Studying protein-DNA interactions using atomic force microscopy

Semin Cell Dev Biol. 2018 Jan;73:220-230. doi: 10.1016/j.semcdb.2017.06.028. Epub 2017 Jun 30.


Atomic force microscopy (AFM) has made significant contributions to the study of protein-DNA interactions by making it possible to topographically image biological samples. A single protein-DNA binding reaction imaged by AFM can reveal protein binding specificity and affinity, protein-induced DNA bending, and protein binding stoichiometry. Changes in DNA structure, complex conformation, and cooperativity, can also be analyzed. In this review we highlight some important examples in the literature and discuss the advantages and limitations of these measurements. We also discuss important advances in technology that will facilitate the progress of AFM in the future.

Keywords: Atomic force microscopy; Binding specificity; DNA bending; Protein-DNA interaction; Stoichiometry.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • DNA / chemistry*
  • DNA / ultrastructure*
  • Humans
  • Microscopy, Atomic Force*
  • Proteins / chemistry*
  • Proteins / ultrastructure*


  • Proteins
  • DNA