DNA/RNA Flexibility

Abstract

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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References

Akiyama T and Hogan ME (1996) The design of an agent to bend DNA. Proceedings of the National Academy of Sciences of the USA 93: 12122–12127.

Crothers DM (1998) DNA curvature and deformation in protein‐DNA complexes: a step in the right direction. Proceedings of the National Academy of Sciences of the USA 95: 15163–15165.

Crothers DM, Haran TE and Nadeau JG (1990) Intrinsically bent DNA. Journal of Biological Chemistry 265: 7093–7096.

Crothers DM, Drak J, Kahn JD and Levene SD (1992) DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods in Enzymology 212: 3–29.

Hagerman PJ (1985) Application of transient electric birefringence to the study of biopolymer structure. Methods in Enzymology 117: 198–219.

Hagerman PJ (1997) Flexibility of RNA. Annual Review of Biophysics and Biomolecular Structure 26: 139–156.

Levene SD and Crothers DM (1986) Ring closure probabilities for DNA fragments by Monte Carlo simulation. Journal of Molecular Biology 189: 61–72.

Luger K, Mader AW, Richmond RK, Sargent DF and Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389: 251–260.

Olson WK, Gorin AA, Lu XJ, Hock LM and Zhurkin VB (1998) DNA sequence‐dependent deformability deduced from protein–DNA crystal complexes. Proceedings of the National Academy of Sciences of the USA 95: 11163–11168.

Reinert KE (1991) DNA‐helix bending, stiffening and elongation on ligand binding; analysis for several DNA–drug systems, general viscometric DNA response and stereochemical implications. Journal of Biomolecular Structure and Dynamics 9: 331–352.

Schellman JA and Harvey SC (1995) Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. Biophysical Chemistry 55: 95–114.

Shore D, Langowski J and Baldwin RL (1981) DNA flexibility studied by covalent closure of short fragments into circles. Proceedings of the National Academy of Sciences of the USA 78: 4833–4837.

Taylor WH and Hagerman PJ (1990) Application of the method of phage T4 DNA ligase‐catalyzed ring‐closure to the study of DNA structure. II. NaCl‐dependence of DNA flexibility and helical repeat. Journal of Molecular Biology 212: 363–376.

Tsen H and Levene SD (1997) Supercoiling‐dependent flexibility of adenosine‐tract‐containing DNA detected by a topological method. Proceedings of the National Academy of Sciences of the USA 94: 2817–2822.

Vologodskii AV and Cozzarelli NR (1994) Conformational and thermodynamic properties of supercoiled DNA. Annual Review of Biophysics and Biomolecular Structure 23: 609–643.

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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How to Cite close
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]