Multicolor molecular beacons for allele discrimination

Nat Biotechnol. 1998 Jan;16(1):49-53. doi: 10.1038/nbt0198-49.


Molecular beacons are hairpin-shaped oligonucleotide probes that report the presence of specific nucleic acids in homogenous solutions. When they bind to their targets they undergo a conformational reorganization that restores the fluorescence of an internally quenched fluorophore. We found that their hairpin conformation enables the use of a wide variety of differently colored fluorophores. Using several molecular beacons, each designed to recognize a different target and each labeled with a different fluorophore, we demonstrate that multiple targets can be distinguished in the same solution, even if they differ from one another by as little as a single nucleotide. A comparison of "hairpin probes" with corresponding "linear probes" confirms that the presence of the hairpin stem in molecular beacons significantly enhances their specificity.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Alleles*
  • DNA Primers
  • Fluorescent Dyes
  • Mutation / genetics*
  • Nucleic Acid Hybridization
  • Oligonucleotide Probes*
  • Polymerase Chain Reaction
  • Spectrometry, Fluorescence
  • p-Dimethylaminoazobenzene / analogs & derivatives


  • DNA Primers
  • Fluorescent Dyes
  • Oligonucleotide Probes
  • 4-(4-dimethylaminophenylazo)benzoic acid
  • p-Dimethylaminoazobenzene