DNA binding proteins that alter nucleic acid flexibility

Micah McCauley, Philip R. Hardwidge, L. James Maher, Mark C. Williams

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

1 Scopus citations

Abstract

Dual - beam optical tweezers experiments subject single molecules of DNA to high forces (∼ 300 pN) with 0.1 pN accuracy, probing the energy and specificity of nucleic acid - ligand structures. Stretching phage X-DNA reveals an increase in the applied force up to a critical force known as the overstretching transition. In this region, base pairing and stacking are disrupted as double stranded DNA (dsDNA) is melted. Proteins that bind to the double strand will tend to stabilize dsDNA, and melting will occur at higher forces. Proteins that bind to single stranded DNA (ssDNA) destabilize melting, provided that the rate of association is comparable to the pulling rate of the experiment. Many proteins, however, exhibit some affinity for both dsDNA and ssDNA. We describe experiments upon DNA + HMGB2 (box A), a nuclear protein that is believed to facilitate transcription. By characterizing changes in the structure of dsDNA with a polymer model of elasticity, we have determined the equilibrium association constant for HMGB2 to be Kds = 0.15 ± 0.7 × 109 M-1 for dsDNA binding. Analysis of the melting transition reveals an equilibrium association constant for HMGB2 to ssDNA to be Kss = 0.039 ± 0.019 × 109 M -1 for ssDNA binding.

Original languageEnglish (US)
Title of host publicationOptical Trapping and Optical Micromanipulation IV
DOIs
StatePublished - Dec 1 2007
EventOptical Trapping and Optical Micromanipulation IV - San Diego, CA, United States
Duration: Aug 26 2007Aug 29 2007

Publication series

NameProceedings of SPIE - The International Society for Optical Engineering
Volume6644
ISSN (Print)0277-786X

Other

OtherOptical Trapping and Optical Micromanipulation IV
CountryUnited States
CitySan Diego, CA
Period8/26/078/29/07

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Keywords

  • DNA protein binding
  • Force induced melting
  • Optical tweezers

ASJC Scopus subject areas

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

Cite this

McCauley, M., Hardwidge, P. R., Maher, L. J., & Williams, M. C. (2007). DNA binding proteins that alter nucleic acid flexibility. In Optical Trapping and Optical Micromanipulation IV [664405] (Proceedings of SPIE - The International Society for Optical Engineering; Vol. 6644). https://doi.org/10.1117/12.736306