Claims
- 1. A method of identifying or classifying organisms on a species-specific or taxon-specific level comprising:
(a) providing a surface plasmon resonance-capable substrate having immobilized thereon one or more species- or taxon-specific nucleic acid probes; then (b) contacting the substrate with a sample known to, or suspected of, containing target nucleic acids from an organism to be identified or classified, under conditions and for a time sufficient for sequence-specific hybridization to occur between target nucleic acids present in the sample and the nucleic acid probes immobilized on the substrate; and then (c) analyzing the substrate by surface plasmon resonance, whereby sequence-specific hybridization between the target nucleic acids present in the sample and the nucleic acid probes immobilized on the substrate is detected.
- 2. The method of claim 1, wherein in step (a) is provided a substrate having a plurality of DNA probes arranged in an array.
- 3. The method of claim 1, wherein in step (a) is provided a substrate having a plurality of RNA probes arranged in an array.
- 4. The method of claim 1, wherein in step (b), the substrate is contacted with a sample containing DNA.
- 5. The method of claim 1, wherein in step (b), the substrate is contacted with a sample containing RNA.
- 6. The method of claim 1, wherein in step (b), the substrate is contacted with a sample containing ribosomal RNA.
- 7. The method of claim 1, wherein in step (c) the substrate is analyzed by surface plasmon resonance imaging.
- 8. The method of claim 1, wherein step (b) further comprises fragmenting the nucleic acids present in the sample before contacting the substrate to the sample.
- 9. The method of claim 8, wherein the nucleic acids present in the sample are fragmented by applying sufficient pressure to the sample to cause nucleic acid fragmentation.
- 10. The method of claim 8, wherein the nucleic acids present in the sample are fragmented by heating the sample to a sufficient temperature and for a sufficient amount of time to cause nucleic acid fragmentation.
- 11. A method of analyzing expression of a gene of interest comprising:
(a) providing a surface plasmon resonance-capable substrate having immobilized thereon one or more nucleic acid probes specifically reactive with mRNA or cDNA corresponding to a gene of interest; then (b) contacting the substrate with a sample known to, or suspected of, containing mRNA or cDNA corresponding to the gene of interest, under conditions and for a time sufficient for sequence-specific hybridization to occur between the mRNA or cDNA present in the sample and the nucleic acid probes immobilized on the substrate; and then (c) analyzing the substrate by surface plasmon resonance, whereby sequence-specific hybridization between mRNA or cDNA present in the sample and the nucleic acid probes immobilized on the substrate is detected.
- 12. The method of claim 11, wherein in step (a) is provided a substrate having a plurality of DNA probes arranged in an array.
- 13. The method of claim 11, wherein in step (a) is provided a substrate having a plurality of RNA probes arranged in an array.
- 14. The method of claim 11, wherein in step (b), the substrate is contacted with a sample containing cDNA.
- 15. The method of claim 11, wherein in step (b), the substrate is contacted with a sample containing mRNA.
- 16. The method of claim 11, wherein in step (c) the substrate is analyzed by surface plasmon resonance imaging.
- 17. The method of claim 11, wherein step (b) further comprises boiling the sample for a period of time sufficient to denature the mRNA or cDNA present in sample before contacting the substrate to the sample.
- 18. The method of claim 11, wherein step (b) further comprises fragmenting the mRNA or cDNA present in the sample before contacting the substrate to the sample.
- 19. The method of claim 18, wherein the nucleic acids present in the sample are fragmented by applying sufficient pressure to the sample to cause nucleic acid fragmentation.
- 20. The method of claim 18, wherein the nucleic acids present in the sample are fragmented by heating the sample to a sufficient temperature and for a sufficient amount of time to cause nucleic acid fragmentation.
- 21. A method of detecting and quantifying sequence-specific hybridization of nucleic acids comprising:
(a) depositing an ω-modified alkanethiol monolayer on a metal substrate; (b) reacting hydrophobic protecting groups with the monolayer; (c) patterning the monolayer to create an array of exposed metal substrate areas; (d) depositing ω-modified alkanethiol in the areas of exposed metal substrate, thereby yielding an array of discrete, unprotected ω-modified alkanethiol spots; (e) attaching nucleic acid probes to the discrete, unprotected ω-modified alkanethiol spots, thereby yielding an array of discrete spots having nucleic acid probes immobilized thereon; (f) removing the protecting groups of step (b); and (g) making the monolayer resistant to non-specific protein binding; and then (h) contacting the substrate of step (g) with a sample known to, or suspected of, containing target nucleic acids at a concentration not greater than 500 mM, under conditions and for a time sufficient for sequence-specific hybridization to occur between target nucleic acids present in the sample and the nucleic acid probes immobilized on the substrate; and then (i) analyzing the substrate by surface plasmon resonance, whereby sequence-specific hybridization between the target nucleic acids present in the sample and the nucleic acid probes immobilized on the substrate is detected.
- 22. The method of claim 21, wherein in step (e), DNA molecules are attached to the discrete, unprotected ω-modified alkanethiol spots.
- 23. The method of claim 21, wherein in step (e), RNA molecules are attached to the discrete, unprotected ω-modified alkanethiol spots.
- 24. The method of claim 21, wherein in step (h), the substrate is contacted with a sample containing DNA.
- 25. The method of claim 21, wherein in step (h), the substrate is contacted with a sample containing RNA.
- 26. The method of claim 21, wherein in step (h), the substrate is contacted with a sample containing ribosomal RNA.
- 27. The array of claim 21, wherein in step (a), the ω-modified alkanethiol monolayer is deposited on a gold substrate.
Parent Case Info
[0001] This is a continuation-in-part of co-pending application Ser. No. 09/456,038, filed Dec. 3, 1999, which is a divisional of Ser. No. 09/368,991, filed Aug. 5, 1999 and issued Oct. 3, 2000 as U.S. Pat. No. 6,127,129, which claims priority to provisional application Serial No. 60/132,342, filed May 4, 1999, all of which are incorporated herein by reference.
Government Interests
[0002] This invention was made with United States government support awarded by the National Institutes of Health, Grant No: NIH GM59622. The United States has certain rights in this invention.
Provisional Applications (1)
|
Number |
Date |
Country |
|
60132342 |
May 1999 |
US |
Divisions (1)
|
Number |
Date |
Country |
Parent |
09368991 |
Aug 1999 |
US |
Child |
09456038 |
Dec 1999 |
US |
Continuation in Parts (1)
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Number |
Date |
Country |
Parent |
09456038 |
Dec 1999 |
US |
Child |
09998551 |
Nov 2001 |
US |