Method of sequencing by hybridization of oligonucleotide probes

• US 5,695,940 A
• Filed: 06/05/1995
• Issued: 12/09/1997
• Est. Priority Date: 04/01/1987
• Status: Expired due to Fees

• Current Assignee: Hyseq, Inc. (Arca Biopharma, Inc.)
• Original Assignee: Hyseq, Inc. (Arca Biopharma, Inc.)
• Inventors: Drmanac, Radoje T., Crkvenjakov, Radomir B.
• Primary Examiner(s): KETTER, JAMES S
• Application Number:
  US08/460,853
• Time in Patent Office: 918 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 536/24.33
• US Class Current: 435/6.18
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2565/50 Detection characterised by immobilisation to a surface
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly

Abstract

The conditions under which oligonucleotide probes hybridize preferentially with entirely complementary and homologous nucleic acid targets are described. Using these hybridization conditions, overlapping oligonucleotide probes associate with a target nucleic acid. Following washes, positive hybridization signals are used to assemble the sequence of a given nucleic acid fragment. Representative target nucleic acids are applied as dots. Up to to 100,000 probes of the type (A,T,C,G) (A,T,C,G)N8(A,T,C,G) are used to determine sequence information by simultaneous hybridization with nucleic acid molecules bound to a filter. Additional hybridization conditions are provided that allow stringent hybridization of 6-10 nucleotide long oligomers which extends the utility of the invention. A computer process determines the information sequence of the target nucleic acid which can include targets with the complexity of mammalian genomes. Sequence generation can be obtained for a large complex mammalian genome in a single process.

Claims

1. A method of sequencing a target nucleic acid of unknown sequence comprising the steps of:

(a) using conditions which differentiate an exactly complementary oligonucleotide probe and an oligonucleotide probe having a single mismatched nucleotide;

(b) contacting a plurality of oligonucleotides, each from six to ten nucleotides in length, with said target nucleic acid;

(c) forming a duplex between the target nucleic acid and the plurality of oligonucleotides;

(d) washing the duplex;

(e) detecting oligonucleotides positively hybridizing as part of said duplex; and

(f) compiling a sequence of the target nucleic acid from overlapping positively-hybridizing oligonucleotides.

2. A method for partial sequencing of a target nucleic acid, comprising the steps of:

(a) using conditions which differentiate an exactly complementary oligonucleotide probe and an oligonucleotide probe having a single mismatched nucleotide;

(b) contacting a target nucleic acid in a reaction mixture with a plurality, but less than a totality, of oligonucleotide probes of given length, each at least six nucleotides in length;

(c) forming a duplex between the target nucleic acid and the plurality of oligonucleotides;

(d) washing the duplex;

(e) detecting oligonucleotides positively hybridizing as part of said duplex; and

(f) compiling a partial sequence of said target nucleic acid from a subset of said oligonucleotide probes which form a duplex with said target nucleic acid and which overlap with a least one other member of said oligonucleotide probes.

3. The method according to claim 2, wherein said oligonucleotide probes are each from six to ten nucleotides in length.