A computer model for the analysis of DNA replication intermediates by two-dimensional agarose gel electrophoresis

Gene. 1998 Sep 14;217(1-2):41-9. doi: 10.1016/s0378-1119(98)00375-8.

Abstract

We present a computer model to predict the patterns expected for the replication intermediates (RIs) of DNA fragments analyzed by neutral/neutral two-dimensional (2D) agarose gel electrophoresis. The model relies on the mode of replication (uni- or bi-directional), the electrophoretic mobility of linear DNA fragments and the retardation caused by the three-dimensional shape of non-linear molecules. The utility of this model is demonstrated with two examples: replication analysis of the plasmids pBR322 and pHH5.8 in Escherichia coli after digestions with EcoRI and HindIII, respectively.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation*
  • DNA / biosynthesis*
  • DNA / chemistry
  • DNA Replication*
  • Deoxyribonuclease EcoRI
  • Deoxyribonuclease HindIII
  • Electrophoresis, Agar Gel
  • Electrophoresis, Gel, Two-Dimensional
  • Escherichia coli / genetics*
  • Oligodeoxyribonucleotides / chemistry*
  • Oligodeoxyribonucleotides / isolation & purification
  • Plasmids*
  • Restriction Mapping

Substances

  • Oligodeoxyribonucleotides
  • DNA
  • Deoxyribonuclease EcoRI
  • Deoxyribonuclease HindIII