A computer model for the analysis of DNA replication intermediates by two-dimensional agarose gel electrophoresis.
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.
Viguera
E
E
Departamento de Biología Celular y del Desarrollo, CIB (CSIC), Velázquez 144, 28006, Madrid, Spain.
Rodríguez
A
A
Hernández
P
P
Krimer
D B
DB
Trellez
O
O
Schvartzman
J B
JB
D003198:Computer Simulation; D004247:DNA / Q000096:biosynthesis* / Q000737:chemistry; D004261:DNA Replication; D015246:Deoxyribonuclease EcoRI; D015247:Deoxyribonuclease HindIII; D004587:Electrophoresis, Agar Gel; D015180:Electrophoresis, Gel, Two-Dimensional; D004926:Escherichia coli / Q000235:genetics*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000302:isolation & purification; D010957:Plasmids; D015183:Restriction Mapping
D009838:Oligodeoxyribonucleotides; D004247:DNA; D015246:Deoxyribonuclease EcoRI; D015247:Deoxyribonuclease HindIII