A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions

Nucleic Acids Res. 1988 Aug 11;16(15):7351-67. doi: 10.1093/nar/16.15.7351.


Specific, end-labeled DNA fragments can be simply and rapidly prepared using the polymerase chain reaction (PCR). Such fragments are suitable for use in DNase I protection footprint assays, chemical sequencing reactions, and for the production and analysis of paused RNA polymerase transcription complexes. Moreover, a general means of introducing a specific mutation at any position along the length of such PCR-generated fragments is described. These procedures, which can circumvent the need for large-scale phage or plasmid growths, preparative gel-electrophoresis and the screening of molecular clones, can facilitate the rapid study of sequence-specific interactions of proteins and DNA. A rapid means of removing excess oligonucleotide primers from completed PCRs is also described.

Publication types

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

MeSH terms

  • Base Sequence*
  • DNA Mutational Analysis*
  • DNA-Directed RNA Polymerases / metabolism*
  • Escherichia coli
  • Gene Amplification*
  • In Vitro Techniques
  • Promoter Regions, Genetic*
  • Transcription, Genetic


  • DNA-Directed RNA Polymerases