Sequence Dependent Rigidity of Single Stranded DNA

Noel L. Goddard, Grégoire Bonnet, Oleg Krichevsky, and Albert Libchaber
Phys. Rev. Lett. 85, 2400 – Published 11 September 2000
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Abstract

Single stranded DNA (ssDNA) equilibrium dynamics are investigated using a fluorophore/quencher-labeled hairpin structure which thermally fluctuates between open and closed states. Temporal correlations of the fluorescence fluctuations are used to determine the energy barrier to conformational change. We find that ssDNA distortion is purely entropic for poly(T) but requires an additional enthalpy of +0.5kcal̇mol1̇base1 for poly(A), consistent with the disruption of base stacking. Such sequence dependent dynamics challenge the classical model of ssDNA as a completely flexible coil.

  • Received 27 March 2000

DOI:https://doi.org/10.1103/PhysRevLett.85.2400

©2000 American Physical Society

Authors & Affiliations

Noel L. Goddard1, Grégoire Bonnet1, Oleg Krichevsky2, and Albert Libchaber1

  • 1Center for Studies in Physics and Biology, The Rockefeller University, New York, New York 10021
  • 2Université Louis Pasteur, 67000 Strasbourg, France

Comments & Replies

Goddard et al. Reply:

Noel Goddard, Grégoire Bonnet, Oleg Krichevsky, and Albert Libchaber
Phys. Rev. Lett. 88, 069802 (2002)

Misfolded Loops Decrease the Effective Rate of DNA Hairpin Formation

A. Ansari, Y. Shen, and S. V. Kuznetsov
Phys. Rev. Lett. 88, 069801 (2002)

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Vol. 85, Iss. 11 — 11 September 2000

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