleic acids

Abstract

This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

Inventors:

Fu, Dong-Jing ^[1]; Cantor, Charles R ^[2]; Koster, Hubert ^[3]; Smith, Cassandra L ^[2]

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+ Show Inventor Affiliations

1. Waltham, MA
2. Boston, MA
3. Concord, MA

Issue Date:

Tue Jan 01 00:00:00 EST 2002

Research Org.:

Boston University

OSTI Identifier:

874666

Patent Number(s):

6436635

Assignee:

Boston University (Boston, MA); Sequenom, Inc. (San Diego, CA)

Patent Classifications (CPCs):

B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01J - CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

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B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01J - CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY

B01J19/0046 - {Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides
B01J2219/00527 - Sheets
B01J2219/00529 - DNA chips
B01J2219/0059 - Sequential processes
B01J2219/00605 - the compounds being directly bound or immobilised to solid supports
B01J2219/0061 - The surface being organic
B01J2219/00612 - the surface being inorganic
B01J2219/00626 - Covalent
B01J2219/0063 - Other, e.g. van der Waals forces, hydrogen bonding
B01J2219/00637 - by coating it with another layer
B01J2219/00648 - by the use of solid beads
B01J2219/00659 - Two-dimensional arrays
B01J2219/00722 - Nucleotides

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

C12Q1/6816 - characterised by the detection means
C12Q1/6837 - using probe arrays or probe chips
C12Q1/6872 - involving mass spectrometry
C12Q1/6874 - involving nucleic acid arrays, e.g. sequencing by hybridisation
C12Q2525/161 - incorporating target specific and non-target specific sites
C12Q2565/501 - being an array of oligonucleotides
C12Q2565/537 - characterised by the capture oligonucleotide acting as a primer
C12Q2565/627 - being a mass spectrometer

C - CHEMISTRY C40 - COMBINATORIAL TECHNOLOGY C40B - COMBINATORIAL CHEMISTRY

C40B40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof

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DOE Contract Number:  

FG02-93ER61609

Resource Type:

Patent

Country of Publication:

United States

Language:

English

Subject:

solid; phase; sequencing; double-stranded; nucleic; acids; relates; methods; detecting; target; acid; sequences; probes; arrays; useful; kits; systems; contain; involve; hybridizing; represent; complementary; homologous; array; probe; single-stranded; portion; optional; variable; sequence; molecular; weights; hybridized; set; determined; mass; spectroscopy; fragments; biological; samples; patient; biopsies; environmental; fixed; support; hybridization; chip; facilitate; automated; determination; identification; nucleic acid; molecular weight; acid sequence; solid support; acid probe; stranded nucleic; /435/999/