Sugar phosphate backbone, conformational

Thibaudeau C, Chattopadhyaya J (1998) The information transmission from the nucleobase drives the sugar-phosphate backbone conformation in the nucleotide wire. Nucleosides Nucleotides 17 1589-1603... 

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. 

Theoretical conformational analysis provides a basis for understanding the unique features of double-stranded DNA In terms of its chemical architecture. The well-known stiffness of the chain as a whole derives from the sequence of heterocyclic bases, while the local mobility of the constituent nucleotides reflects the structural complexity of the sugar-phosphate backbone. 

As RNA molecules are highly negatively charged due to their sugar-phosphate backbone, the conformational state of these molecules is strongly dependent on the concentration of positively charged counterions. In the absence of Mg2+ or other polyvalent counterions, and in low monovalent salt concentrations, RNA becomes denatured as a result of ineffective Debye screening of the repulsive forces between different parts of the polymer. 

Watson and Crick also found that the two complementary strands of DNA are coiled into a helical conformation about 20 A in diameter, with both chains coiled around the same axis. The helix makes a complete turn for every ten residues, or about one turn in every 34 A of length. Figure 23-27 shows the double helix of DNA. In this drawing, the two sugar-phosphate backbones form the vertical double helix with the heterocyclic bases stacked horizontally in the center. Attractive stacking forces between the pi clouds of the aromatic pyrimidine and purine bases are substantial, further helping to stabilize the helical arrangement. 

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