Correlated Local Bending of a DNA Double Helix and Its Effect on DNA Flexibility in the Sub-Persistence-Length Regime.
Mechanical characteristics of DNA in the sub-persistence-length (lP ≈ 150 base pairs) regime are vital to many of its biological functions but not well understood. Recent experimental studies in this regime have shown a dramatic departure from the traditional worm-like chain model, which is designed for long DNA chains and predicts a constant flexibility at all length scales. Here, we report an improved model with explicit considerations of a new length scale lD ≈ 10 base pairs, over which DNA local bend angles are correlated. In this correlated worm-like chain model, a finite length correction term is analytically derived, and DNA flexibility is found to be contour-length-dependent. While our model reduces to the traditional worm-like chain model at length scales much larger than lP, it predicts that DNA becomes much more flexible at shorter sizes, in good agreement with recent cyclization measurements of short DNA fragments around 100 base pairs.
†Department of Chemistry, Massachusetts Institue of Technology, Cambridge, Massachusetts 02139, United States.|‡Pillar of Engineering Product Development, Singapore University of Technology and Design, 20 Dover Drive, 138682 Singapore.
Xinliang
X
Xu
‡Pillar of Engineering Product Development, Singapore University of Technology and Design, 20 Dover Drive, 138682 Singapore.
Beng Joo Reginald
BJ
Thio
†Department of Chemistry, Massachusetts Institue of Technology, Cambridge, Massachusetts 02139, United States.|§Singapore-MIT Alliance for Research and Technology (SMART), 1 Create Way, #10-01 Create Tower, 138602 Singapore.
Jianshu
J
Cao
DNA cyclization; DNA mechanics; coarse-grained model; correlated worm-like chain; single-molecule study