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Investigating Polarity Effects in DNA Base Stacking.

Jibin Abraham Punnoose1,2, Chai S Kam1,3, Tristan Melfi1

  • 1The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States.

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|December 26, 2025
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Summary
This summary is machine-generated.

Strand polarity significantly impacts DNA base stacking energetics, with specific purine-pyrimidine arrangements showing greater stability. This finding is crucial for designing short DNA sequences in biotechnology.

Keywords:
DNAbase stackingmolecular dynamicsnucleic acidssingle-molecule

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Structural Biology

Background:

  • Nucleic acid structures rely on base pairing and base stacking for stability.
  • The energetic contributions of base stacking are not fully understood, unlike base pairing.

Purpose of the Study:

  • To investigate how strand polarity affects base-stacking energetics in DNA.
  • To quantify the energetic contributions of base stacking and their dependence on polarity.

Main Methods:

  • Utilized single-molecule force-clamp assays with a Centrifuge Force Microscope (CFM).
  • Employed molecular dynamics (MD) simulations to visualize stacking interfaces.
  • Designed DNA constructs with reversed stacking polarities and no-stack controls.

Main Results:

  • Observed polarity-dependent differences in base-stacking energetics.
  • Purine-purine and certain purine-pyrimidine interactions showed the most pronounced polarity effects.
  • A 5' purine stacked on a 3' pyrimidine was generally more stable than the reverse.

Conclusions:

  • Base polarity is a key factor modulating DNA stacking stability.
  • These findings are important for designing short DNA duplexes, such as overhangs.
  • Consideration of polarity is essential in molecular biology and biotechnology applications.