Mapping structurally perturbed sites in DNA by replication arrest and run-off replication.
We describe a technique for rapid fine mapping of sites of torsion-induced perturbations of DNA structure. The technique involves strand scission or chemical base modification at structurally perturbed sites, replication arrest in a double-strand DNA sequencing reaction, and size analysis of replication products by electrophoresis on sequencing gels. Besides being less complicated and faster than site identification by conventional end-labeling methods, the technique assures high sequence specificity through the use of oligomeric sequencing primers. This property should be useful for in vivo mapping of DNA structural perturbations with known sequence within complex genomes.
D000079:Acetaldehyde / Q000031:analogs & derivatives; D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D004261:DNA Replication; D004262:DNA Restriction Enzymes; D010957:Plasmids
C038235:bromoacetaldehyde; D004247:DNA; D004262:DNA Restriction Enzymes; D000079:Acetaldehyde