Double helices conformational flexibility

The furanose rings of the deoxyribose units of DNA are conformationally labile. All flexible forms of cyclopentane and related rings are of nearly constant strain and pseudorotations take place by a fast wave-like motion around the ring The flexibility of the furanose rings (M, Levitt, 1978) is presumably responsible for the partial unraveling of the DNA double helix in biological processes. 

The viscosity of xanthan solutions is also distinct from that of flexible polyelectrolyte solutions which generally shows a strong Cs dependence [141]. In this connection, we refer to Sho et al. [142] and Liu et al. [143], who measured the intrinsic viscosity and radius of gyration of Na salt xanthan at infinite dilution which were quite insensitive to Cs ( > 0.005 mol/1). Their finding can be attributed to the xanthan double helix which is so stiff that its conformation is hardly perturbed by the intramolecular electrostatic interactions. In fact, it has been shown that the electrostatic persistence length contributes only 10% to the total persistence length even at as low a Cs as 0.005 mol/1 [142]. Therefore, the difference in viscosity behavior between xanthan and flexible polyelectrolyte... 

The double helix of the DNA can only to a first approximation be considered a linear, rod-like structure with the typical coordinates of B-DNA. Actually, DNA possesses considerable flexibility and conformational variability. The flexibility and structural polymorphism of DNA are prerequisites for many of the regulatory processes on the DNA level (review Alleman and Egli, 1997). Local deviation from the classical B-structure of DNA, as well as bending of the DNA, are observed in most protein-DNA complexes. 

Given the conformational flexibility of the monomer imits, it is no surprise that the double helical secondary structure can actually be subdivided into families of structurally distinct pol5miorphs (see Table 1 for helix parameters) (6). DNA double helices most commonly adopt the B-form, while A-form helices are the most common RNA secondary structures. These helices have a right-handed helix sense and utilize the Watson-Crick base pairing mentioned above (Fig. 3). In addition, both the A- and B-form orient the glycosidic bond in the anti conformation. A major difference between the A- and B-form structures is the positioning of the base pairs relative to the hefix axis. In B-DNA the base pairs are centered... 

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