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Related Experiment Video

Updated: Jun 19, 2026

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Published on: October 13, 2011

Structural basis of pathway-dependent force profiles in stretched DNA.

Daniel R Roe¹, Anne M Chaka

¹Physics Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8443, Gaithersburg, Maryland 20878-8443, USA.

The Journal of Physical Chemistry. B

|October 23, 2009

Summary

Stretching double-stranded DNA from the 3' ends is more stable than from the 5' ends. This difference in DNA mechanical properties is due to how the force is dissipated through the phosphate backbone versus base pair hydrogen bonds.

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Area of Science:

Molecular Biophysics
Structural Biology
Computational Biology

Background:

DNA's mechanical properties, including flexibility, are crucial for its biological functions.
Single-molecule experiments reveal differential stability of double-stranded DNA when stretched from 3' versus 5' termini at high loading rates.
The structural basis for this observed mechanical difference remains unclear.

Purpose of the Study:

To investigate the structural mechanisms underlying the differential stability of double-stranded DNA when stretched from its 3' and 5' termini.
To compare the stability and structural changes of DNA oligomers under 3'-terminal and 5'-terminal stretching using computational methods.

Main Methods:

Molecular dynamics simulations were employed to model DNA stretching.
Umbrella sampling techniques were utilized to analyze the potential energy landscape during stretching.
A 30 base pair double-stranded DNA oligomer was simulated.

Main Results:

At extensions exceeding 1.7 times the original length, DNA stretched from the 3' termini is more stable than when stretched from the 5' termini.
The 3' stretched structure maintains significantly more hydrogen bonds (80%) between base pairs and exhibits enhanced base stacking.
Force dissipation occurs primarily through phosphate backbone flexibility in 3' stretching, while 5' stretching directly stresses base pair hydrogen bonds, leading to rupture and major groove widening.

Conclusions:

3' and 5' terminal stretching of double-stranded DNA are fundamentally distinct mechanical processes.
Differential hydrogen bond stability and force dissipation mechanisms explain the observed differences in DNA mechanical behavior.
Computational simulations provide structural insights into DNA's response to mechanical forces.