Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis

Nat Biotechnol. 1998 Apr;16(4):359-63. doi: 10.1038/nbt0498-359.


We developed a new approach to DNA sequence analysis that uses fluorogenic reporter molecules--molecular beacons--and demonstrated their ability to discriminate alleles in real-time PCR assays of genomic DNA. A set of overlapping molecular beacons was used to analyze an 81-bp region of the Mycobacterium tuberculosis rpoB gene for mutations that confer resistance to the antibiotic rifampin. In a blinded study of 52 rifampin-resistant and 23 rifampin-susceptible clinical isolates, this method correctly detected mutations in all of the resistant strains and in none of the susceptible strains. The assay was carried out entirely in sealed PCR tubes and was simple to perform and interpret. This approach can be used to analyze any DNA sequence of moderate length with single base pair accuracy.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Antibiotics, Antitubercular / pharmacology
  • DNA-Directed RNA Polymerases
  • Drug Resistance, Microbial / genetics*
  • Microbial Sensitivity Tests
  • Mycobacterium tuberculosis / drug effects*
  • Mycobacterium tuberculosis / genetics
  • Plant Proteins / genetics
  • Point Mutation*
  • Polymerase Chain Reaction
  • Rifampin / pharmacology


  • Antibiotics, Antitubercular
  • Plant Proteins
  • RpoB protein, Oryza sativa
  • DNA-Directed RNA Polymerases
  • Rifampin