title: A computer model for the analysis of DNA replication intermediates by two-dimensional agarose gel electrophoresis.
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.
authors.affiliation: Departamento de Biología Celular y del Desarrollo, CIB (CSIC), Velázquez 144, 28006, Madrid, Spain.
authors.forename: E
authors.initials: E
authors.lastname: Viguera
authors.forename: A
authors.initials: A
authors.lastname: Rodríguez
authors.forename: P
authors.initials: P
authors.lastname: Hernández
authors.forename: D B
authors.initials: DB
authors.lastname: Krimer
authors.forename: O
authors.initials: O
authors.lastname: Trellez
authors.forename: J B
authors.initials: JB
authors.lastname: Schvartzman
mesh_terms: 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
chemical_list: D009838:Oligodeoxyribonucleotides; D004247:DNA; D015246:Deoxyribonuclease EcoRI; D015247:Deoxyribonuclease HindIII