The use of Brownian dynamics simulations to investigate the presence of structural (kinks) and dynamic (bulges) anomalies in short DNA stretches is analyzed in connection with a string-of-beads model. A scaling method to choose the hydrodynamic translational and rotational parameters of the beads is proposed and tested on straight, kinked and bulged DNA fragments 17 nm long. The model reproduces the rigid-body rotational diffusion for the straight DNA and for the fluorescence polarization anisotropy decay of the kinked and bulged DNAs the model predicts a different behavior which is found experimentally.
Chirico, G., Collini, M. (1999). Study of flexible joints and permanent bends in DNA fragments by brownian dynamics simulations. THEORETICAL CHEMISTRY ACCOUNTS, 101(1-3), 126-130 [10.1007/s002140050418].
Study of flexible joints and permanent bends in DNA fragments by brownian dynamics simulations
CHIRICO, GIUSEPPE;COLLINI, MADDALENA
1999
Abstract
The use of Brownian dynamics simulations to investigate the presence of structural (kinks) and dynamic (bulges) anomalies in short DNA stretches is analyzed in connection with a string-of-beads model. A scaling method to choose the hydrodynamic translational and rotational parameters of the beads is proposed and tested on straight, kinked and bulged DNA fragments 17 nm long. The model reproduces the rigid-body rotational diffusion for the straight DNA and for the fluorescence polarization anisotropy decay of the kinked and bulged DNAs the model predicts a different behavior which is found experimentally.
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