Double helix electrostatic interactions

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]. 

Two examples of aquation/anation studies of chloro-platinum(II) complexes of possible medical relevance appeared in subsection 1 above 202,207). Aquation of cisplatin is slower in the presence of DNA but not in the presence of phosphate 220). DNA also inhibits substitution in [Pt(terpy)(py)]2+ and related complexes. For reaction of these charged complexes with iodide ion inhibition is attributable to electrostatic interactions - the complex is concentrated on the double helix and thus separated from the iodide, which distances itself from the helix. Intercalation of these complexes within the helix also serves to make nucleophilic approach by neutral reagents such as thiourea more difficult 221). 

De Mendoza reported the first example of anion-directed helix formation in 1996 [91]. The assembly of this helical structure relies, not only on electrostatic interactions between the anionic template and the positively charged strands, but also on hydrogen bonding. The tetraguanidinium strand 69 (see Scheme 34) self-assembles around a sulfate anion via hydrogen bonding to produce a double helical structure. The formation of this assembly and its anion-dependence was proposed on the basis of NMR and CD spectroscopic studies. 

The external binding mode (Fig. 5) is due mostly to the electrostatic interaction of cations with the negatively charged phosphate backbone at the periphery of the double helix [33]. 

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 different structural forms of the double helix lead to different dynamic interactions, and the geometry of the grooves is important in allowing or preventing access to the bases. Electrostatic interactions play a crucial role in the transition between right-handed B-DNA and left-handed Z-DNA [8], which is one of the best characterized conformational changes in double-stranded DNA. 

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. 

Noncovalent Bonds. Noncovalent bonds are weaker than covalent bonds but arc crucial for biochemical processes such as the formation of a double helix, hour lundamental noncovalent bond types are electrostatic interactions, hydrot en bonds, van der Waals interactions, and hydrophobic inlerac-turns. T hey differ in geometry, strength, and specificity. Furthermore, these bunds are allected in vastly different ways by the presence of water. Let us consider the characteristics of each ... 

Figure 1.13 Electrostatic interactions in DNA. Each unit within the double helix includes a phosphate group (the phosphor us atom being shown in purple) that bears a negative charge. 

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