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Two-state model of conformational fluctuation in a DNA hairpin-loop

Two-state model of conformational fluctuation in a DNA hairpin-loop,10.1016/S0009-2614(00)01425-1,Chemical Physics Letters,Liming Ying,Mark I. Wallace

Two-state model of conformational fluctuation in a DNA hairpin-loop   (Citations: 15)
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Stretched exponential kinetics have been observed in the conformational fluctuation of a DNA hairpin-loop under equilibrium conditions. In this paper, we employ a simple multiple-pathway two-state jump model to calculate single-molecule proximity ratio distributions. The simulation can reasonably reproduce the experimental single-molecule data of the conformational fluctuations in water, indicating that static disorder is dominant. In contrast, there exists significant discrepancy between the two-state simulation and experiment in buffer (2.5 mM Tris-HCl, 250μM EDTA, 100 mM NaCl), suggesting that both static and dynamic disorder may contribute to the non-exponential kinetics.
Journal: Chemical Physics Letters - CHEM PHYS LETT , vol. 334, no. 1, pp. 145-150, 2001
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    • ...<{[SECTION]}>5 where G(b 1) is the gamma function (31)...
    • ...Stretched-exponential decays have been shown to be consistent with both static and dynamic disorder (31,47,53), where static disorder involves a number of pathways connecting open and closed hairpin states through multiple transition rates, and dynamic disorder exhibits temporal changes of transition rates...
    • ...(multiple states connected by various transition rates) or dynamic (the rate constants change over time) (31,47,53)...

    Jiho Kimet al. The initial step of DNA hairpin folding: a kinetic analysis using fluo...

    • ...The formation of the stem‐ loop structure between self-complementary sequences at the ends of a molecular beacon is driven by a favorable free energy difference DGs that depends on the stem length Ls, stem sequence, ionic conditions, and the temperature q (8,44)...

    Andrew Tsourkaset al. Hybridization kinetics and thermodynamics of molecular beacons

    • ...yields a collapse time of tcoll � 8 ms, consistent with previous measurements of hairpin closing rates at or near 300 K (Ansari et al., 2001; Bonnet et al., 1998; Goddard et al., 2000; Shen et al., 2001; Wallace et al., 2000, 2001; Ying et al., 2001)...
    • ...Both this approximation and the apparent unfolding rate above are consistent with previous measurements for similar hairpins (Ansari et al., 2001; Bonnet et al., 1998; Goddard et al., 2000; Shen et al., 2001; Wallace et al., 2000, 2001; Ying et al., 2001)...
    • ...Unlike previous experimental studies, however, which commonly measure only hairpin collapse rather than full formation of folding interactions (Bonnet et al., 1998; Goddard et al., 2000; Wallace et al., 2000; Ying et al., 2001), the dynamics observed suggest a complex landscape with multiple local...
    • ...Consistent with previous experimental and theoretical assessments (Ansari et al., 2001; Bonnet et al., 1998; Goddard et al., 2000; Grunwell et al., 2001; Kuznetsov et al., 2001; Shen et al., 2001; Wallace et al., 2000; Ying et al., 2001; Zhang and Chen, 2002), our results indicate an essentially two-state energy surface...

    Eric J. Sorinet al. Insights into Nucleic Acid Conformational Dynamics from Massively Para...

    • ...Others have suggested that misfolded states contribute to folding kinetics by roughening the folding energy landscape (Ansari et al., 2001; Ying et al., 2001)...

    Daniel P. Aalbertset al. Single-Strand Stacking Free Energy from DNA Beacon Kinetics

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