Multiplex assay for nucleic acids employing transponders

• US 6,001,571 A
• Filed: 05/19/1997
• Issued: 12/14/1999
• Est. Priority Date: 11/30/1995
• Status: Expired due to Term

• Current Assignee: PharmaSeq, Inc.
• Original Assignee: PharmaSeq, Inc.
• Inventors: Mandecki, Wlodek
• Primary Examiner(s): Campbell, Eggerton A.
• Application Number:
  US08/858,363
• Time in Patent Office: 939 Days
• Field of Search: 435/6, 435/91.2
• US Class Current: 435/6.19
• CPC Class Codes: B01J 2219/00567 Transponder chips
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• 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: G01N 15/14 Optical investigation techniques, e.g. flow cytometry
• CPC Class Codes: G01N 33/54313 the carrier being characterised by its particulate form
• CPC Class Codes: G01N 33/54373 involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings

Abstract

Disclosed are materials and methods for performing multiplex assays for nucleic acids, in which a transponder is associated with the bead(s) forming the solid phase used in the assay, nucleic acid probes are bound to the surface of the particles, and data concerning the assay is encoded on the transponder. A dedicated read/write device is used to remotely encode or read the data.

Claims

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

(a) providing a solid phase comprising particles having transponders, the transponders having memory elements, the particles having a nucleic acid probe attached to a surface of the solid phase particles, the probe having a sequence complementary to a target sequence, the transponders having an index number encoded in the memory element;

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

(c) denaturing nucleic acids in the sample mixture;

(d) hybridizing nucleic acids in the sample mixture whereby target nucleic acid sequences hybridize to the probe;

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

(g) decoding the data encoded on transponders using the dedicated read/write scanner to identify the class of transponders to which analytes are bound.

2. The method of claim 1, wherein the index number is encoded on the transponder memory element during the transponder manufacturing process.

3. The method of claim 1, wherein the index number is encoded on the transponder memory element by the user with a read/write scanner device.

4. The method of claim 1 wherein the label is bound to the target nucleic acid.

5. The method of claim 1 wherein the label is bound to a second oligonucleotide probe, the second probe having a sequence complementary to a second target sequence.

6. The method of claim 1, wherein the label comprises a fluorophore, a chromophore, a radiolabel, a chemiluminescent agent or a bioluminescent agent.

7. The method of claim 1, wherein an outer surface of the transponders is glass, plastic or latex.

8. The method of claim 1 wherein the data comprises the sequence of the oligonucleotide probe deposited on solid phase.

9. The method of claim 1 wherein the data comprises characteristics of the sample.

10. A method of performing a multiplex solid phase assay for target nucleic acids in a sample, comprising the steps of:

(a) providing a particulate solid phase, the particles of the solid phase having transponders, the transponders having memory elements, and an oligonucleotide probe attached to a surface of the particle, the oligonucleotide probe complementary to a target sequence;

(b) the transponders comprising two or more classes of encoded transponders, each class having a different oligonucleotide bound to the surface of the particle, and each class having a different index number encoded on the transponders memory elements;

(c) contacting the solid phase with a sample to form a sample mixture, the sample mixture containing two more transponders of different classes;

(e) denaturing nucleic acids in the sample mixture;

(f) hybridizing nucleic acids in the sample mixture whereby target nucleic acids hybridize to the nucleic acid probe;

(g) removing unbound sample components from the sample mixture;

(h) analyzing the solid phase to detect a label indicative of the presence of bound analytes; and

(i) decoding the data encoded on the transponders to identify the class of transponder to which an analyte is bound.

11. A method of detecting target nucleic acids in a sample, 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 attached to its surface, a first population having an oligonucleotide probe that hybridizes to a different target nucleic acid 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 target nucleic acids to the oligonucleotide probes;

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

(e) decoding the transponder to identify the probe.

12. The solid phase of claim 11, wherein the solid phase comprises at least three populations of solid phase particles, each particle having a transponder and having an oligonucleotide probe 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.