Study of flexible joints and permanent bends in DNA fragments by brownian dynamics simulations |
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| Authors: | Giuseppe Chirico Maddalena Collini |
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| Institution: | (1) Istituto Nazionale di Fisica della Materia, Università degli Studi di Milano, Dipartimento di Fisica, via Celoria 16, I-20133 Milan, Italy, IT |
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| 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.
Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 23 November 1998 |
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| Keywords: | : Brownian dynamics Fluorescence polarization anisotropy DNA flexibility |
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