DNA/RNA Flexibility


Flexibility of DNA and RNA molecules are characteristics that describe resistance of these polymers to conformational distortion. The bending flexibility of nucleic acid molecules is an important factor that governs local interactions involved in protein–nucleic acid recognition and RNA folding as well as global properties such as supercoiling and genome organization.

Keywords: worm‐like chain; rotational diffusion; ring‐closure kinetics; intrinsic bend

Figure 1.

Several conformations of an intrinsically straight worm‐like chain with L = P. Conformations were simulated by a Monte‐Carlo computer algorithm; each chain consisted of 150 rigid segments and all chains were fixed at a common origin and assigned identical initial directions of propagation.

Figure 2.

Transient electric birefringence decay (TEBD) curve for a 124‐bp DNA fragment. The decay curve was obtained from an average of 100 pulses (10 kV cm−1, 5 μs pulse width). The solid line gives the best fit to the terminal component of the decay curve.

Figure 3.

Ring‐closure probabilities for DNA, J, as a function of DNA size. (a) Solid circles are the data of (Shore et al., ) and the solid curve is the best fit of the torsion‐independent component of J with P = 47.5 nm. The upper and lower dashed curves give the maxima and minima in J, respectively, for an analysis that includes the torsion‐dependent part of the ring‐closure probability. (b) Full, torsion‐dependent values of J from (a) over a narrow range of DNA size near 250 bp.



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Further Reading

Bloomfield VA, Crothers DM and Tinoco I Jr. (2000) Nucleic Acids: Structures, Properties and Functions. Herndon, VA: University Science Books.

Calladine CR and Drew HR (1997) Understanding DNA: The Molecule and How It Works. London: Academic Press.

Cozzarelli N and Wang J (eds) DNA Topology and its Biological Effects. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Levene S (1994) Conformation and energetics of supercoiled DNA: experimental and theoretical studies. In: Eckstein F and Lilley DMJ (eds) Nucleic Acids and Molecular Biology, vol. 8, pp. 119–132. Heidelberg, Germany: Springer‐Verlag.

Olson WK and Zhurkin VB (2000) Modeling DNA deformations. Current Opinion in Structural Biology 10: 286–297.

Vologodskii A (1992) Topology & Physics of Circular DNA. Boca Raton, FL: CRC Press.

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Levene, Stephen D(Mar 2002) DNA/RNA Flexibility. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0003125]