Poly double helices

The systematic catenation of cyclotetrasilane rings gives rise to a double helix structure of two poly silane main chains. 

Isotactic poly(methyl methacrylate), also, is an intricate case, resolved only after a 20-year debate. The repetition period along the chain axis is 10.40 A corresponding to S monomer units the entire cell contains 20 monomer units (four chains). At first, the stmcture was resolved as a 5/1 helix (183) with = 180° and 62 — 108° but no reasonable packing was found using this assumption. Further conformational calculations showed that helices like 10/1 or 12/1 should be more stable than the 5/1 helix. The structure was solved by Tadokoro and co-workers (153b) who proposed the presence of a double helix. Two chains, with the same helical sense and the same direction but displaced by 10.40 A one from the other are wound on each other, each chain having 10 monomer units per turn [i(10/l)] and a 20.80-A repeat period. As a result, the double helix has a 10.40-A translational identity period, identical to that found in the fiber spectmm. The conformational parameters are Of = 179° and 2 = -148°. Energy calculations indicate that the double helix is more stable by 4.4 kcal per-mole of monomer units than two isolated 10/1 helices, a result that is in line with the well-known capacity of this polymer to form complexes in solution (184). 

The most important feature of DNA is that it usually consists of two complementary strands coiled about one another to form a double helix (Figure 7.3). Each strand is the poly nucleotide. The... 

The distortions induced in the DNA double helix by the interstrand cross-links have been characterized by several techniques. As judged by chemical probes (diethyl pyrocarbonate, hydroxylamine, osmium tetroxide), antibodies to cisplatin-modified poly(dG-dC)-poly(dG-dC), natural (DNase I) and artificial (1,10-phenanthroline-copper complex) nucleases, the cytosine residues are accessible to the solvent, and the distortions are located at the level of the adduct [48-50]. From the electrophoretic mobility of the multimers of double-stranded oligonucleotides containing a single interstrand cross-link [50] it is deduced that the DNA double helix is unwound (79°) and its axis is bent (45°). 

DNA Bending Assume that a poly(A) tract five base pairs long produces a 20° bend in a DNA strand. Calculate the total (net) bend produced in a DNA if the center base pairs (the third of five) of two successive (dA)5 tracts are located (a) 10 base pairs apart (b) 15 base pairs apart. Assume 10 base pairs per turn in the DNA double helix. 

Due to the toxicity of the co-(cyclopolymer) 8, the capability of interferon induction of a great number of polymers has been tested. Thus, interferon is formed by the presence of natural double helix RNA, which occurs in some viruses (Reo-viruses), but also by the synthetically produced complex (40) from poly(inosinic acid) and poly(cytidylic acid) (1 1). An improved and extended interferon induction of such poly(nucleic acid)s can be achieved by complexing with synthetic polycations, as for example diethylaminodextrane (41) or with a polycation (42) of composition 9. 

The double helix formed by poly(G) poly(C) does not disproportionate. The reason is that it forms an extremely stable Watson-Crick duplex and that the Hoogsteen base pair could only form if poly(C) were protonated (legend to Fig. 16.16). 

Fig. 20.10. Base pairs found in homopolymer nucleic add self-complexes. The unsymmetrical uridine U-U and 2-thiouridine s2U-s2U base pairs lead to antiparaUel orientation of polynucleotide chains similar to the RNA double helix. In the symmetrical AH+ -AH+ and C-CH+ base pairs, the dyad axis coinddes with the helix axis and gives rise to parallel polynucleotide chains. For the same reason, the four polynucleotide chains in [poly(G)]4 are related by a fourfold rotation axis and are also parallel

In the homopolymers formed by uridine or 2-thiouridine, base pairs with twofold symmetry are feasible, as described in Part II, Chapter 16 [529, 699]. The situation is more complex, however, because the homopolymer folds back on itself, giving rise to a hairpin-like structure where the polynucleotide strands are necessarily antiparallel and the base pairs are of the form shown in Fig. 20.10. Not surprisingly, a comparable double helix is also observed for polyxanthylic acid poly (X) [700]. The purine base of xanthosine displays the same hydrogen-bonding functional groups as uracil and therefore, the same base pair can be formed, but the purine-purine pair requires a larger separation between the glycosidic links and consequently a wider helix radius. 

Mazumdar SK, Saenger W, Scheit KH (1974) Molecular structure of poly-2-thiouridylic acid, a double helix with non-equivalent polynucleotide chains. J Mol Biol 85 213-229... 

The helical structure observed here may be stabilized by interactions which is revealed by the formation of a double helix of poly A in acidic aqueous solution74. With rising pH of the system, helicity of the polymer increases due to release of the electrostatic repulsion between positively charged side chains. Above pH 2.5, the spectra cannot be measured, as the polymer begins to precipitate in aqueous solution. By adding EG, helicity tends to increase (Fig. 22). In EG, however, poly-L-lysine - HBr still exists in a random coil structure. Therefore, it can be assumed that EG rather depresses the electrostatic repulsion between piotonated adenine units. 

Some experimental data show that the double-helix DNA macromolecules exist in poly(ethylene oxide) solution in the so-called compact form, which is very similar to the toroidal globule considered in Sect. 5. Electron micrographs definitely reveal the existence of cavities in the center of the globules. Of course, the development of an adequate theory of the compact form of DNA requires the consideration of some more refined peculiarities of the system and, primarily, of the role of poly-(ethylene oxide) (see recent works ). However, we emphasize that the existence of the cavity in the middle of the globule is apparently the fundamental consequence of the absence of the points of easy bending in the polymer chain. Hence, more refined theories must use as.a starting point the simple consideration of Sect. 5.6 of this paper. 

To form double-stranded poly(A)-poly(U), equimolar amounts of the two homopolymers are mixed at a concentration of 0.6-1.5 fiM nucleotide (about 200-500 /iig/ml) in 0.1 A/ NaCl, 0.01 M phosphate pH 7 at room temperature and allowed to anneal for a few hours. Hypochromicity occurs at 260 nm when a double helix is formed and at both 260 and 280 nm when a triple helix is formed. At room temperature and 0.1 Af NaCl, only the stoichiometry determines which helix will form. At high ionic strength (0.7 M NaCl), and at high temperature, even a 1 1 mixture will form a triple helix with time triple-strand formation is also favored by... 

Poly(I) and poly(C) form only a double helix, and hypochromicity is greatest at 250 nm. Since poly(I) can form helical structure by itself, this mixture of homopolymers is heated to 100° in a boiling water bath to melt the poly (I) structure, and the mixture is allowed to cool slowly to room... 

James P. Lewis, Pablo Ordejon, and Otto F. Sankar, Electric-structure-based molecular-dynamics method for large biological systems Application to the 10 basepair poly(dG) poly(dC) DNA double helix. Physical Review B, 55, 6880-6887 (1997). 

Diffraction patterns obtained by Davies and Baldwin [12] indicated that poly d(A-T).poly d(A-T) could assume a conformation with axial periodicity about 24.5 A which they named D-DNA. Similar diffraction patterns were obtained from poly d(I-C).poly d(I-C) by Mitsui et al. [46]. They proposed a novel left-handed double helix with anti-parallel strands and Watson-Crick base-pairs. This eightfold helix contained sugars with an unusual pucker and the bases were placed about 2 A behind the helix axis i.e. on the opposite side from the position of the base-pairs in the A form of DNA. Arnott et al. [47] obtained better quality D-form diffraction patterns from poly d(A-T).poly d(A-T) which they analysed using the linked atom least squares technique. They rejected the left-handed model of Mitsui et al. [46] and claimed... 

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