Amplification and separation of nucleic acid sequences using strand displacement amplification and bioelectronic microchip technology

• US 20060110754A1
• Filed: 10/14/2005
• Published: 05/25/2006
• Est. Priority Date: 04/12/1999
• Status: Abandoned Application

• Current Assignee: Nanogen, Inc.
• Original Assignee: Nanogen, Inc.
• Inventors: Nerenberg, Michael I., Edman, Carl F., Spargo, Catherine A., Walker, George Terrance
• Application Number:
  US11/251,229
• Publication Number:
  US 20060110754A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 2531/119 Strand displacement amplification [SDA]
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode

Abstract

Described and disclosed are devices, methods, and compositions of matter for the multiplex amplification and analysis of nucleic acid sequences in a sample using novel strand displacement amplification technologies in combination with bioelectronic microchip technology. Specifically, a nucleic acid in a sample is amplified to form amplicons, the amplicons are addressed to specified electronically addressable capture sites of the bioelectronic microchip, the addressed amplicons are captured and labeled, and then the capture sites are analyzed for the presence of label. Samples may be amplified using strand displacement amplification. The invention is also amenable to other amplification methodologies well known by those skilled in the art. The capture and label steps may be by a method of universal capture with sequence specific reporter, or by a method of sequence specific capture with universal reporter. The label may be detected by fluorescence, chemiluminescence, elecrochemiluminescence, or any other technique as are well known by those skilled in the art. This invention further allows for analyzing multiple nucleic acid targets on a single diagnostic platform wherein the nucleic acids may be amplified while either in direct contact with microchip components or in solution above the microchip array.

Claims

1. A method for the amplification, multiplex assaying, and detection target nucleic acids of interest using a bioelectronic microchip, comprising the steps of:

a) introducing at least one of the target nucleic acids onto a bioelectronic microchip having a plurality of electronically addressable capture sites;

b) amplifying said target nucleic acids to form amplicons of said target nucleic acids;

c) providing for said amplicons to contact capture probes located on capture sites by a process wherein said process comprises either (1) biasing any of said plurality of electronically addressable capture sites with an electronic bias sufficient to attract said amplicons to said biased capture sites, or (2) hybridizing said amplicons with said capture probes without electronic biasing;

d) capturing said amplicons onto specified electronically addressable capture sites of (c) by a capture probe that has specificity for said amplicons; and

e) detecting the presence of said amplicons;

wherein amplification of the target nucleic acid is by strand displacement amplification.

2. The method of claim 1, wherein said amplification, multiplex assaying and detecting are carried out either consecutively or simultaneously in relation to one another.

3. The method of claim 1, wherein detection of amplicons is by at least one of fluorescence, chemiluminescence, and electrochemiluminescence.

4. The method of claim 1, wherein target nucleic acids of interest are derived from a source selected from the group consisting of blood, sputum, stool, tissue, media, semen, hair, urine, food, water, and culture inoculated with at least one of blood, sputum, stool, tissue, media, semen, hair, urine, food, water.

5. The method of claim 1, wherein the target nucleic acid of interest is derived from a source selected from a group consisting of a bacterium, a virus, a human, an animal, or a plant.

6. A method of amplification, multiplex assaying, and the detection of target nucleic acids of interest using a bioelectric microchip comprising the steps of:

a) introducing at least one of the target nucleic acids onto a bioelectronic microchip having a plurality of electronically addressable capture sites;

b) electronically biasing any of said plurality of electronically addressable capture sites with an electronic bias sufficient to attract said target nucleic acids of interest to at least one of said capture sites;

c) amplifying said target nucleic acids to form-amplicons of said target nucleic acids;

d) capturing said amplicons of said target nucleic acids onto specified capture sites of said microchip by a capture probe that has specificity for said amplicons; and

e) detecting the presence of said captured amplicons;

wherein amplification of the target nucleic acid is by strand displacement amplification.

7. The method of claim 6, wherein said amplification, multiplex assaying and detecting are carried out either consecutively or simultaneously in relation to one another.

8. The method of claim 6, wherein detection of amplicons is by at least one of fluorescence, chemiluminescence, and electrochemiluminescence.

9. The method of claim 6, wherein target nucleic acids of interest are derived from a source selected from the group consisting of blood, sputum, stool, tissue, media, semen, hair, urine, food, water, and culture inoculated with at least one of blood, sputum, stool, tissue, media, semen, hair, urine, food, water.

10. The method of claim 6, wherein the target nucleic acid of interest is derived from a source selected from a group consisting of a bacterium, a virus, a human, an animal, or a plant.

11. A method for detecting specific nucleic acid sequences in multiple samples on an electronically addressable microchip having an array comprising a plurality of electronically addressable capture sites comprising the steps of:

a) introducing said samples onto said microchip;

b) sequentially subjecting each of said introduced samples, prior to the introduction of a subsequent sample, to a nucleic acid amplification reaction to form amplicons of specified nucleic acids contained in said samples;

c) capturing said amplicons formed from each introduced sample in (b) by specified said capture sites for their respective immobilization -prior to introduction of each next sample;

d) following addition, amplification and capture of said samples of steps (a), (b), and (c), introducing onto said microchip a label that has specificity for immobilized amplicons derived from any of said samples; and

f) detecting the presence of labeled amplicons hybridized to said immobilized amplicons;

wherein amplification of the target nucleic acids is by stand displacement amplification.

12. The method of claim 11, wherein said capturing of amplicons in (c) is carried out by hybridization.

13. The method of claim 11, wherein said label comprises sets of labeled oligonucleotides each set having a nucleotide sequence complimentary to a specific sample, said sets further being introduced to said microchip sequentially and electronically biased to capture sites containing their respective immobilized amplicons.

14. The method of claim 11 wherein said label comprises sets of labeled oligonucleotides each set having a nucleotide sequence complimentary to a specific sample, said sets further being introduced to said microchip sequentially and captured onto capture sites containing their respective immobilized amplicons.

15. The method of claim 11, wherein said amplification, capture and detecting are carried out either consecutively or simultaneously in relation to one another.

16. The method of claim 11, wherein presence of labeled amplicons is detected by at least one of fluorescence, chemiluminescence, and electrochemiluminescence.

17. The method of claim 11, wherein said samples are derived from a group consisting of blood, sputum, stool, tissue, media, semen, hair, urine, food, water, and culture inoculated with at least one of blood, sputum, stool, tissue, media, semen, hair, urine, food, water.

18. The method of claim 11, wherein the nucleic acid of interest is derived from a source selected from the group consisting of a bacterium, a virus, a human, an animal or a plant.

19. A method for detecting specific nucleic acid sequences in multiple samples on an electronically addressable microchip having an array comprising a plurality of electronically addressable capture sites comprising the steps of:

a) subjecting each of said samples to a nucleic acid amplification reaction to form amplicons of specified nucleic acids contained in each of said samples;

b) introducing onto said microchip each of said samples following said reaction;

c) subjecting each of said introduced samples of (b) to electronically directed biasing of said samples to specified electronically addressable capture sites prior to the introduction of a subsequent introduced sample;

d) immobilizing electronically directed samples of (c) to the capture sites;

e) following immobilization of said samples in (d), introducing onto said microchip a label that has specificity for immobilized amplicons derived from any of said samples; and

f) detecting the presence of labeled amplicons hybridized to said immobilized amplicons.

20. The method of claim 19, wherein said samples are introduced and amplified sequentially.

21. The method of claim 19, wherein said label comprises sets of labeled oligonucleotides each set having a nucleotide sequence complimentary to a specific sample, said sets further being introduced to said microchip sequentially and electronically biased to capture sites containing their respective immobilized amplicons.

22. The method of claim 19 wherein said label comprises sets of labeled oligonucleotides each set having a nucleotide sequence complimentary to a specific sample, said sets further being introduced to said microchip sequentially and captured onto capture sites containing their respective immobilized amplicons.

23. The method of claim 19, wherein said amplification, capture and detecting are carried out either consecutively or simultaneously in relation to one another.

24. The method of claim 19, wherein presence of labeled amplicons is detected by at least one of fluorescence, chemiluminescence, and electrochemiluminescence.

25. The method of claim 19, wherein said samples are derived from a group consisting of blood, sputum, stool, tissue, media, semen, hair, urine, food, water, and culture inoculated with at least one of blood, sputum, stool, tissue, media, semen, hair, urine, food, water.

26. The method of claim 19, wherein the nucleic acid of interest is derived from a source selected from the group consisting of a bacterium, a virus, a human, an animal or a plant.