Structure of B-DNA

Modulation of DNA structure and dynamics is also possible using base-pair mismatches. Mismatches exert little influence on the global structure of B-DNA duplexes. Locally, the extent of base stacking perturbation depends sensitively on the nature of the mismatch [139-141]. Therefore, while a CA mismatch introduces a significant distortion in local stacking, the well-stacked GA mismatch is, by many criteria, barely perceptible. The dynamics of mismatched base-pairs may also be significantly distinct from matched Watson-Crick base pairs [9]. We exploit these features of DNA mismatches to probe the sensitivity of DNA-mediated CT to base structure and dynamics. 

Figure 1.30 The double helical structure of B -DNA. Interchanging of either the bases of a base pair and/or base pair with base pair does not affect the geometry of this structure. Reproduced by permission of Prentice Hall from Chemistry for Pharmacists and the Life Sciences by G Thomas...

Minasov G, Tereshko V, Egli M. Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions 46. on conformation and packing. J. Mol. Biol. 1999 291 83-99. 

The thermodynamic and spectroscopic properties of short segments of duplex DNA containing a single CPD indicate that cis-syn CPD can be accommodated in the double helical structure of B-DNA such that hydrogen bonding with the opposite A residues is possible (41). The crystal structure of... 

T.K. Chiu and R E. Dickerson. 2000. 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium J. Mol. Biol. 301 915-945. (PubMed)... 

Figure 2 Structure of B-DNA depicting the major and minor grooves...

In addition to the major B form, three additional DNA structures have been described. Two of these are compared to B DNA in Figure 4-4. In very low humidity, the crystallographic structure of B DNA changes to the A form RNA-DNA and RNA-RNA helices exist in this form in cells and in vitro. Short DNA molecules composed of alternating purlne-pyrlmldlne nucleotides (especially Gs and Cs) adopt an alternative left-handed configuration Instead of the normal right-handed helix. This structure is called Z DNA because... 

See also DNA, Nucleic Acid Structures, Structure of B-DNA, Twists, Linking Number, Supercoiling, Writhing, Topoisomerases... 

See also Nucleic Acid Sequences, Primary, Secondary, Tertiary Structure of Nucleic Acids, History of DNA, Structure of B-DNA... 

The internal torsion angles, which are characteristic for the furanose ring of deoxyribose (noted by T0-T4) determine the appearance of endo- and exo-conformations of deoxyribose. The Watson-Crick model corresponds to B-DNA type, having the deoxyribose in the C-2 -endo conformational form. The secondary structure of B-DNA... 

Figure 4. Stereo view of structures of B-DNA and alternating B-DNA (16), superimposed as far as possible. The alternating structure is not necessarily the same as that present in solution.

Berger I, Tereshko V, Ikeda H, Marquez VE, Egli M (1998) Crystal structures of B-DNA with incorporated 2 -deoxy-2 fluoro-arabino-furanosyl thymines implications of conformational preorganization for duplex stability. Nucleic Acids Res 26 2473-2480... 

Figure 12.2. The double helical structure of B-DNA. One pitch represents 10 nucleotides which are composed of a single turn of DNA. See also Color Insert.

Figure 29-2. Section of the basic structure of B-DNA with about three turns of the double helix and with large furrow at 2.2 nm and small furrow at 1.2 nm. The periodicity is 3.4 nm.

Figure 6.8 Structure of B-DNA. [Reproduced by permission of A. L. Brogden, University of Reading]...

Under normal conditions the described procedure is not possible, because both G and A are purine bases and therefore for a G-A base pair there would not be enough space in the double helical structure of B DNA. On the other hand if the double helix becomes through the binding of a chemical carcinogen (especially... 

In the last years the problem of the proper theoretical treatment of solvation effects in DNA has been solved to a great extent (17). In a number of publications the interaction energy between water molecules and the nucleotide bases (28), base pairs (29), single (30), and double helices (31) of DNA has been calculated. Recently, also the complete solvent structure of a B-DNA double helix fragment with 12 base pairs and the corresponding sugar and phosphate units has been determined (32). In these Monte Carlo simulations, 447 water molecules have been included and their interaction energies and probability distributions (at a temperature of 300 K) have been calculated. In recent publications the Na+ ion structure of B-DNA at different humidities, ionic concentrations and temperature has been presented (33). 

T. K. Chiu and R. E. Dickerson,/. Molec. Biol., 301, 915 (2000). 1 A Crystal Structures of B-DNA Reveal Sequence-Specific Binding and Groove-Specific Bending of DNA by Magnesium and Calcium. 

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