A COMPUTER-MODEL FOR THE ANALYSIS OF DNA-REPLICATION INTERMEDIATES BY2-DIMENSIONAL AGAROSE-GEL ELECTROPHORESIS

We present a computer model to predict the patterns expected for the r eplication intermediates (RIs) of DNA fragments analyzed by neutral/ne utral two-dimensional (2D) agarose gel electrophoresis. The model reli es on the mode of replication (unior hi-directional), the electrophore tic 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 p lasmids pBR322 and pHH5.8 in Escherichia coli after digestions with Ec oRI and HindIII, respectively. (C) 1998 Elsevier Science B.V. All righ ts reserved.