Sequence dependent rigidity of single stranded DNA - PubMed (original) (raw)

Sequence dependent rigidity of single stranded DNA

N L Goddard et al. Phys Rev Lett. 2000.

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 +0.5 kcal x mol(-1) x base(-1) 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.

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Comment in

• Misfolded loops decrease the effective rate of DNA hairpin formation.
  Ansari A, Shen Y, Kuznetsov SV. Ansari A, et al. Phys Rev Lett. 2002 Feb 11;88(6):069801. doi: 10.1103/PhysRevLett.88.069801. Epub 2002 Jan 25. Phys Rev Lett. 2002. PMID: 11863867 No abstract available.

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