Double helix, stability

In some organisms, 5-methy cytosine or 5-hydroxymethylcytosine replaces some of the cytosine. The fact that A = T and G C, and that A -f C = G + T (sum of the amino bases equals the sum of the keto bases) together with X-ray diffraction studies led to the idea that DNA is a double helix stabilized by hydrogen bonding (Fig. 2-12). 

The double helix stability is determined by a longitudinal interaction of neighboring bases, called base stacking, which results from complex interactions ofTt-electron orbitals of the planar bases, dipole, dipole-induced dipole, London dispersion forces, and hydrophobic Interactions. The stability of base stacking is of the order purine-purine > purine-pyrimidine > pyrimidine-pyrimidine. The G/C pairs are more stable than A/T pairs, because they have three hydrogen bonds as opposed to two (Fig. 6.7). Therefore, stacked dimers high in G/C content are energetically preferred to those rich in A/T content (13). 

In our opinion the new concept ( )of sol-gel transition given by Rees and coworkers is not enough to interpret the specific role of counterions in the double helix stabilization and consequently in the gel formation. 

Section 28 8 The most common form of DNA is B DNA which exists as a right handed double helix The carbohydrate-phosphate backbone lies on the outside the punne and pyrimidine bases on the inside The double helix IS stabilized by complementary hydrogen bonding (base pairing) between adenine (A) and thymine (T) and guanine (G) and cytosine (C)... 

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>. 

Fig. 24.—(a) Stereo view of slightly over a turn of the 3-fold double helix of i-carrageenan (23). The two chains are distinguished by open and filled bonds for clarity. The vertical line is the helix axis. Six interchain hydrogen bonds per turn among the galactose residues stabilize the double helix. The sulfate groups lined up near the periphery are crucial for intermolecular 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 stability of the double helix is affected by the GC content. A GC base pair has three hydrogen bonds, while an AT base pair has only two. For this reason, sequences of DNA that are GC-rich form more stable structures than AT-rich regions. 

Hg2 + selectively binds the AT region, apparently due to its great affinity for thymine. Thus, Hg2+ interacts with DNA at nitrogen atoms, replacing hydrogen between the thymine and adenine bases [114]. This interaction results in increased helix stability and an increased diameter of the double helix, approximating the difference between the atomic radius of hydrogen and mercury [116]. 

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