Universal molecular beacon-based tracer system for real-time polymerase chain reaction

Anal Chem. 2006 Nov 15;78(22):7886-90. doi: 10.1021/ac061518+.

Abstract

DNA diagnostic has been moving from expensive, low-throughput, multistep methods to inexpensive, higher throughput, closed-tube, and automated methods. Fluorescence is the favored signaling technology for such assays. In this method, we describe a universal molecular beacon (U-MB) as the fluorescent tracer in the real-time PCR technique. A 5'-universal template primer (5'-UT primer) has been designed with a tail in complementary to the loop and 5'-side arm sequence of U-MB at the 5'-end of forward target specific primer. As PCR cycles increase, a new DNA fragment with a 5'-UT primer tail is synthesized, which is used as the template for next PCR cycle. As the reverse primer extends to the 5'-UT primer tail, the U-MB hybridized is displaced and the fluorescence from the fluorophore of the U-MB is quenched, indicating that the allele-specific PCR is in progress. This tracing system combined with an allele-specific reverse primer and vent (exo-) DNA polymerase, a polymerase that lacks 3'- to 5'-exonuclease activity, was used for the detection of point mutations of base G in codon 259 (AGA) of exon 7 of p53 gene on a panel of breast cancer individuals.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breast Neoplasms / genetics
  • Codon / genetics
  • DNA Primers / chemistry*
  • DNA Primers / genetics
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism
  • Exons / genetics
  • Female
  • Genetic Testing
  • Genotype
  • Humans
  • Mutation
  • Oligonucleotide Probes / chemistry
  • Polymerase Chain Reaction / methods*
  • RNA / chemistry*
  • RNA / genetics
  • Templates, Genetic
  • Tumor Suppressor Protein p53 / genetics
  • Tumor Suppressor Protein p53 / physiology

Substances

  • Codon
  • DNA Primers
  • Oligonucleotide Probes
  • RNA primers
  • Tumor Suppressor Protein p53
  • RNA
  • DNA-Directed RNA Polymerases