Double helix hydrophobic interactions

The DNA double helix is stabilized by hydrophobic interactions resulbng from the individual base pairs stacking on top of each other in the nonpolar interior of the double helix (Figs. 4-1 and 4-2). The hydrogen bonds, like the hydrogen bonds of proteins, contribute somewhat to the overall stability of the double helix but contribute greatly to the specificity for forming the correct base pairs. An incorrect base pair would not... 

The influence of DNA on the photo-electron transfer process between a variety of donor-acceptor couples has been examined during the last ten years. For all the systems studied, the metal complex interacts with the DNA and plays the role of electron acceptor or donor in the hydrophobic DNA microenvironment, whereas the other partner of the process, i.e. the reducing or oxidising agent in the ground state, is localised either on the DNA double helix, or does not interact with the nucleic acid and remains in the aqueous phase. Thus three... 

We encountered the properties of hydrophilic and hydrophobic molecules in our thoughts about driving forces for formation of three-dimensional protein structures. Specifically, proteins fold in a way that puts most of the hydrophobic amino acid side chains into the molecular interior, where they can enjoy each other s company and avoid the dreaded aqueous environment. At the same time, they fold to get the hydrophilic amino acid side chains onto the molecular surface, where they happily interact with that enviromnent. The same ideas are important for the double-stranded helical structure of DNA. The hydrophobic bases are localized within the double hehx, where they interact with each other, and the strongly hydrophilic sugar and phosphate groups are exposed on the exterior of the double helix to the water environment. Now, we need to understand something more about structural features that control these properties. 

Lipophilic compounds, such as the various terpenoids, tend to associate with other hydrophobic molecules in a cell these can be biomembranes or the hydrophobic core of many proteins and of the DNA double helix [10,18,24,25]. In proteins, such hydrophobic and van der Waals interactions can also lead to conformational changes, and thus protein inactivation. A major target for terpenoids, especially saponins, is the biomembrane. Saponins (and, among them, the steroid alkaloids) can change the fluidity of biomembranes, thus reducing their function as a permeation barrier. Saponins can even make cells leaky, and this immediately leads to cell death. This can easily be seen in erythrocytes when they are attacked by saponins these cells burst and release hemoglobin (hemolysis) [1,6,17]. Among alkaloids, steroidal alkaloids (from Solanaceae) and other terpenoids have these properties. 

Since the first crystal structure of IPNS (108), which is an enzyme closely related to the Fe/20G-dependent oxygenases, stractures have been determined for many Fe(II)-/20G-dependent oxygenases, all revealing a consensus core double-stranded P-helix (DSBH) fold or jelly-roll motif (66, 102). Typically this core consists of two four-stranded antiparallel P-sheets, with the major sheet supported by closely packed a-helices. The DSBH core is stabilized even more by internal hydrophobic interactions. The active site and HXD/E... H iron binding motif reside within this core stmcture. Additional or varying stmctural features from the DSBH domain define different structural subfamilies of this class of enzyme (66). 

The structure relies crucially on the pairing up of nucleic acid bases between the two chains. Adenine pairs only with thymine via two hydrogen bonds, whereas guanine pairs only with cytosine via three hydrogen bonds. Thus, a bicyclic purine base is always linked with a smaller monocyclic pyrimidine base to allow the constant diameter of the double helix. The double helix is further stabilized by the fact that the base pairs are stacked one on top of each other, allowing hydrophobic interactions... 

---