Method of identifying hairpin DNA probes by partial fold analysis

Miller, Benjamin L; Strohsahl, Christopher M

Method of identifying hairpin DNA probes by partial fold analysis

Patent · 06 October 2009

OSTI ID:1003001

Miller, Benjamin L ^[1]; Strohsahl, Christopher M ^[2]

Penfield, NY
Saugerties, NY

Method of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

Research Organization:: Infotonics Tech Center Inc

Sponsoring Organization:: USDOE

DOE Contract Number:: FG02-02ER63410

Assignee:: University of Rochester (Rochester, NY)

Patent Number(s):: 7,598,034

Application Number:: 10/584,875

OSTI ID:: 1003001

Country of Publication:: United States

Language:: English

References (8)

Effect of Secondary Structure on the Thermodynamics and Kinetics of PNA Hybridization to DNA Hairpins Kushon, Stuart A.; Jordan, Jason P.; Seifert, Jennifer L. Journal of the American Chemical Society, Vol. 123, Issue 44 https://doi.org/10.1021/ja016310e	journal	November 2001
Hybridization of single-stranded DNA targets to immobilized complementary DNA probes: comparison of hairpin versus linear capture probes Riccelli, P. V. Nucleic Acids Research, Vol. 29, Issue 4 https://doi.org/10.1093/nar/29.4.996	journal	February 2001
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Zuker, Michael; Stiegler, Patrick Nucleic Acids Research, Vol. 9, Issue 1 https://doi.org/10.1093/nar/9.1.133	journal	January 1981
Thermodynamic basis of the enhanced specificity of structured DNA probes Bonnet, G.; Tyagi, S.; Libchaber, A. Proceedings of the National Academy of Sciences, Vol. 96, Issue 11 https://doi.org/10.1073/pnas.96.11.6171	journal	May 1999
Stem-loop oligonucleotides: a robust tool for molecular biology and biotechnology Broude, Natalia E. Trends in Biotechnology, Vol. 20, Issue 6 https://doi.org/10.1016/S0167-7799(02)01942-X	journal	June 2002
Rapid Identification of Candida dubliniensis Using a Species-Specific Molecular Beacon Park, Steven; Wong, May; Marras, Salvatore A. E. Journal of Clinical Microbiology, Vol. 38, Issue 8 https://doi.org/10.1128/JCM.38.8.2829-2836.2000	journal	January 2000
Single-mismatch detection using gold-quenched fluorescent oligonucleotides Dubertret, Benoit; Calame, Michel; Libchaber, Albert J. Nature Biotechnology, Vol. 19, Issue 4 https://doi.org/10.1038/86762	journal	April 2001
Hybridization-Based Unquenching of DNA Hairpins on Au Surfaces: Prototypical “Molecular Beacon” Biosensors Du, Hui; Disney, Matthew D.; Miller, Benjamin L. Journal of the American Chemical Society, Vol. 125, Issue 14 https://doi.org/10.1021/ja0290781	journal	April 2003

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