DNA crystal structure

Eisenstein, M., Shakked, Z.i Hydration patterns and intermolecnlar interactions in A-DNA crystal structures. Implications for DNA recognition. J. Mol. Biol. 248 (1995) 662-678... 

In recent years an astonishing structural variety has been rmcovered for DNA. Crystal structures have shown that, apart from the structural motifs of the A-, B- and Z-forms of DNA, other, sequence-dependent structural variations exist which are observed when smaller sequence fragments are examined in detail. 

Fig. 14.8. DNA binding domain of the tnmor suppressor protein p53 in complex with DNA. Crystal structure of the core domain of p53 (amino acids 102-292) in complex with a double-stranded DNA that contains a specific binding site for p53 (Cho et al., 1994). The amino acid positions are highhghted at which frequent oncogenic mutations are observed (see Fig. 14.9). MOLSKRIPT representation according to Krauhs, (1991).

This problem lies at the heart of all enzyme electrode manufacture. Proteins are biological molecules, and there is an apocryphal tale concerning Bragg when he was head of the Cavendish Laboratory, and Frances Crick told him he was going to study DNA crystal structure. Bragg s reply was gruff, and as it turned out quite apt, thats no... 

Table 1 Parameters describing complementary base-pair geometry in high-resolution DNA crystal structures ...

Ma B, Pan Y, Gunasekaran K, Venkataraghavan RB, Levine AJ, Nussinov R (2005) Comparison of the protein-protein interfaces in the p53-DNA crystal structures Towards elucidation of the biological interface. Proc Natl Acad Sci USA 102 3988-3993... 

Figure 2. Histograms of consecutive phosphorus - phosphorus distances for the structures generated during the simulations with the CHARMM23 potential, structures determined by NMR spectroscopy, and high resolution B-DNA and A-DNA crystal structures, as listed in the Materials section.

Svozil D, Kalina J, Omelka M, Schneider B (2008) DNA conformations and their sequence preferences. Nucleic acids res 36 3690-3706. doi 10.1093/nar/gkn260 Schneider B, Neidle S, Berman HM (1997) Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42 113-124. doi 10.1002/(SICI)1097-0282(199707)42 1<113 AID-BIP10>3.0.CO 2-0... 

Neidle S, Parkinson GN (2008) Quadruplex DNA crystal structures and drug design. Biochi-mie 90 1184-1196... 

Sponer, J., Hobza, P. (1994). Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study. Journal of the American Chemical Society, 116, 709. 

A certain number of MD simulations have been carried out by Pettitt and co-workers in order to study the dynamics and the hydration properties of triplex systems as well as the equilibrium distribution and dynamical behavior of counter-and co-ions in their vicinity. For that purpo.se, this group simulated different triplexes in a box of water at a 1.0 M NaCl concentration using the Ewald summation method. From a 500 ps MD simulation, a spine of water molecules in one of the grooves of the triplex, analogous to those described in B-DNA crystal structures, was found to contribute to its stabilization (Figure 7). Then, a 1.3 ns MD simulation of the same d(CG-G)7 triple helix was conducted, displaying an rms deviation value close to 1.6 A from the modeled structure. In view of... 

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