title: Sequence dependent rigidity of single stranded DNA.
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.
authors.affiliation: Center for Studies in Physics and Biology, The Rockefeller University, New York, New York 10021, USA.
authors.forename: N L
authors.initials: NL
authors.lastname: Goddard
authors.forename: G
authors.initials: G
authors.lastname: Bonnet
authors.forename: O
authors.initials: O
authors.lastname: Krichevsky
authors.forename: A
authors.initials: A
authors.lastname: Libchaber
mesh_terms: D004277:DNA, Single-Stranded / Q000737:chemistry*; D005456:Fluorescent Dyes; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D004277:DNA, Single-Stranded; D005456:Fluorescent Dyes