Method of Identifying a Base in a Nucleic Acid

• US 5,968,740 A
• Filed: 03/05/1997
• Issued: 10/19/1999
• Est. Priority Date: 07/24/1995
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lipshutz, Robert J., Huang, Xiaohua, Fodor, Stephen P. A.
• Primary Examiner(s): Houtteman, Scott W.
• Application Number:
  US08/811,829
• Time in Patent Office: 958 Days
• Field of Search: 435/6, 536/24.3, 536/24.31, 536/24.32
• US Class Current: 506/5
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• 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: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

Claims

1. A method of identifying a base in a target nucleic acid with a plurality of nucleic acid probes, said probes having fewer bases than said target, comprising the steps of:

contacting said probes with said target;

identifying a first probe that has the highest binding affinity to said target;

selecting a first set of extension probes comprising at least two of said first probes which are extended differently from each other by the addition at one end of A, C, T, U or G, with or without a deletion at he other end of said extension probes; and

identifying one of said first set of extension probes that hybridizes specifically to said target more strongly than others of said first set of extension probes, whereby said one of said extension probes identifies a base in said target nucleic acid.

2. A method as recited in claim 1 wherein substantially all of said nucleic acid probes comprise n nucleotides, and wherein said extension probes comprise n-1 nucleotides of said first probe.

3. A method as recited in claim 1 further comprising the steps of:

selecting a second set of A, C, T, U, and G extension probes that extend in a direction opposite of said first set of extension probes; and

identifying one of said second set of extension probes that hybridizes specifically to said target more strongly than others of said second set of extension probes., whereby said one of said second set of extension probes identifies a second base in said target nucleic acid.

4. The method as recited in claim 1 further comprising the step of:

repeating said steps of selecting sets of extension probes and identifying extension probes five or more times.

5. The method as recited in claim 1 wherein said step of identifying further comprises the steps of:

identifying single base mismatch probes, said single base mismatch probes comprising at least two of A, C, T, U, and G monosubstitutions of said first set of extension probes;

recording hybridization affinity data of said single base mismatch probes; and

selecting one of said first set of extension probes as a correct extension of said first probe when said hybridization affinity data conform to expected hybridization affinity data of said single base mismatch probes.

6. The method as recited in claim 5 wherein said expected hybridization data comprise:

higher binding affinity for probe/target complexes with a mismatch at termini of said extension probes; and

lower binding affinity for probe/target complexes with a mismatch at internal portions of said complexes.

7. The method as recited in claim 6 wherein:

said hybridization data are normalized to a hybridization value for one of said extension probes; and

said step of identifying comprises selecting one of said extension probes having terminal single base mismatch probes that do not have normalized hybridization values higher than a normalized value of said one of said extension probes.

8. The method as recited in claim 1 wherein the step of identifying comprises the step of selecting one of said set of extension probes that exhibits a higher binding affinity to said target than other extension probes.

9. The method as recited in claim 1 wherein said step of identifying is conducted in an appropriately programmed computer.

10. A method of determining if a nucleotide sequence of a target nucleic acid is the same as a sequence of a first nucleic acid comprising:

contacting said target nucleic acid with a plurality of nuclei acid probes to determine a core probe subsequence;

determining the affinity of said target nucleic acid to probes identical to, but for a single base mismatch, of said core probe subsequence; and

determining that said nucleotide sequence of said target is the same as said first nucleic acid if said affinity of said target to probes identical to but for a single base mismatch follows a predetermined pattern.

11. The method as recited in claim 10 wherein said predetermined pattern comprises affinity of said single base mismatch probes normalized to affinity of a perfect complement of said subsequence.

12. The method as recited in claim 11 wherein said affinity of single base mismatch probes are plotted as affinity versus mismatch position, and normalized to said affinity of a perfect complement of said subsequence.

13. The method as recited in claim 10 further comprising the step of determining that said nucleotide sequence of said target is not the same as said first nucleic acid if said affinity of said target to probes complementary to single base mismatches does not follow a predetermined pattern.