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Force Spectroscopy of DNA and RNA: Structure and Kinetics from Single-Molecule Experiments

  • Rebecca Bolt Ettlinger
  • Michael Askvad Sørensen
  • Lene Broeng OddershedeEmail author
Chapter
Part of the Nucleic Acids and Molecular Biology book series (NUCLEIC, volume 29)

Abstract

Force spectroscopy of individual DNA and RNA molecules provides unique insights into the structure and mechanics of these for life so essential molecules. Observations of DNA and RNA molecules one at a time provide spatial, structural, and temporal information that is complementary to the information obtained by classical ensemble methods. Single-molecule force spectroscopy has been realized only within the last decades, and its success is crucially connected to the technological development that has allowed single-molecule resolution. This chapter provides an introduction to in vitro force spectroscopy of individual DNA and RNA molecules including the most commonly used techniques, the theory and methodology necessary for understanding the data, and the exciting results achieved. Three commonly used single-molecule methods are emphasized: optical tweezers, magnetic tweezers, and nanopore force spectroscopy. The theory of DNA stretch and twist under tension is described along with related experimental examples. New principles for extracting kinetic and thermodynamic information from nonequilibrium data are outlined, and further examples are given including the opening of DNA and RNA structures to reveal their energy landscape. Finally, future perspectives for force spectroscopy of DNA and RNA are offered.

Keywords

Energy Landscape Optical Tweezer Chromatin Fiber Force Spectroscopy Extension Curve 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Nomenclature

ΔG

Gibbs free energy change

ΔG

Activation energy

CFT

Crooks fluctuation theorem

dsDNA

Double-stranded DNA

EWLC

Extensible worm-like chain model

FJC

Freely jointed chain model

JE

Jarzynski equality

k(F)

Rate of transition at force F

k0

Rate of transition at zero force

K0

Elasticity

Lc

Contour length

Lp

Persistence length

MT

Magnetic tweezers

NFS

Nanopore force spectroscopy

OT

Optical tweezers

ssDNA

Single-stranded DNA

TWLC

Twistable worm-like chain model

WLC

Worm-like chain model

x

Distance to the transition state

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Rebecca Bolt Ettlinger
    • 1
  • Michael Askvad Sørensen
    • 2
  • Lene Broeng Oddershede
    • 1
    Email author
  1. 1.The Niels Bohr InstituteUniversity of CopenhagenCopenhagenDenmark
  2. 2.The Department of BiologyUniversity of CopenhagenCopenhagenDenmark

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