Promoter unwinding and promoter clearance by RNA polymerase: detection by single-molecule DNA nanomanipulation.

ABSTRACT: By monitoring the end-to-end extension of a mechanically stretched, supercoiled, single DNA molecule, we have been able directly to observe the change in extension associated with unwinding of approximately one turn of promoter DNA by RNA polymerase (RNAP). By performing parallel experiments with negatively and positively supercoiled DNA, we have been able to deconvolute the change in extension caused by RNAP-dependent DNA unwinding (with approximately 1-bp resolution) and the change in extension caused by RNAP-dependent DNA compaction (with approximately 5-nm resolution). We have used this approach to quantify the extent of unwinding and compaction, the kinetics of unwinding and compaction, and effects of supercoiling, sequence, ppGpp, and nucleotides. We also have used this approach to d

SUBMITTER: Revyakin A 

PROVIDER: S-EPMC387324 | biostudies-literature | 2004 Apr

REPOSITORIES: biostudies-literature