Self-avoiding wormlike chain model for double-stranded-DNA loop formation.

Area of Science:

• Biophysics
• Computational Biology
• Polymer Physics

Background:

• Understanding DNA loop formation is crucial for molecular biology.
• Excluded volume effects, or the physical space occupied by DNA segments, can influence chain conformation and cyclization probability.
• Previous models often simplified DNA as non-self-avoiding chains.

Purpose of the Study:

• To compute the impact of excluded volume on the probability of double-stranded DNA (dsDNA) forming a loop.
• To investigate how excluded volume affects the J factor, a measure of cyclization probability.
• To compare simulation results with existing scaling theories and experimental observations.

Main Methods:

• Utilized a Monte Carlo algorithm to generate large ensembles of self-avoiding wormlike chains.
• Calculated the J factor across various length scales for both self-avoiding and non-self-avoiding chain models.
• Analyzed chain end-to-end distribution and anisotropy in the elastic regime.

Main Results:

• Confirmed a power-law drop-off of -1.92 in the entropic regime for self-avoiding chains, stronger than the -1.5 predicted for non-self-avoiding chains.
• Observed highly anisotropic end-to-end chain distribution in the elastic regime due to excluded volume.
• Found that excluded volume increases the J factor by approximately half an order of magnitude compared to non-self-avoiding chains.

Conclusions:

• Excluded volume significantly enhances the propensity of dsDNA to form loops.
• The findings provide a potential explanation for increased loop formation observed in short dsDNA molecules during recent cyclization experiments.
• This study highlights the importance of incorporating excluded volume in models of DNA conformational dynamics.