Research Papers

Modeling Deoxyribose Nucleic Acid as an Elastic Rod Inlaid With Fibrils

[+] Author and Article Information
Bin Chen

Department of Engineering Mechanics,
Zhejiang University,
Hangzhou, China
e-mail: chenb6@zju.edu.cn

Chenling Dong

Department of Engineering Mechanics,
Zhejiang University,
Hangzhou, China

Manuscript received February 5, 2014; final manuscript received March 2, 2014; accepted manuscript posted March 6, 2014; published online April 1, 2014. Editor: Yonggang Huang.

J. Appl. Mech 81(7), 071005 (Apr 01, 2014) (4 pages) Paper No: JAM-14-1055; doi: 10.1115/1.4026988 History: Received February 05, 2014; Revised March 02, 2014; Accepted March 06, 2014

A classical view of the double-stranded deoxyribose nucleic acid (DNA) as an isotropic elastic rod fails to explain its high flexibility manifested in the formation of sharp loops that are essential in gene regulation and DNA storage. Since the basic structure of DNA can be divided into the external highly polar backbone and the internal hydrophobic bases, here we model DNA as an elastic rod inlaid with fibrils. If the fibrils are much stiffer than the rod, we find that the persistence length of short DNA can be much smaller than that of long DNA with an adapted shear lag analysis. Consequently, the cyclization rate for short DNA is found to be much higher than the previous prediction of the worm-like chain model, which is interestingly in consistency with experiments. Our analysis suggests that the bending of short DNAs can be facilitated if there exists a specific structural heterogeneity.

Copyright © 2014 by ASME
Topics: DNA , Modeling
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Fig. 1

Model of DNA as an elastic rod inlaid with fibrils. The rod is fixed on one end and free on the other end.

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Fig. 2

Long DNA can be regarded as a collection of segments of Kuhn length freely jointed with each other and segment “AB” is half of Kuhn length

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Fig. 3

Variation of persistence length of short DNA against contour length. In the figure, Lc is the characteristic length for stress transfer and ρ∞ is the intrinsic persistence length of DNA.

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Fig. 4

Apparent j factor for looping of short DNA: solid lines are for r = 0, dashed lines for r = 5 nm, blue lines for WLC, red lines for Lc = 5 nm, black lines for Lc = 6.5 nm, green lines for Lc = 10 nm, and the experimental data from Ref. [11] are represented as triangles

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Fig. 5

Variation of critical bending angle for instability with contour length when Lc = 6 nm and ρ∞ = 60 nm

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Fig. 6

Dependence of the effective bending modulus EIeff of a simple heterogeneous structure on its length, where the stiffness of the upper layer and the lower layer is much larger than that of the middle layer. Stars are the simulation results and the solid line is the curve fitted with Eq. (9): EIMax = 0.24 × 10-6 N·m2 and Lc = 62 μm.




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