Double helix conformations

Sanger develops his sequence analysis for amino acids in proteins Nobel Prize Chemistry to Hermann Staudinger for contributions to the understanding of macromolecular chemistry Watson and Crick discover the double helix conformation of DNA, the break-through in bio-polymer science... 

The three main families of nucleic acid double helix conformations... 

Amylopectin is responsible for the crystalline character of the starch granule and its structure can be modelled as a hyperbranched molecule [10,11, 28,29]. The model for the amylopectin molecule proposed by Robin [14] is illustrated in Figure 4.1(c). The A-chains, which are short segments of 15 D-glucopyranosyl residues, are the portion responsible for the crystalline structure of amylopectin. Starch crystallites are thus formed by compact areas made up of A-chains with DP 15. The crystallinity index of regular corn starch with 73% amylose is equivalent to that of waxy maize starch which is 100% amylose this confirms that amylose content has little effect on granule crystallinity. Starch crystallites formed in compact areas are made up of vicinal A-chains in a compact double helix conformation with two extended helices possessing 6 residues per turn that repeat every 21 A [1]. 

The UV-induced generation of cyclobutane dimers is greatly dependent on double-helix conformational factors. In dormant spores of various bacillus species, for example, a group of small, acid-soluble proteins specifically bind to DNA, thereby enforcing a particular conformation that is unfavorable for the formation of harmful cyclobutane-type lesions. As a consequence, these dormant spores are much more resistant to UV radiation than the corresponding grooving cells, in which DNA strands reassume conformations favorable for the formation of cyclobutane-type lesions [31]. 

Mechanochemical degradation in solution of the dezoxiribo-nu-cleic acid, ADN, by capillaries shear, had as effect the transversal splitting of ADN macromolecule, with a double helix conformation, and not the scission of the secondary hydrogen bonds that assure the maintaining of this conformation in solution [1034-1037]. 

The biopolymers when present in aqueous solution are in double helix conformation but at certain temperature the double helix domains aggregate and form physical cross-links due to hydrophobic interaction, thus resulting in gelation. These polymers are in sol form at higher temperature and gelate at lower temperature, thus correspond to UCST system. 

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. 

FIGURE 7.31 The favored conformation of agarose in water is a double helix with a threefold screw axis. 

H bonding also vitally influences the conformation and detailed structure of the polypeptide chains of protein molecules and the complementary intertwined polynucleotide chains which form the double helix in nucleic acids.Thus, proteins are built up from polypeptide chains of the type shown at the top of the next column. 

One of the most thoroughly investigated examples of polymeric biomolecules in regard to the stabilization of ordered structures by hydration are the DNAs. Only shortly after establishing the double-helix model by Watson and Crick 1953 it became clear, that the hydration shell of DNA plays an important role in stabilizing the native conformation. The data obtained by the authors working in this field up until 1977 are reviewed by Hopfinger155>. 

Small-angle X-ray scattering (SAXS), circular dichroism (CD), and UV spectroscopy at different temperatures were used to investigate the nature of calf-thymus DNA in aqueous solution, in the presence of [Me Sn] " (n = 1-3) species. The results demonstrate that the [MeSn(IV)] moiety does not influence the structure and conformation of the DNA double helix, and does not degrade DNA, as indicated by agarose gel electrophoresis. Inter alia, the radii of gyration, Rg, of the cross section of native calf-thymus DNA, determined by SAXS in aqueous solution in the presence of [Me Sn] " (n = 1-3) species are constant and independent of the nature and concentration of the [Me Sn] species. 

Recent advances of the Seeman group led to the construction of a nanomechanical device from DNA [89]. In this molecular apparatus, the ion-dependent transition of B-DNA into the Z-conformation is used to alter the distance between two DNA DX domains attached to the switchable double helix. Atomic displacements of about 2-6 nm were attained. Ionic switching of nanoparticles by means of DNA supercoiling has also been reported [53]. Additional advances regarding the use of DNA is nanomechanical devices have been reported by Fritz et al., who showed that an array of cantilevers can be used to... 

The tveak and reversible binding of these complexes to calf-thymus DNA (ct DNA) suggests a dominant electrostatic mode of interaction nevertheless, relevant conformational distortions of the double helix are caused [50]. A multinuclear NMR study of the reactivity of [Au(en)Cl2]Cl and [Au(en)2]Cl3 vith guanosine 5 -monopho-sphate (5 -GMP) reveals that in an aqueous solution only [Au(en)Cl2]Cl binds very weakly to 5 -GMP via N(7) to give a 1 1 adduct [48]. 

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