Mutational scanning of PCR products by subtractive oligonucleotide hybridization analysis

Biotechniques. 1999 Feb;26(2):308-16. doi: 10.2144/99262rr01.

Abstract

Here, we describe a new approach for mutational scanning of PCR products through hybridization analysis between complementary oligonucleotides. Sets of overlapping probe oligonucleotides complementary to wild-type (WT) sequence are hybridized to microbead-immobilized PCR products under solution-like conditions. Mismatch-hybridization situations between a mutant sample and probe oligonucleotides result in higher remaining concentrations in solution of involved probe oligonucleotides. Post-hybridization supernatants are subsequently analyzed for their probe oligonucleotide compositions using surface plasmon resonance-based biosensor technology. Relative remaining probe oligonucleotide concentrations are monitored in real-time through hybridization analysis between probe oligonucleotides and their corresponding sensor-chip immobilized complementary counterparts. This allows for the construction of composition diagrams revealing the existence and approximate location of a mutation within an investigated sample DNA sequence. Applied on PCR products derived from clinical samples of microdissected tumor biopsies, single mutations in exons 6 and 7 of the human p53 tumor-suppressor gene were successfully detected and approximately localized.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biosensing Techniques / methods
  • Cloning, Molecular / methods
  • DNA Mutational Analysis / methods*
  • DNA, Neoplasm / analysis*
  • DNA, Single-Stranded / genetics
  • Exons
  • Humans
  • Nucleic Acid Hybridization / methods*
  • Oligonucleotide Probes*
  • Polymerase Chain Reaction / methods
  • Tumor Suppressor Protein p53 / genetics

Substances

  • DNA, Neoplasm
  • DNA, Single-Stranded
  • Oligonucleotide Probes
  • Tumor Suppressor Protein p53