Extreme bendability of DNA double helix due to bending asymmetry

• Published in: The Journal of chemical physics Vol. 143; no. 10; p. 104904
• Main Authors: Salari, H, Eslami-Mossallam, B, Naderi, S, Ejtehadi, M R
• Format: Journal Article
• Language: English
• Published: United States 14-09-2015
• Subjects: Computer Simulation; DNA - chemistry; Elasticity; Models, Genetic; Models, Molecular; Monte Carlo Method; Nucleic Acid Conformation
• ISSN: 1089-7690
• DOI: 10.1063/1.4929994

Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study [B. Eslami-Mossallam and M. R. Ejtehadi, Phys. Rev. E 80, 011919 (2009)]. Exploiting a coarse grained representation of the DNA molecule at base pair (bp) level and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that the DNA molecule has a larger J-factor compared to the WLC model which is in excellent agreement with recent experimental data.