Effects of Sequence Disorder on DNA Looping and Cyclization

Abstract

Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of cyclization probabilities. For short DNA segments, the range of the distribution reaches several orders of magnitude for even completely random sequences. The ensemble averaged values of the cyclization probability are also calculated, and the connection to the recent experiments is discussed.

8 pages, 4 figures, LaTeX; accepted to Physical Review E; v2: a substantially revised version; v3: references added, conclusions expanded, minor editorial corrections to the text; v4: a substantially revised and expanded version (total number of pages doubled); v5: new Figure 4, captions expanded, minor editorial improvements to the text

References in corpus (2)

• Exact theory of kinkable elastic polymers
• Distribution Functions, Loop Formation Probabilities and Force-Extension Relations in a Model for Short Double-Stranded DNA Molecules

Cited by in corpus (8)

• J-factors of short DNA molecules
• Effect of Bending Anisotropy on the 3D Conformation of Short DNA Loops
• Disordered, stretched, and semiflexible biopolymers in two dimensions
• Sequence-Dependent Effects on the Properties of Semiflexible Biopolymers
• Anisotropic Elastic Model for Short DNA Loops
• Gaussian fluctuations of spatially inhomogeneous polymers
• Mechanical behavior of a wormlike chain with variable bending rigidity along the chain contour in free space
• Statistical method for A-RNA and B-DNA