Phosphates backbone structure

Figure 12.16), can insert between the stacked base pairs of DNA. The bases are forced apart to accommodate these so-called intercalating agents, causing an unwinding of the helix to a more ladderlike structure. The deoxyribose-phosphate backbone is almost fully extended as successive base pairs are displaced 0.7 nm from one another, and the rotational angle about the helix axis between adjacent base pairs is reduced from 36° to 10°. 

The secondary biological cycles stem from the crucial roles that phosphates and particularly organophosphates play in all life processes. Thus organophosphates are incorporated into the backbone structures of DNA and RNA which regulate the reproductive processes of cells, and they... 

Protons bound to heteroatoms in heterocyclic compounds are likely to be very mobile in solution and, where two or more heteroatoms are present in a structure, different isomers (tautomers) may be in equilibrium. As a case in point, consider the nucleotide bases (indicates the point of attachment to the sugar-phosphate backbone). 

The structure of DNA. (a) A ball-and-stick model, with the sugar-phosphate backbone colored blue and the bases colored red. b) A space-filling model, showing C atoms in blue, N atoms in dark blue, H atoms in white, O atoms in red, and P atoms in yellow. 

The structures of DNA and RNA are similar in that each has a sugar-phosphate backbone with one organic base bound to each sugar. However, there are four distinct differences between RNA and DNA ... 

Fig. 1 The w-stack of double helical DNA. In this idealized model of B-DNA the stack of heterocyclic aromatic base pairs is distinctly visible within the sugar-phosphate backbone (schematized by ribbons) a view perpendicular to the helical axis b view down the helical axis. It is the stacking of aromatic DNA bases, approximately 3.4 A apart, that imparts the DNA with its unique ability to mediate charge transport. Base stacking interactions, and DNA charge transport, are exquisitely sensitive to the sequence-depen-dent structure and flexibility of DNA...

The structures shown in Fig. 4-1 are for B-form DNA, the usual form of the molecule in solution. Different double-helical DNA structures can be formed by rotating various bonds that connect the structure. These are termed different conformations. The A and B conformations are both right-handed helices that differ in pitch (how much the helix rises per turn) and other molecular properties. Z-DNA is a left-handed helical form of DNA in which the phosphate backbones of the two antiparallel DNA strands are still arranged in a helix but with a more irregular appearance. The conformation of DNA (A, B, or Z) depends on the temperature and salt concentration as well as the base composition of the DNA. Z-DNA appears to be favored in certain regions of DNA in which the sequence is rich in G and C base pairs. 

In forming the double-helix polymeric DNA structure, the two sugar-phosphate backbones twist around the central stack of base pairs, generating a major and minor groove. Several conformations, known as DNA polymorphs, are possible. 

Figure 4.16 The structure of yeast tRNAplle (a) the cloverleaf form of the base sequence tertiary base-pairing interactions are represented by thin red lines connecting the participating bases. Bases that are conserved in all tRNAs are circled by solid and dashed lines, respectively. The different parts of the structure are colour-coded, (b) The X-ray structure showing how the different base-paired stems are arranged to form an L-shaped molecule. The sugar-phosphate backbone is represented as a ribbon with the same colour scheme as in (a). (From Voet and Voet, 2004. Reproduced with permission from John Wiley Sons., Inc.)...

Figure 13.4 Oligonucleotide structure. The nucleotides are joined via the phospho-diester bridges between sugar residues. The bases stick out away from the sugar-phosphate backbone.

Figure 12.3 The double hehx of DNA. The sugar-phosphate backbones wind about the periphery of the molecule in opposite directions. The hydrogen-bonded base pairs occupy the core of the structure and are basically flat and lie perpendicular to the long axis of the helix. (Illustration, Irving Geis/Geis Archives Trust. Howard Hughes Medical Institute. Reproduced with permission.)...

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