title: The dynamic response of upstream DNA to transcription-generated torsional stress.
abstract: The torsional stress caused by counter-rotation of the transcription machinery and template generates supercoils in a closed topological domain, but has been presumed to be too short-lived to be significant in an open domain. This report shows that transcribing RNA polymerases dynamically sustain sufficient torsion to perturb DNA structure even on linear templates. Assays to capture and measure transcriptionally generated torque and to trap short-lived perturbations in DNA structure and conformation showed that the transient forces upstream of active promoters are large enough to drive the supercoil-sensitive far upstream element (FUSE) of the human c-myc into single-stranded DNA. An alternative non-B conformation of FUSE found in stably supercoiled DNA is not accessible dynamically. These results demonstrate that dynamic disturbance of DNA structure provides a real-time measure of ongoing genetic activity.
authors.affiliation: Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland 20892-1500, USA.
authors.forename: Fedor
authors.initials: F
authors.lastname: Kouzine
authors.forename: Juhong
authors.initials: J
authors.lastname: Liu
authors.forename: Suzanne
authors.initials: S
authors.lastname: Sanford
authors.forename: Hye-Jung
authors.initials: HJ
authors.lastname: Chung
authors.forename: David
authors.initials: D
authors.lastname: Levens
mesh_terms: D001483:Base Sequence; D002843:Chromatin / Q000737:chemistry; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004278:DNA, Superhelical / Q000737:chemistry; D015180:Electrophoresis, Gel, Two-Dimensional; D004926:Escherichia coli / Q000378:metabolism; D016259:Genes, myc; D006160:Guanosine Triphosphate / Q000378:metabolism; D008274:Magnesium / Q000737:chemistry; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry; D011995:Recombination, Genetic; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D004278:DNA, Superhelical; D012313:RNA; D006160:Guanosine Triphosphate; D004247:DNA; D008274:Magnesium