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Protoplasma

, 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

Abstract

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.

Keywords

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

Abbreviations

AFM

Atomic force microscopy

ALEX

Alternating-laser excitation

ATP

Adenosine tri-phosphate

BVA

Burst variance analysis

bp

Base pair

CAP

Catabolite activator protein

DNA

Deoxyribonucleic acid

dsDNA

Double-stranded deoxyribonucleic acid

dNTP

Deoxyribonucleoside tri-phosphate

FRET

Förster resonance energy transfer

FPS

FRET-restrained positioning and screening

MFD

Multiparameter fluorescence detection

NMR

Nuclear magnetic resonance

NPS

Nano-positioning system

PDA

Probability distribution analysis

PIFE

Protein-induced fluorescence enhancement

Pol

Polymerase

quFRET

Quenchable Förster resonance energy transfer

RNA

Ribonucleic acid

RNAP

RNA polymerase

rNTP

Ribonucleoside tri-phosphate

smFRET

Single-molecule Förster resonance energy transfer

SSB

Single-stranded DNA binding protein

ssDNA

Single-stranded deoxyribonucleic acid

TIRF

Total internal reflection fluorescence

TBP

TATA box binding protein

TF

Transcription factor

Notes

Acknowledgments

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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