Inter double helices

Fig. 37.—(a) Stereo view of one turn of the 3-fold double helix of welan (43). The two chains are drawn in open and filled bonds for distinction. The vertical line represents the helix axis. Both intra-and inter-chain hydrogen bonds and side chains, hydrogen bonded to carboxylate groups, stabilize the double helix. Calcium ions (crossed circles) are present near the carboxylate groups, but outside the helix to make inter double-helical connections. 

In the crystal structures, neighboring doublehelices have the same rotational orientation and the same translation of half a fiber repeat as in the PARA 1 model. Only the Ax vector is slightly larger in the calculated interaction (1.077 nm) than in the observed ones 1.062 nm and 1.068 nm in the A type and B type, respectively. This may be due to the fact that in the crystal structures the helices depart slightly from perfect 6-fold symmetry. Also, no interpenetation of the van der Waals surfaces is allowed in the calculations, whereas some of them may occur in the cristallographic structure. It is quite interesting to note that the network of inter double-helices hydrogen bonds found in the calculated PARA 1 model reproduces those found in the crystalline structures. 

Fic. 10.—Parallel packing arrangement of 6-fold, A-amylose (8) molecules, (a) A stereo side view of less than 2 turns of a pair of double helices 10.62 A (=al2) apart. The two strands in each helix are distinguished by open and filled bonds, and the helix axis is also drawn, for convenience. Note that atom 0-6 mediates both intra- and inter-double helix hydrogen bonds. 

Fig. 30. — Packing arrangement of 4-fold antiparallel double helices of potassium hyaluronate (32). (a) Stereo view of a unit cell approximately normal to the line of separation of the two helices. The two chains in each duplex, drawn in open and filled bonds for distinction, are linked by not only direct hydrogen bonds, but also water bridges. Inter double-helix hydrogen bonds are mediated between hydroxymethyl and iV-acetyl groups. Potassium ions (crossed circles) at special positions have only a passive role in the association of hyaluronate chains.

Figure 6. Molecular drawings of the best arrangement of two anti-parallel double-helices, a) Projection perpendicular to the chain axis, b) Projection along the chain axis. Inter double-helix hydrogen bonds are shown as dotted lines.

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. 

In the case of 10-fold helices, the two chains in a double helix would be related by 2-fold symmetry coincident with the helix axis. Starting from several grid points, the intra-and inter-molecular short contacts within a double helix were minimized. Only the double helix model with 10 chains could be constructed without any fatal contacts. However, we could not pack this model successfully in the unit cell because of the large helical radii for several atoms. The results of these calculations are summarized in Table II. 

The bases contained in DNA are quite complex units which are built into the double inter-linked helix molecule of DNA. There are four main types of base, A, T, C and G, standing for adenine, thymine, cytosine and guanine, (see also Chapter 5), but they can also be protonated, i.e. pick up an H+, by reacting with an acid. 

In 1962, the Nobel Prize winners for Physiology and Medicine were Francis Crick, James Watson and Maurice Wilkins. They used chromatography to separate the complex mixture of amino acids making up proteins. This led to the characterization of the structure of a protein by X-ray analysis and in particular the realization that the three-dimensional structure of DNA was an inter-linked double helix. 

This antiparallel double helix has a central cavity which is filled by the polyiodide chain or, in other terms, the polyiodide chain serves as a matrix around which the p-nitrophenyl-a-maltohexaoside molecules are arranged. The complex is stabilized by the inter- and intramolecular hydrogen bonds, the coordination of Ba2+ to hydroxyl groups and 0(5) atoms, and by the stacking interactions between p-nitrophenyl groups [583, 583 a]. 

Discussions then focus on why it is such a challenge for scientists to understand how the simple building blocks of life could have come together to form proteins and DNA. Students are fascinated by the chemical complexity demonstrated by life, and how their own lives are dependent on molecular level processes. They also begin to appreciate the challenges faced by scientists. The role of self-assembly, which was first introduced in discussions on water and inter-molecular Interactions, is also emphasized here in considerations of the secondary structure of proteins and the double-helix of DNA. 

A DNA triple helix contains three strands, two of the DNA double helix, with the third strand winding around the major groove of the DNA double helix forming a triplex. There are two types of triplexes, inter-molecular and intra-molecular, depending on the source of the third... 

Several works have shown that the aggregation of isotactic and syndiotactic chains leads to the formation of stereoeomplexes for which the iso/syndio stoichiometry is found equal to 1/2, probably with a structure composed of a double-stranded helix of a 30/4 helicoidal isotactic chain surroxmded by a 60/4 helicoidal syndiotactic chain. Syndiotactic PMMA self-aggregates exhibit similar structures, with conformations close to extended chains. Experimental data indicate that, in self-aggregated syndiotactic PMMA in solution, some of the ester groups are close in contact, probably in a double helix slructure with solvent molecules included in the cavities of inner- and inter-helices. Isotactic PMMA self-aggregates also exhibit conformational helix structures. 

Chemical denaturation of the double helix at neutral pH can be effected by addition of urea or formamide. These have the effect of disrupting the H-bonding systems which in turn reduces the inter-base hydrophobic forces which otherwise help to stabilise the double helix. These stabilising forces can also be curtailed by the action of alkali which shifts the bases into enol forms (10.70). 

There are enzymes called gyrases and topoisomerases which will assist in the inter-conversion of these forms. The left-handed superhetical form has been observed most frequently moreover, transition from the relaxed circular form appears to favour unwinding of the double helix (Figure 11.38). 

Hydrogen bonding is frequently involved in intercalation and interaction of many drugs with the DNA double helix. Denaturation and separation of the component strands will involve rupture of all the inter-base N-H-0 bonding. 

These data have been combined to suggest a model for gellan gelatin (Figure 3). In the TMA form inter-chain crystallization of gellan fibrils is taken to be suppressed. Helix formation on cooling is considered to promote end-to-end association, via double helix formation, into fibrils. Thickening or bifurcation of these fibrils could arise by a chain end... 

Approximately 75% of DNA alkylations are monofunctional and the cross-linking alkylations account for only 25% of DNA alkylations the relative proportion of these lesions in DNA is constant, and the total number of alkylations in DNA has a linear relationship with SM dose. The ratio of inter- to intra-strand cross-links is 1 2. The significance of inter-strand cross-links between double helix DNA strands is that cell division ceases because DNA polymerase is ineffeetive on such a structure the cross-linking lesions are approximately 10-fold more toxic to the cell than is the case for the monofunctional adducts of SM. The effect of SM on rapidly dividing cells is particularly severe (notably in the gut and bone marrow). ... 

The molecular structure of DNA (double helix) consists of two inter-twined spirals of sugar and phosphate molecules linked by hydrogen-bonded base pairs (see Fig. 1). The phosphate backbone is negatively charged with H- - or Na-t-to balance the neutrality. The width of the double helix is about two nanometres and the length of the DNA molecule depends on the number of base pairs (about a third of a nanometre per base pair). For practical use, natural DNA, derived from salmon milt, which is normally a waste product of the salmon-fishing industry is attractive... 

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