Thermodynamic basis of the enhanced specificity of structured DNA probes

Grégoire Bonnet, Sanjay Tyagi, Albert Libchaber, Fred Russell Kramer

Research output: Contribution to journalArticlepeer-review

564 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)6171-6176
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number11
StatePublished - May 25 1999
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General


  • Fluorescence quenching
  • Mismatch discrimination
  • Molecular beacons
  • Molecular recognition
  • Phase diagram

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