A method for quantifying the force dependence of initiation by T7 RNA polymerase

Bennett S. Kalafut, Gary M. Skinner, Koen Visscher

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

To access the genetic code to be transcribed to RNA, RNA polymerases must first open a "transcription bubble" in the DNA. Structural studies suggest that the minimal model of initiation by T7 bacterophage RNA polymerase (T7 RNAP) consists of two distinct steps: initial binding, in which the T7 RNAP binds to and bends the DNA, and opening, achieved by "scrunching" of the DNA. Since both steps involve mechanical deformation of the DNA, both may be affected by downstream DNA tension. Using an oscillating two-bead optical tweezers assay, we have measured the lifetime of single T7 RNAP-DNA initation complexes under tension. Global maximumlikelihood fitting of force-dependent and non-force-dependent versions of this minimal model shows that there is no conclusively discernible force-dependence of initiation in the measured 0-2 pN DNA tension range.

Original languageEnglish (US)
Title of host publicationOptical Trapping and Optical Micromanipulation VI
DOIs
StatePublished - 2009
EventOptical Trapping and Optical Micromanipulation VI - San Diego, CA, United States
Duration: Aug 2 2009Aug 6 2009

Publication series

NameProceedings of SPIE - The International Society for Optical Engineering
Volume7400
ISSN (Print)0277-786X

Other

OtherOptical Trapping and Optical Micromanipulation VI
CountryUnited States
CitySan Diego, CA
Period8/2/098/6/09

Keywords

  • Rna polymerase
  • Single molecule
  • T7 rna polymerase
  • Transcription initiation

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics
  • Computer Science Applications
  • Applied Mathematics
  • Electrical and Electronic Engineering

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  • Cite this

    Kalafut, B. S., Skinner, G. M., & Visscher, K. (2009). A method for quantifying the force dependence of initiation by T7 RNA polymerase. In Optical Trapping and Optical Micromanipulation VI [740005] (Proceedings of SPIE - The International Society for Optical Engineering; Vol. 7400). https://doi.org/10.1117/12.827659