Basepair parameters

Average global helical parameters, intra basepair parameters, Cl cylinder radius (rci) and phosphate cylinder radius (rp) for fibre model [83], crystal structure [12] and M.D. average structures. The average values from middle three tetrads are listed for both the M.D. average structures. Rotational parameters are in degrees and translational parameters are in A. Standard deviations are shown within parentheses. 

Figure 4. Two dimensional histograms for selected pairwise combinations of the six geometrical parameters describing the conformation of basepair steps. Gray represents the space sampled by the simulations, and the black lines are isopopulation contours. The black asterisks are data from structures determined by NMR spectroscopy, and high resolution B-DNA and A-DNA crystal structures (listed in the Materials section).

The intra as well as inter-basepair structural parameters were calculated for the middle three tetrads taking all four strands pairwise and using the NUPARM software [63], For both simulations, local dinucleotide step, intra base-pair and global helical parameters were calculated for the GG base pairs in the middle three tetrads and averaged between 100 to 1100 ps. Only the global helical and... 

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