title: Thermodynamic basis of the enhanced specificity of structured DNA probes.
abstract: Molecular beacons are DNA probes that form a stem-and-loop structure and possess an internally quenched fluorophore. When they bind to complementary nucleic acids, they undergo a conformational transition that switches on their fluorescence. These probes recognize their targets with higher specificity than probes that cannot form a hairpin stem, and they easily discriminate targets that differ from one another by only a single nucleotide. Our results show that molecular beacons can exist in three different states: bound to a target, free in the form of a hairpin structure, and free in the form of a random coil. Thermodynamic analysis of the transitions between these states reveals that enhanced specificity is a general feature of conformationally constrained probes.
authors.affiliation: Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021, USA.
authors.forename: G
authors.initials: G
authors.lastname: Bonnet
authors.forename: S
authors.initials: S
authors.lastname: Tyagi
authors.forename: A
authors.initials: A
authors.lastname: Libchaber
authors.forename: F R
authors.initials: FR
authors.lastname: Kramer
mesh_terms: D001483:Base Sequence; D015342:DNA Probes / Q000138:chemical synthesis / Q000737:chemistry*; D005452:Fluoresceins; D006358:Hot Temperature; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D012996:Solutions; D013816:Thermodynamics
chemical_list: D015342:DNA Probes; D005452:Fluoresceins; D009838:Oligodeoxyribonucleotides; D012996:Solutions