A-DNA helix

A -DNA The Watson-Crick model of DNA is based on the x-ray diffraction patterns of B-DNA. Most DNA is B-DNA however, DNA may take on two other conformations, A-DNA and Z-DNA. These conformations are greatly favored by the base sequence or by bound proteins. When B-DNA is slightly dehydrated in the laboratory, it takes on the A conformation. A-DNA is very similar to B-DNA except that the base pairs are not stacked perpendicular to the helix axis rather, they are tilted because the deoxyribose moiety puckers differently. An A-DNA helix is wider and shorter than the B-DNA helix. 

The molecular dynamics unit provides a good example with which to outline the basic approach. One of the most powerful applications of modem computational methods arises from their usefulness in visualizing dynamic molecular processes. Small molecules, solutions, and, more importantly, macromolecules are not static entities. A protein crystal structure or a model of a DNA helix actually provides relatively little information and insight into function as function is an intrinsically dynamic property. In this unit students are led through the basics of a molecular dynamics calculation, the implementation of methods integrating Newton s equations, the visualization of atomic motion controlled by potential energy functions or molecular force fields and onto the modeling and visualization of more complex systems. 

FIGURE 24-10 Supercoils. A typical phone cord is coiled like a DNA helix, and the coiled cord can itself coil in a supercoil. The illustration is especially appropriate because an examination of phone cords helped lead Jerome Vinograd and his colleagues to the insight that many properties of small circular DNAs can be explained by super-coiling. They first detected DNA supercoiling, in small circular viral DNAs, in 1965. 

Fig. 3 Thermal denaturation transition of a DNA helix, (a) UV absorbance increases with temperature, following the unstacking of bases, following a sigmoidal shape. AD and Au are lower and upper baselines, also slightly dependent on temperature, (b) Fraction of single strands 6 extracted from data in (a), which defines the melting temperature corresponding to 9 = 0.5. Adapted with permission from [7]...

Replication, which starts at the end of a DNA helix, continues until the entire structure has been duplicated. The same result is obtained when replication starts at the centre of a DNA helix. In this case unwinding continues in both directions until the complete molecule is duplicated. This latter situation is more common. 

Murphy CJ, Arkin MR, Jenkins Y, et al. Long-range photoinduced electron transfer through a DNA helix. Science 1993 262 1025-9. 

When the ruthenium-modified oligomer is annealed to its unmetal-lated complement, the metal complex intercalates and intense luminescence is observed (77). By contrast, the ruthenium-modified oligonucleotide alone or in the presence of noncomplementary single-stranded DNA displays little luminescence. These results are consistent with previous studies luminescence is observed in aqueous solution only when the stacked bases of a DNA helix provide a platform for intercalation of the dppz ligand. 

The results for covalently bound analogues of [Ru(phen)2(dppz)]2+ and [Rh(phi)2(phen)]3+ intercalated into a 15-mer oligonucleotide therefore demonstrate that photoinduced electron transfer between intercalators can occur rapidly over >40 A through a DNA helix over a pathway consisting of 7r-stacked base pairs. The DNA 7r-stack may be considered a remarkably effective medium for electronic coupling of intercalated species. 

Brown T, Kennard O, Kneale G, Rabinovich D (1985) High resolution structure of a DNA helix containing mismatched base pairs. Nature (Lond) 315 604- 606... 

Kneale G, Brown T, Kennard O, Rabinovich D (1985) G-T base-pairs in a DNA helix the crystal structure of d(GGGGTCCQ. J Mol Biol 186 805 - 814... 

How strong can the bend be on a DNA helix from cisplatin DFT and MP2 quantum chemical calculations of cisplatin-bridged DNA purine bases70... 

In DNA replication and other processes, the two strands of the double helix must be separated from each other, at least in a local region. The two strands of a DNA helix readily come apart when the hydrogen bonds between base pairs are disrupted. In the laboratory, the double helix can be disrupted by heating a solution of DNA or by adding acid or alkali to ionize its bases. The dissociation of the double helix is called melting because it occurs abruptly at a certain temperature. The melting temperature (Tj ) is defined as the... 

The results of Crothers and coworkers are in agreement with the analysis of crystal data of bZIP Fos-Jun bound to AP-1 DNA [23,20]. The data indicate a DNA helix that is only marginally bent (less than 10°) [23]. 

Diameter of a DNA helix Silicon lattice constant Diameter of a carbon atom... 

When the oxidizing species, an electron acceptor, and the electron donor are both embedded within a biological macromolecule (e.g., in a protein or DNA molecules), the reaction kinetics are entirely different from those in solution in which both species can diffuse freely and encounter one another in order to undergo chemical reaction. An example of such intramolecular processes is the one-electron oxidation of guanine (G) by a 2AP neutral radical, both site-specifi-cally positioned within a DNA duplex [28]. Here, both reaction partners are fixed within a DNA helix and the bimolecular reaction model is not suitable for describing the reaction kinetics (4.16). Instead, the kinetics of oxidation of G by 2AP(-H) radicals in double-stranded DNA follow first-order kinetics with the magnitudes... 

Dado G P and Gellman S H 1993 Redox control of secondary structure in a designed peptide J. Am. Chem. Soc. 115 12609-10 Murphy C J, Arkin M R, Jenkins Y, Ghatlia N D, Bossmann S H, Tlirro N J and Barton J K 1993 Long-range photoinduced electron transfer through a DNA helix Science 262 1025-9... 

The linking number is the total number of times two strands of a DNA helix cross each other by means of either twist or writhe this equals the number of times the two strands are interlinked. It reflects both the winding of the native DNA helix and the presence of any supercoiling. 

Indicate the role of deoxyribose puckering in determining the structural differences between A-DNA and B-DNA helices. Compare the structures of double-strand RNA and RNA-DNA hybrids with that of the A-DNA helix. 

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