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Related Experiment Video

Updated: Jun 9, 2025

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

13.0K

Stacking correlation length in single-stranded DNA.

Xavier Viader-Godoy1,2, Maria Manosas1,3, Felix Ritort1,3

  • 1Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain.

Nucleic Acids Research
|October 26, 2024
PubMed
Summary
This summary is machine-generated.

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Base stacking is vital for nucleic acid stability. Optical tweezers experiments reveal stacking energies in DNA and RNA, showing DNA stacking is cooperative and crucial for double-helix stability.

Area of Science:

  • Biophysics
  • Molecular Biology
  • Biochemistry

Background:

  • Base stacking is fundamental for nucleic acid structure and function, influencing DNA hybridization and protein binding.
  • Quantifying stacking energy in single-stranded DNA (ssDNA) is challenging due to its interplay with hydrogen bonding.

Purpose of the Study:

  • To experimentally measure the stacking energy per base in short DNA and RNA sequences.
  • To investigate the cooperative nature and correlation length of base stacking.
  • To elucidate the contribution of base stacking to overall DNA double-helix stability.

Main Methods:

  • Utilized optical tweezers to perform unzipping experiments on short poly-purine DNA sequences (dA, dGdA).
  • Developed and applied a helix-coil model incorporating finite length effects to analyze force-extension curves.

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Related Experiment Videos

Last Updated: Jun 9, 2025

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

13.0K
Studying DNA Looping by Single-Molecule FRET
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  • Analyzed stacking stability and correlation length in poly-rA and poly-rC RNA sequences.

    • Main Results:

    • Derived salt-independent stacking energies: 0.14(3) kcal/mol for poly-dA and 0.07(3) kcal/mol for poly-dGdA.
    • Demonstrated predominantly cooperative stacking in DNA sequences with a correlation length of ~4 bases at zero force.
    • Observed maximum correlation lengths of ~10 (poly-dA) and ~5 (poly-dGdA) bases at transition forces.
    • RNA sequences (poly-rA, poly-rC) exhibited greater stacking stability but shorter correlation lengths (~2 bases).

    Conclusions:

    • Base stacking is a primary driver of DNA double-helix stability, as evidenced by agreement with hybridization energy salt dependencies.
    • Stacking interactions in DNA are cooperative, with length scales influenced by sequence and force.
    • RNA stacking is stronger but less cooperative compared to DNA, suggesting sequence-specific contributions to nucleic acid stability.