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

• US 6,046,003 A
• Filed: 01/26/1998
• Issued: 04/04/2000
• Est. Priority Date: 11/30/1995
• Status: Expired due to Fees

• Current Assignee: PharmaSeq, Inc.
• Original Assignee: PharmaSeq, Inc.
• Inventors: Mandecki, Wlodek
• Primary Examiner(s): FREDMAN, JEFFREY NORMAN
• Application Number:
  US09/013,114
• Time in Patent Office: 799 Days
• Field of Search: 435/6, 435/91.2, 435/810, 435/973, 340/825.06, 340/825.54, 340/870.17, 436/501, 436/520, 436/519, 536/23.1, 536/24.3
• US Class Current: 506/38
• 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 solid phase support comprising:

(a) a transponder which is a monolithic integrated circuit which can transmit via electromagnetic radiation data stored within said integrated circuit; and

(b) an oligonucleotide probe attached to the surface of the integrated circuit, wherein said probe is capable of binding to a nucleic acid.

3. The solid phase support of claim 1, wherein said monolithic integrated circuit comprises a photovoltaic cell that can be activated by light.

4. The solid phase support of claim 3, wherein said data stored in the memory of said monolithic integrated circuit are encoded by a manufacturer of said integrated circuit.

5. The solid phase support of claim 4, wherein said data stored in the memory of the monolithic integrated circuit are encoded by a user with a scanner device.

2. A solid phase support comprising:

(a) a transponder which is a monolithic integrated circuit which can transmit via electromagnetic radiation data stored within said integrated circuit;

(b) at least one layer of a coating deposited on the surface of the integrated circuit, (c) an oligonucleotide probe attached to the coating layer, wherein said probe is capable of binding to a target nucleic acid.

6. The solid phase support of claim 2, wherein said monolithic integrated circuit comprises (a) a photovoltaic cell that can be activated by light and (b) said coating is at least partially transmissible to light.

7. The solid phase support of claim 6, wherein said data stored in the memory of said monolithic integrated circuit are encoded by a manufacturer of said integrated circuit.

8. The solid phase support of claim 7, wherein said data stored in said memory of the monolithic integrated circuit are encoded by a user with a scanner device.

9. 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 (i) a transponder and (ii) an oligonucleotide probe bound to its surface; and

(b) at least one label reagent.

10. The kit of claim 9, wherein the label reagent comprises a reagent that labels the target nucleic acid.

11. The kit of claim 9, wherein the label reagent comprises a labeled nucleotide.

12. The kit of claim 9, further comprising:

(a) a sample diluent buffer solution; and

(b) an enzyme reaction buffer solution.

13. A kit of claim 9, wherein the transponder is a monolithic integrated circuit.

14. The kit of claim 13, wherein the label reagent comprises a reagent that labels the target nucleic acid.

15. The kit of claim 13, wherein the label reagent comprises a labeled nucleotide for use in a chain extension reaction using DNA polymerase.

16. The kit of claim 13, further comprising:

(a) a sample diluent buffer solution; and

(b) an enzyme reaction buffer solution.