Base pair step parameters

Fig. 13.16 Probability density distributions of inter base pair helical parameters of 6L tind 6 from molecular dynamics simulations, (a) rise distance, (b) tilt angle, (c) slide distemce, (d) twist angle, (e) shift distance and (f) roll angle for TT steps in single stranded systems 2L blue line) tmd 2 (green line) and double stianded systems 6L (red line) tmd 6 (teal line)...

Fig. 13.17 Probability density distributions of intra base pair helical parameters for 6L and 6 from molecular dynamics simulations (a) buckle, (b) propeller, and (c) opening angles for the 5 tind 3 A-T base pair of the TT step in 6 (blue line and red line) and the 5 and 3 A-T base ptiir of the TT step in 61. (green line and teal line)...

Fig.1 The six step parameters that define the conformation of a Watson-Crick base pair inDNA...

This limitation has been overcome with a special NDDO-HT parameterization for calculating hole coupling matrix elements in DNA-related systems [72]. As reference data, coupling matrix elements were calculated for a set of 130 structures of WCP dimers with different step parameters at the HF/6-31G level. As discussed below in more detail, electronic couplings between neighboring pairs are extremely sensitive to conformational fluctuations of the DNA structure. For instance, the matrix element between base pairs in... 

Recently, the effects of static and dynamic structural fluctuations on the electron hole mobility in DNA were studied using a time-dependent self-consistent field method [33]. The motion of holes was coupled to fluctuations of two step parameters of a duplex, rise and twist (Fig. 1), namely the distances and the dihedral angles between base pairs, respectively. The hole mobility in an ideally ordered poly(G)-poly(C) duplex was found to be decreased by two orders of magnitude due to twisting of base pairs and static energy disorder. A hole mobility of 0.1 cm V s was predicted for a homogeneous system the mobility of natural duplexes is expected to be much lower [33]. In this context, one can mention several theoretical studies, based on band structure approaches, to estimate the electrical conductivity of DNA [85-87]. 

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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