Detection of polynucleotide hybridization
First Claim
1. A method of detecting hybridization between a polynucleotide probe and a target polynucleotide having a nucleic acid sequence that is complementary to a nucleic acid sequence in the polynucleotide probe, wherein a first end of the polynucleotide probe is coupled to a matrix and a second end of the polynucleotide probe is coupled to a detectable marker, the method comprising observing a change in the conformation of the polynucleotide probe that is the result of hybridization between the polynucleotide probe and the target polynucleotide.
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Abstract
The invention disclosed herein provides a new detection scheme to monitor hybridization between complimentary polynucleotides such as DNA and/or RNA. Embodiments of the invention disclosed herein localized electromagnetic radiation to provide an optimized analysis of polynucleotide hybridization in contexts such as the polynucleotide microarrays typically used on gene chips.
21 Citations
20 Claims
- 1. A method of detecting hybridization between a polynucleotide probe and a target polynucleotide having a nucleic acid sequence that is complementary to a nucleic acid sequence in the polynucleotide probe, wherein a first end of the polynucleotide probe is coupled to a matrix and a second end of the polynucleotide probe is coupled to a detectable marker, the method comprising observing a change in the conformation of the polynucleotide probe that is the result of hybridization between the polynucleotide probe and the target polynucleotide.
- 12. A method of detecting hybridization between a polynucleotide probe and a target polynucleotide having a nucleic acid sequence that is complementary to a nucleic acid sequence in the polynucleotide probe, wherein the polynucleotide probe has a first end labeled with a detectable marker and a second end attached to a matrix having a negative charge, the method comprising using evanescent wave illumination to observe a reduction in the height of a detectable marker coupled to the polynucleotide probe'"'"'s free end above the surface of the matrix to which the polynucleotide probe is attached.
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16. A method of detecting hybridization between a polynucleotide probe and a target polynucleotide having a nucleic acid sequence that is complementary to a nucleic acid sequence in the polynucleotide probe, wherein the polynucleotide probe has a bound end coupled to a matrix and a free end coupled to a detectable marker, the method comprising:
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(a) determining an height of the detectable marker coupled to the polynucleotide probe'"'"'s free end above the surface of the matrix to which the probe is attached in the absence of a complementary polynucleotide sequence;
(b) allowing the polynucleotide probe and the target polynucleotide sequence to come into contact with one another under conditions favorable to hybridization;
(c) using evanescent wave illumination to measure the height of the detectable marker coupled to the polynucleotide probe'"'"'s free end above the surface of the matrix to which the probe is attached in the presence of the target polynucleotide sequence;
(d) comparing the height of the detectable marker in step (a) with the height of the detectable marker in step (c);
wherein a reduction the height of the detectable marker in step (a) as compared to step (d) is indicative of hybridization between a polynucleotide probe and a target polynucleotide having a nucleic acid sequence that is complementary to a nucleic acid sequence in the polynucleotide probe.
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17. An apparatus for detecting hybridization between a polynucleotide probe and a target polynucleotide having a nucleic acid sequence that is complementary to a nucleic acid sequence in the polynucleotide probe, wherein the hybridization is detected using evanescent wave illumination, the apparatus comprising:
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(a) a matrix on which a first end of a polynucleotide probe attached, wherein the second end of the polynucleotide probe is coupled to a detectable marker consisting of a fluorophore or a light scattering marker;
(b) a coupling mechanism which optically couples the probe to an optical guide to obtain an evanescent wave on the surface of the matrix;
(c) an optical arrangement which measures the fluorescent or scattered intensity both before and after depositing a solution containing a target polynucleotide sequences on the probe under conditions which favor hybridization of the probe and a target polynucleotide sequences that are complementary to a nucleic acid sequence in the polynucleotide probe; and
(d) a detector which records the difference of fluorescent intensity or scattering before and after subjecting the probe DNA to the target polynucleotide sequences.
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18. A kit comprising a container, a label on said container, and a polynucleotide probe composition contained within said container;
- wherein a first end of the polynucleotide probe is coupled to a matrix and a second end of the polynucleotide probe is coupled to a detectable marker; and
instructions for using the polynucleotide probe composition in methods of detecting hybridization between a polynucleotide probe and a target polynucleotide having a nucleic acid sequence that is complementary to a nucleic acid sequence in the polynucleotide probe by observing a change in the conformation of the polynucleotide probe that is the result of hybridization between the polynucleotide probe and the target polynucleotide. - View Dependent Claims (19, 20)
- wherein a first end of the polynucleotide probe is coupled to a matrix and a second end of the polynucleotide probe is coupled to a detectable marker; and
Specification