Studying RNAP-promoter interactions using atomic force microscopy

Methods. 2015 Sep 15;86:4-9. doi: 10.1016/j.ymeth.2015.05.018. Epub 2015 May 22.


The most fundamental step in gene expression is transcription, during which DNA is transcribed to a corresponding RNA strand by the action of RNA polymerases (RNAPs). Over the past two decades, atomic force microscopy (AFM) has been used as one of the key tools in the investigation of transcriptional events at the single-molecule level. AFM studies have provided significant insights into the structure-function relationships of RNAP-DNA complexes in different stages of transcription. Here, we begin by illustrating the basic setup of AFM, followed by an introduction of the applications of AFM techniques, including high-speed AFM (HS-AFM) imaging, to investigate RNAP-DNA interactions with a special focus on promoter-search processes and open promoter formations. The combination of AFM with a newly developed experimental technique, DNA origami nanotechnology, will also be described.

Keywords: Atomic force microscopy; DNA origami; Promoter; RNA polymerase; Transcription.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • DNA-Directed RNA Polymerases / genetics*
  • DNA-Directed RNA Polymerases / ultrastructure
  • Gene Expression
  • Microscopy, Atomic Force
  • Nanotechnology
  • Promoter Regions, Genetic*
  • Transcription, Genetic*


  • DNA-Directed RNA Polymerases