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- W2051284120 abstract "Polyelectrolytes, or charged polymers, are prevalent in biological systems, yet their physical properties are far less well understood than those of neutral polymers. We report on measurements using small angle x-ray scattering to study bulk ensemble-averaged properties of small (up to 100 bases) poly-deoxythymine (poly-dT) and poly-deoxyadenine (poly-dA) molecules. By studying homomeric single stranded DNA (ssDNA), we can observe their polymeric properties without interference from secondary structure formation. This gives us insight to the conformational space explored by single stranded nucleic acids in folding processes, and the nucleotide dependence of loop flexibility of DNA and RNA junctions. We observe, as is consistent with base-stacking of purines, that poly-dA is stiffer than poly-dT. For poly-dT, the radius of gyration (Rg) scales with the number of monomers with a Flory exponent (ν) which decreases slowly with increasing salt, but drops sharply below that expected for a self-avoiding random walk (SAW) polymer (ν ∼ 0.588) with more than 500 mM of added sodium acetate. This is perhaps due to the condensation of charges around the DNA and/or the change in solvent quality with added salt. The ratio (r) of the square of the maximum pair-wise distance (Dmax) to Rg fluctuates around 10, suggesting that ssDNA compacts locally. Assuming that Dmax is a fair estimate of the end-to-end distance of the polymer, a value of 12 is expected for r in the case of a rod, and about 6.3 for a SAW polymer. This localized clustering is consistent with the electrostatic blob model of de Gennes et al. The persistence length of poly-dT - determined by fitting the data to a worm-like chain model - increases in a sublinear fashion with increasing Debye screening length, unlike the behaviors predicted by polyelectrolyte theories." @default.
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- W2051284120 date "2009-02-01" @default.
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- W2051284120 title "Scaling Behavior of Single Stranded DNA Measured by Small Angle X-ray Scattering" @default.
- W2051284120 doi "https://doi.org/10.1016/j.bpj.2008.12.1744" @default.
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