Conformational Dynamics of Poly(T) Single-Stranded DNA at the Single-Molecule Level

Area of Science:

• Biophysics
• Polymer Physics
• Materials Science

Background:

• Single-stranded DNA (ss-DNA) conformational dynamics are crucial for DNA replication, repair, and as a material for engineering.
• Polythymidine (poly(T)) serves as a model ss-DNA due to its inherent flexibility and lack of secondary structure.
• Previous studies lacked experimental data on longer poly(T) chains relevant to biological and material applications.

Purpose of the Study:

• To experimentally investigate the conformational dynamics of longer polythymidine (poly(T)) chains (130-170 nucleotides) at the single-molecule level.
• To develop a model for DNA hairpin folding kinetics based on self-avoiding walks (SAW) to describe poly(T) dynamics.
• To determine the influence of salt concentration on ss-DNA flexibility and conformational dimensionality.

Main Methods:

• Utilized single-molecule Förster resonance energy transfer (smFRET) to monitor DNA hairpin folding kinetics.
• Employed a DNA hairpin construct where folding is dictated by the conformational dynamics of the poly(T) sequence.
• Developed a theoretical model for hairpin folding kinetics derived from self-avoiding-walk (SAW) principles.

Main Results:

• Observed that poly(T) folding kinetics deviate significantly from standard flexible polymer models.
• The derived SAW-based model accurately describes the conformational dynamics of poly(T).
• Estimated conformational dimensionality indicates ss-DNA is fully flexible at ≥100 mM NaCl but not at 50 mM NaCl.

Conclusions:

• The conformational dynamics of ss-DNA are salt-dependent, influencing its behavior in biological systems and engineered materials.
• The developed SAW model provides a robust framework for understanding ss-DNA conformational dynamics.
• This study offers insights into ss-DNA behavior critical for understanding biological mechanisms and advancing DNA-based materials engineering.