Abstract
The sequence-directed flexibility of double helical DNA is examined with color-coded representations of the spatial probability density distributions of the chain ends. The distributions are derived from Monte Carlo simulations that incorporate local sequence-dependent bending of neighboring Watson-Crick base pairs. The density functions are compared with typical rigid representations of the double helix and with sample Monte Carlo trajectories. Applications are presented for three short fragments of kinetoplast DNA from Crithidia fasciculata, which exhibit dramatically different behavior on nondenaturing polyacrylamide gels. The distributions (based on 10 6 configurations per chain) are useful descriptors of overall chain flexibility, illustrating the effects of chain length and base sequence on macromolecular configuration and revealing characteristic differences between curved and rodlike DNA.
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