, Volume 251, Issue 2, pp 317–332 | Cite as

Studying DNA–protein interactions with single-molecule Förster resonance energy transfer

  • Shazia Farooq
  • Carel Fijen
  • Johannes HohlbeinEmail author
Special Issue: New/Emerging Techniques in Biological Microscopy


Single-molecule Förster resonance energy transfer (smFRET) has emerged as a powerful tool for elucidating biological structure and mechanisms on the molecular level. Here, we focus on applications of smFRET to study interactions between DNA and enzymes such as DNA and RNA polymerases. SmFRET, used as a nanoscopic ruler, allows for the detection and precise characterisation of dynamic and rarely occurring events, which are otherwise averaged out in ensemble-based experiments. In this review, we will highlight some recent developments that provide new means of studying complex biological systems either by combining smFRET with force-based techniques or by using data obtained from smFRET experiments as constrains for computer-aided modelling.


Single-molecule Förster resonance energy transfer Fluorescence Enzymes DNA DNA–protein interactions 



Atomic force microscopy


Alternating-laser excitation


Adenosine tri-phosphate


Burst variance analysis


Base pair


Catabolite activator protein


Deoxyribonucleic acid


Double-stranded deoxyribonucleic acid


Deoxyribonucleoside tri-phosphate


Förster resonance energy transfer


FRET-restrained positioning and screening


Multiparameter fluorescence detection


Nuclear magnetic resonance


Nano-positioning system


Probability distribution analysis


Protein-induced fluorescence enhancement




Quenchable Förster resonance energy transfer


Ribonucleic acid


RNA polymerase


Ribonucleoside tri-phosphate


Single-molecule Förster resonance energy transfer


Single-stranded DNA binding protein


Single-stranded deoxyribonucleic acid


Total internal reflection fluorescence


TATA box binding protein


Transcription factor



We thank Herbert van Amerongen and Arjen Bader for critically reading the manuscript and providing helpful suggestions. S.F. acknowledges funding from the Foundation for Fundamental Research on Matter (FOM), which is part of the Netherlands Organisation for Scientific Research (NWO).

Conflict of interest

The authors declare that they have no conflict of interest.


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Copyright information

© Springer-Verlag Wien 2013

Authors and Affiliations

  1. 1.Laboratory of BiophysicsWageningen URWageningenThe Netherlands

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