Crystal structure B-DNA

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... 

Travers, A.A. (1992) The reprogramming of transcriptional competence. Cell 69, 573-575. Velankar, S.S., Soultanas, P., Dillingham, M.S., Subramanya, H.S., and Wigley, D.B. (1999) Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inch-worm mechanism. Cell 97, 75-84. 

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. 

Hopfner, K. P., Eichinger, A., Engh, R. A., Laue, F., Ankenbauer, W., Huber, R., and Angerer, B. (1999). Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius. Proc. Natl. Acad. Sci. USA 96, 3600-3605. 

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... 

Singleton, M. R, Dillinigham, M. S., Gaudier, M., Kowalczykowski, C.. and Wigley, D. B. 2004, Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature... 

Figure 5-5 Comparison of structures of the TT region of (a) duplex 1, and (b) native duplex in B-form DNA. Both strands were cut out of the full duplexes, generated (a) from molecular dynamics simulations incorporating NMR constraints, and (b) from crystal structure data [123], The intruding C7 methylene with the flat solvent-accessible surface in the modified linkage 1 contrasts markedly with the maximally solvent-accessible phosphate of the phosphodiester linkage. The solvent-accessible surfaces are stippled (adapted from [72]).

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... 

B Guenther, R Onrust, A Sail, M O Donnell, J Kuriyan. Crystal structure of the 5 subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell 91 335-345, 1997. 

Early diffraction photographs of such DNA fibers taken by Rosalind Franklin and Maurice Wilkins in London and interpreted by James Watson and Francis Crick in Cambridge revealed two types of DNA structures A-DNA and B-DNA. The B-DNA form is obtained when DNA is fully hydrated as it is in vivo. A-DNA is obtained under dehydrated nonphysiological conditions. Improvements in the methods for the chemical synthesis of DNA have recently made it possible to study crystals of short DNA molecules of any selected sequence. These studies have essentially confirmed the refined fiber diffraction models for A- and B-DNA and in addition have given details of small structural variations for different DNA sequences. Furthermore, a new structural form of DNA, called Z-DNA, has been discovered. 

Figure 9.3 Comparison of the consensus nucleotide sequence of the TATA box (a) and the sequences of the DNA fragments used in the crystal structure determinations of the TATA box-binding proteins from yeast (b) and the plant Arabidopsis thaliana (c).

Interactions that are not sequence specific are also an Important part of the binding and occur between the sugar and phosphate residues of the DNA and the side-chain and main-chain atoms of the protein. In the crystals the DNA fragment retains the B-DNA structure with only minor distortions. 

---