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.
We report a new photophysical phenomenon in which 1.06 mm pulses from a Q-switched Nd:YAG laser induce crystallization in supersaturated solutions of urea in water. Because the solutions are transparent at the incident wavelength, a photochemical mechanism is unlikely. The needle-shaped crystals that initially form tend to be aligned parallel to the electric field vector of the light, suggesting a Kerr-like field-induced alignment of urea molecules that aids in organizing prenucleating clusters. The effect has application to pump-probe nucleation studies and to clean nucleation in sealed systems. [S0031-9007(96)01456-1]
It is shown that laminar thermal convection can drive a chain reaction of DNA replication. The convection is triggered by a constant horizontal temperature gradient, moving molecules along stationary paths between hot and cold regions. This implements the temperature cycling for the classical polymerase chain reaction (PCR). The amplification is shown to be exponential and reaches 100,000-fold gains within 25 min. Besides direct applications, the mechanism might have implications for the molecular evolution of life.
DNA beacons are short single-stranded chains which can form closed hairpin shapes through complementary base pairing at their ends. Contrary to the common polymer theory assumption that only their loop length matters, experiments show that their closing kinetics depend on the loop composition. We have modeled the closing kinetics and in so doing have obtained stacking enthalpies and entropies for single-stranded nucleic acids. The resulting change of persistence length with temperature effects the dynamics. With a Monte Carlo study, we answer another polymer question of how the closing time scales with chain length, finding tau approximately N(2.44+/-0.02). There is a significant crossover for shorter chains, bringing the effective exponent into good agreement with experiment.
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