NMR-based investigations into target DNA search processes of proteins

Methods. 2018 Sep 15:148:57-66. doi: 10.1016/j.ymeth.2018.05.004. Epub 2018 May 10.

Abstract

To perform their function, transcription factors and DNA-repair/modifying enzymes must first locate their targets in the vast presence of nonspecific, but structurally similar sites on genomic DNA. Before reaching their targets, these proteins stochastically scan DNA and dynamically move from one site to another on DNA. Solution NMR spectroscopy provides unique atomic-level insights into the dynamic DNA-scanning processes, which are difficult to gain by any other experimental means. In this review, we provide an introductory overview on the NMR methods for the structural, dynamic, and kinetic investigations of target DNA search by proteins. We also discuss advantages and disadvantages of these NMR methods over other methods such as single-molecule techniques and biochemical approaches.

Keywords: DNA scanning; Dynamics; Kinetics; NMR; Protein-DNA interactions; Target search.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • DNA / analysis*
  • DNA / chemistry
  • DNA / metabolism*
  • Humans
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Protein Binding / physiology
  • Protein Structure, Secondary
  • Proteins / analysis*
  • Proteins / chemistry
  • Proteins / metabolism*

Substances

  • Proteins
  • DNA