Hybridization-based biosensor containing hairpin probes and use thereof
First Claim
1. A sensor chip comprising:
- a fluorescence quenching surface;
a first nucleic acid molecule comprising first and second ends with the first end bound to the fluorescence quenching surface, a first region, and a second region complementary to the first region, the first nucleic acid molecule having, under appropriate conditions, either a hairpin conformation with the first and second regions hybridized together or a non-hairpin conformation; and
a first fluorophore bound to the second end of the first nucleic molecule;
whereby when the first nucleic acid molecule is in the hairpin conformation, the fluorescence quenching surface substantially quenches fluorescent emissions by the first fluorophore, and when the first nucleic acid molecule is in the non-hairpin conformation fluorescent emissions by the fluorophore are substantially free of quenching by the fluorescence quenching surface.
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Abstract
A sensor chip that includes: a fluorescence quenching surface; a nucleic acid probe that contains first and second ends with the first end bound to the fluorescence quenching surface, a first region, and a second region complementary to the first region, the nucleic acid probe having, under appropriate conditions, either a hairpin conformation with the first and second regions hybridized together or a non-haipin conformation; and a first fluorophore bound to the second end of the first nucleic acid molecule. When the first nucleic acid molecule is in the hairpin conformation, the fluorescence quenching surface substantially quenches fluorescent emissions by the first fluorophore; and when the first nucleic acid molecule is in the non-hairpin conformation, fluorescent emissions by the fluorophore are substantially free of quenching by the fluorescence quenching surface. Various nucleic acid probes, methods of making the sensor chip, biological sensor devices that contain the sensor chip, and their methods of use are also disclosed.
44 Citations
66 Claims
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1. A sensor chip comprising:
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a fluorescence quenching surface;
a first nucleic acid molecule comprising first and second ends with the first end bound to the fluorescence quenching surface, a first region, and a second region complementary to the first region, the first nucleic acid molecule having, under appropriate conditions, either a hairpin conformation with the first and second regions hybridized together or a non-hairpin conformation; and
a first fluorophore bound to the second end of the first nucleic molecule;
whereby when the first nucleic acid molecule is in the hairpin conformation, the fluorescence quenching surface substantially quenches fluorescent emissions by the first fluorophore, and when the first nucleic acid molecule is in the non-hairpin conformation fluorescent emissions by the fluorophore are substantially free of quenching by the fluorescence quenching surface. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61)
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- 37. A nucleic acid probe comprising first and second ends, the first end being modified for coupling to a surface and the second end being bound to a fluorophore, the nucleic acid probe further comprising a first region, and a second region complementary to the first region, wherein, under appropriate conditions, the nucleic acid probe has either a hairpin conformation with the first and second regions hybridized together or a non-hairpin conformation, with one or both of the first and second regions being adapted for hybridization to a target nucleic acid molecule.
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62. A method of making a sensor chip, the method comprising:
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providing a fluorescence quenching surface;
exposing the fluorescence quenching surface to a plurality of first nucleic acid molecules each comprising first and second ends with the first end being modified for coupling to the fluorescence quenching surface, a first region, and a second region complementary to the first region, and each first nucleic acid molecule having, under appropriate conditions, either a hairpin conformation with the first and second regions hybridized together or a non-hairpin conformation; and
exposing the fluorescence quenching surface to a plurality of spacer molecules each including a reactive group capable of coupling to the fluorescence quenching surface, whereby the plurality of spacer molecules, when bound to the fluorescence quenching surface, inhibit interaction between adjacent first nucleic acid molecules bound to the fluorescence quenching surface. - View Dependent Claims (63, 64, 65, 66)
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Specification