Stacking correlation length in single-stranded DNA

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.
• 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.