Cytosine Denaturation

Nucleic acids can be denatured by heat, as proteins can. What bonds are broken when a DNA molecule is denatured Would DNA of greater percent composition of guanine and cytosine denature more or less readily than DNA of greater percent composition of adenine and thymine ... 

The DNA structure involves two polyanionic phosphodiester strands linked together by hydrogen bonding of base pairs. The strands can be separated by a denaturation process (melting). The melting temperatnre increases with an increase in guanine (G)-cytosine (C) content, since this base pair possess three hydrogen bonds as compared to just two for the adenine (A)-thymine (T) pair. 

Earlier studies using thermal denaturation analysis and spectrophotomet-ric titration with TxA T and CxC-C" containing DNA triplexes showed that coralyne binds strongly to these triplexes by intercalation and does not exhibit a significant sequence-selectivity [222]. In a later study by Morau Allen et al. [217], employing DNase footprinting, thermal denaturation analysis, UV-visible spectrophotometric titrations, circular dichroism and NMR spectroscopy, showed that coralyne is fully intercalated into TxA T triplex DNA whereas in C GxC triplex, it is partially intercalated due to electrostatic repulsion between the cationic alkaloid and the protonated cytosine [217]. Kepler et al. [223] demonstrated that coralyne intercalated to parallel triplex DNA but did not intercalate to antiparallel triplex DNA. Recently Hud and coworkers [219,224] demonstrated that duplex poly(dA) poly(dT) is trans-... 

As with proteins, the nucleic acid polymers can denature, and they have secondary structure. In DNA, two nucleic acid polymer chains are twisted together with their bases facing inward to form a double helix. In doing so, the bases shield their hydrophobic components from the solvent, and they form hydrogen bonds in one of only two specific patterns, called base pairs. Adenine hydrogen bonds only with thymine (or uracil in RNA), and guanine pairs only with cytosine. Essentially every base is part of a base pair in DNA, but only some of the bases in RNA are paired. The double-helix structure... 

Fig. 26. Nucleic acid structures. A The structure of the four bases in DNA, guanine (G), cytosine (C) adenine (A) and thymine (T). Uracil (U) replaces thymine (T) in RNA. B The spontaneous attraction of A for T and C for G allows the recognition of homologous sequences in aqueous solutions and the strong and specific hybridization of one sequence with its homologous sequence. C DNA forms a double helix at body temperature, which can be denatured to separate the strands by heating. D single stranded mRNA structure.

Dependence of the temperature midpoint (Tm) of DNA on the content of guanine and cytosine. As the percentage of G + C increases, the Tm increases. Two curves are shown to illustrate the point that the denaturation temperature is shifted to lower values when the ionic strength is lowered. 

Moreover, natural nucleic acids give rise to two well-separated oxidation peaks in differential pulse voltammograms, which can be used to probe individual adenine-thymine (AT) and guanine-cytosine (GC) pairs in double helical DNA during its conformational changes [38]. Differences in signals obtained at carbon electrodes were observed according to whether, or not, the DNA was denatured [39]. 

Berg et al. 711 proposed that the adenine and cytosine residues in native DNA are reduced by a so-called electron hopping mechanism, the only condition for this being adsorption of protonated DNA at the electrode surface at the reduction potential of these bases. It was also assumed that the DNA is adsorbed in its A-form, exhibiting semi-conducting properties. There is consequently no surface denaturation of the DNA. 

Mitochondria are about the size of bacteria. They have a diameter of 0.2 to 0.5 gm and are 0.5 to 7 p.m long. They are bounded by two lipid bilayers, the inner one being highly folded. These folds are called cristae. The innermost space of the mitochondrion is called the matrix. They have their own DNA in the form of at least one copy of a circular double helix (Chap. 7), about 5 p.m in overall diameter it differs from nuclear DNA in its density and denaturation temperature by virtue of being richer in guanosine and cytosine (Chap. 7). The different density from nuclear DNA allows its separation by isopycnic centrifugation. Mitochondria also have their own type of ribosomes that differ from those in the cytoplasm but are similar to those of bacteria. 

The cytosine-guanine base pah with its three hydrogen bonds is more stable than the adenine-thymine base pah. The more CG bp there are, the more stable the DNA molecule. Structure b, with the least number of CG bp, will therefore denature first... 

Problem 21.57. At high temperatures, deoxynucleic acids become denatured, i.e., they unwind from double helices into disordered single strands. Account for the fact that the higher the content of guanine-cytosine base pairs relative to adenine-thymine base pairs, the higher the temperature required to denature a DNA double helix. 

Apilux, A., Tabata, M., Chailapakul, O. (2007). Electrochemical behaviors of native and thermally denatured fish DNA in the presence of cytosine derivatives and porphyrin by cyclic voltammetry using boron-doped diamond electrode. Bioelectrochemistry 70, 435-439. 

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