Rate of unwinding small DNA

  • Cohen R
  • Crothers D
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The kinetics of the helix-coil transition of low molecular weight DNA was investigated using temperature-jump techniques. The material was sonicated or sheared, then fractionated according to molecular weight using differential solubility in an isopropanol-buffer mixture. To prevent irreversible strand separation the samples were cross-linked with mitomycin C. Kinetic observations (266 nm) were made as a function of molecular weight, fraction coil, perturbation size and salt concentration. The Eigen-DeMaeyer apparatus was used for times between 5 μsec and 2 sec; slower effects required a special instrument. Decay times varying with M1.9down to 6.0 × 105daltons are attributed to fractionally limited unwinding. Some faster effects are from overtones (melting from ends). The rate of unwinding of DNA with a molecular Weight of 1.0 × 105daltons appears to be limited by the breakage of hydrogen bonds. From the data we estimate a rate constant of 4 × 106sec-1for base pair formation. A very fast decay (~30 μsec) is possibly the nucleation of coil at an A + T rich region. Ascribed to protolytic equilibria and to non-specific base-base interaction is an irresolvable (

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  • R. J. Cohen

  • D. M. Crothers

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