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Related Experiment Video

Updated: Jun 12, 2026

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers
08:48

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Published on: October 13, 2011

DNA structural changes under different stretching methods studied by molecular dynamics simulations.

Wenpeng Qi1, Xiaoling Lei, Haiping Fang

  • 1Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China.

Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry
|June 10, 2010
PubMed
Summary

Stretching DNA at its 5' termini caused more untwisting and base pair breakage than stretching at the 3' termini. These DNA stretching dynamics reveal distinct structural responses to force application.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Biology

Background:

  • Understanding DNA mechanics is crucial for molecular biology.
  • DNA's conformational flexibility influences its function.
  • Simulations provide insights into DNA behavior under stress.

Purpose of the Study:

  • To investigate DNA conformational changes under stretching.
  • To compare the effects of stretching 3'-termini versus 5'-termini.
  • To identify key mechanical differences in DNA double helix response.

Main Methods:

  • Molecular dynamics simulations of a 22-mer DNA molecule.
  • Applying tensile force to both 3' and 5' termini.
  • Analyzing DNA structural variations, including untwisting and base pair roll.

Main Results:

  • Stretching 5'-termini required more energy (190 kJ mol(-1)) and showed higher force plateau (~100 pN) than 3'-termini (142 kJ mol(-1), ~80 pN).
  • 5'-termini stretching induced base pair rolling towards the major groove and reduced DNA diameter.
  • 5'-termini stretching led to base pair breakage at the force plateau, significantly disrupting the DNA double helix structure.

Conclusions:

  • The 5'-termini of DNA are more susceptible to mechanical stress, leading to structural instability and base pair dissociation.
  • DNA conformational changes, including base rotation and translation, occur primarily after the force plateau is reached (DNA length > 1.2).
  • Differential stretching of DNA termini reveals distinct mechanical properties and potential implications for DNA repair and replication mechanisms.