Conformational changes in single-strand DNA as a function of temperature by SANS

Area of Science:

• Biophysics
• Structural Biology
• Molecular Biology

Background:

• Single-strand DNA (ssDNA) structural dynamics are crucial for understanding its biological functions.
• Temperature-dependent conformational changes in ssDNA can influence its interactions and stability.
• Accurate characterization of ssDNA behavior is essential for predicting binding affinities.

Purpose of the Study:

• To investigate the temperature-dependent structural transitions of a specific ssDNA sequence (5'-ATGCTGATGC-3').
• To correlate structural changes observed via scattering with thermal transition data.
• To explain thermodynamic discrepancies in ssDNA binding stability measurements.

Main Methods:

• Small-angle neutron scattering (SANS) measurements at varying temperatures (25-80°C).
• Fitting of cylindrical, helical, and random coil models to SANS data.
• Differential scanning calorimetry (DSC) for thermal transition analysis.
• Ultraviolet (UV) optical density measurements for strand melting analysis.

Main Results:

• SANS data indicated ssDNA expansion in diameter and pitch with increasing temperature.
• Conformational changes occurred in distinct phases: 25-43°C (diameter expansion), 43-53°C (pitch expansion), and 53-80°C (dramatic pitch and diameter increase).
• DSC and UV melting scans showed a reversible two-state transition centered around 47.5°C, consistent with base unstacking.

Conclusions:

• The observed structural transitions are attributed to the unstacking of DNA bases.
• The broad thermal transition observed explains discrepancies in binding stability measurements.
• Understanding ssDNA conformational dynamics is key to accurate thermodynamic predictions.