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 Citation (Scopus)

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 publicationProceedings of SPIE - The International Society for Optical Engineering
Volume7400
DOIs
StatePublished - 2009
EventOptical Trapping and Optical Micromanipulation VI - San Diego, CA, United States
Duration: Aug 2 2009Aug 6 2009

Other

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

Fingerprint

RNA
DNA
deoxyribonucleic acid
Minimal Model
DNA-Directed RNA Polymerases
Genetic Code
Optical Tweezers
Dependent
Transcription
Bubble
Maximum Likelihood
Lifetime
Distinct
genetic code
Optical tweezers
Range of data
bacteriophage T7 RNA polymerase
beads
Assays
bubbles

Keywords

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

ASJC Scopus subject areas

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

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 Proceedings of SPIE - The International Society for Optical Engineering (Vol. 7400). [740005] https://doi.org/10.1117/12.827659

A method for quantifying the force dependence of initiation by T7 RNA polymerase. / Kalafut, Bennett S.; Skinner, Gary M.; Visscher, Koen.

Proceedings of SPIE - The International Society for Optical Engineering. Vol. 7400 2009. 740005.

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

Kalafut, BS, Skinner, GM & Visscher, K 2009, A method for quantifying the force dependence of initiation by T7 RNA polymerase. in Proceedings of SPIE - The International Society for Optical Engineering. vol. 7400, 740005, Optical Trapping and Optical Micromanipulation VI, San Diego, CA, United States, 8/2/09. https://doi.org/10.1117/12.827659
Kalafut BS, Skinner GM, Visscher K. A method for quantifying the force dependence of initiation by T7 RNA polymerase. In Proceedings of SPIE - The International Society for Optical Engineering. Vol. 7400. 2009. 740005 https://doi.org/10.1117/12.827659
Kalafut, Bennett S. ; Skinner, Gary M. ; Visscher, Koen. / A method for quantifying the force dependence of initiation by T7 RNA polymerase. Proceedings of SPIE - The International Society for Optical Engineering. Vol. 7400 2009.
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