Method of determining the sequence of nucleic acids employing solid-phase particles carrying transponders

• US 20010044109A1
• Filed: 02/12/2001
• Published: 11/22/2001
• Est. Priority Date: 11/30/1995
• Status: Abandoned Application

• Current Assignee: PharmaSeq, Inc.
• Original Assignee: PharmaSeq, Inc.
• Inventors: Mandecki, Wlodek
• Application Number:
  US09/781,655
• Publication Number:
  US 20010044109A1
• 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 2219/005 Beads
• CPC Class Codes: B01J 2219/00567 Transponder chips
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2563/149 Particles, e.g. beads
• CPC Class Codes: C12Q 2563/185 Nucleic acid dedicated to use as a hidden marker/bar code, e.g. inclusion of nucleic acids to mark art objects or animals
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 70/00 Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: Y10S 435/81 Packaged device or kit
• CPC Class Codes: Y10S 435/973 Simultaneous determination of more than one analyte
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

A method is described for determining the sequence of nucleic acids. The method employs small solid phase particles having transponders, with a primary layer of an oligonucleotide of known sequence attached to the outer surface of the particle. A read/write scanner device is used to encode and decode data on the transponder. The stored data includes the sequence of the oligonucleotide immobilized on the transponder. The sequence of sample nucleic acids is determined by detecting annealing to an oligonucleotide bound to a particle, followed by decoding the transponder to determine the sequence of the oligonucleotide.

Claims

1. A method of determining the sequence of a target nucleic acid sequence in a sample, comprising the steps of:

(a) providing a solid phase comprising particles having transponders, the particles having an oligonucleotide probe attached to a surface of the solid phase particles, the transponders having memory elements and an index number indicating sequence of the probe encoded on the transponders;

(c) contacting the solid phase with a sample to form a sample mixture;

(d) denaturing nucleic acids in the sample mixture;

(e) hybridizing the nucleic acids in the sample mixture, whereby target nucleic acid sequences hybridize to complementary probes;

(f) analyzing the solid phase to detect the presence of a label indicative of binding target nucleic acid to probes;

(g) decoding the data encoded on transponders using the dedicated read/write scanner to identify the sequence of the probes to which target nucleic acids are bound.

2. The method of

claim 1

, further comprising the step of analyzing the sequences of probes to which target nucleic acid bound to determine at least a portion of the sequence of the target nucleic acid.

3. The method of

claim 1

wherein the label is bound to the target nucleic acid.

4. The method of

claim 1

wherein the label is added after the annealing step through a chain extension reaction using DNA polymerase.

5. The method of

claim 1

wherein the data comprises the sequence of the oligonucleotide probe deposited on solid phase.

6. The method of

claim 1

wherein the data comprises characteristics of the sample.

7. A method of determining the sequence of target nucleic acid thought to contain a plurality of subsequences, comprising the steps of:

(a) introducing into the sample at least two populations of solid phase particles, each particle having a transponder and having an oligonucleotide probe corresponding to one of the subsequences attached to its surface, a first population having a different oligonucleotide probe sequence than a second population and the transponders in the first population being encoded with a different identification than the transponders of the second population;

(b) denaturing the nucleic acids in the sample;

(c) hybridizing the nucleic acids in the sample, whereby target nucleic acid sequences hybridize to the oligonucleotide probes;

(c) analyzing the particles to detect a label indicating that target nucleic acid has bound to the probe; and

(d) decoding the transponder to determine the sequence of the probe.

8. The method of

claim 7

, wherein the solid phase comprises at least three populations of solid phase particles, each particle having a transponder and having an oligonucleotide probe corresponding to one of the subsequences attached to its surface, each of the three populations having a different oligonucleotide probe sequence and each of the populations being encoded with a different identification than the transponders of the second population.

9. The method of

claim 7

wherein the surface of the particles is glass, latex or plastic.

10. The method of

claim 7

wherein the oligonucleotide probe is single-stranded.

11. The method of

claim 7

, wherein the-oligonucleotide probe is biotinylated and the particle is coated with a layer of streptavidin.

12. A kit for determining the sequence of target nucleic acids in a sample, comprising:

(a) at least one assay vessel, containing at least one solid phase particle having a transponder, and an oligonucleotide probe bound to a surface of the particle; and

(b) at least one label reagent.

13. The kit of

claim 12

, wherein the label reagent comprises a reagent that labels the target nucleic acid.

14. The kit of

claim 12

, wherein the label reagent comprises a labelled nucleoside for use in a chain extension reaction using DNA polymerase.

15. The kit of

claim 12

, further comprising:

(a) a sample diluent buffer solution; and

(b) an enzyme reaction buffer solution.