Nucleic acids base pairs, stability

Contrary to H-bonded nucleic acid base pairs discussed in the previous section, the nature of intermolecular interactions in complexes of stacked bases was analyzed more extensively. The values of minimal, maximal, and average total stabilization energies, corrected for BSSE, for a set comprising over 80 stacked bases, are plotted in Fig. 20.1. In the case of guanine-adenine and adenine-cytosine complexes, the results are presented for two sequence contexts, i.e., A/G-G/A and A/C-C/A. The symbol AA denotes the 2-oxo-adenine - complexes of oxidized bases, and this... 

I. Dqbkowska, H.V. Gonzales, P. Jurecka, P. Hobza, Stabilization energies of the hydrogen-bonded and stacked stmctures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5,-d(GCGAAGC)-3 hairpin Complete basis set calculations at the MP2 and CCSD(T) levels. J. Phys. Chem. A 109, 1131-1136 (2005)... 

Although the calculations of the transition energies of different tautomeric forms of molecules have been performed in a few cases, the discussion has been restricted to the difference in electronic absorption band positions and not to the change in relative stabilities of the tautomers caused by electronic excitation. The latter problem, however, has been the subject of a few theoretical considerations for nucleic acid base pairs. Most of these studies were motivated by the need for a potential function for double proton transfer between nucleic acid bases that would allow calculation of proton tunneling probabilities for the Lowdin model of mutagenesis (Lowdin, 1965). 

Leonard, G.A., McAuley-Hecht, K., Brown, T., and Hunter, W.N. (1995) Do C-H- O hydrogen bonds contribute to the stability of nucleic acid base pairs Acta Cryst. D51,136-139. Egli, M. and Gessner, R.V. (1995) Stereoelectronic effects of deoxyribose 04 on DNA... 

Starikov, E.B. and Steiner, T. (1997) Computational support for the suggested contribution of C H- O = C interactions to the stability of nucleic acid base pairs, Acta Cryst. D53,345-347. 

Basis set effect on hydrogen bond stabilization energy estimation of the Watson-Crick type nucleic acid base pairs using medium-size basis sets single point MP2... 

In an aqueous solution, the charge on the backbone makes the strands extremely hydrophilic and soluble however, the aromatic nucleic acid base pairs are much more hydrophobic. Therefore, when a double-stranded duplex forms, the stacked nonpolar base pairs are located at the interior of the structure, reducing contact with water and increasing contact with each other. These net changes in intermolecular forces and balance between hydrophobic and hydrophilic substituents add to the stability of the double helix. 

Danilov VI, Zheltovsky NV, Slyusarchuk ON, Poltev VI, Alderfer JL (1997) The study of the stability of Watson-Crick nucleic acid base pairs in water and dimethyl sulfoxide eom-puter simulation by the Monte Carlo method. J Biomol Struct Dyn 15(l) 69-80... 

In this article, we discussed several rigorous ab initio studies, including our own findings, which had recently put the discussion of the nature of intermolecular interactions in nucleic acid base complexes on quantitative basis. The results of computations summarized herein confirm that H-bonded and stacked base pairs are mainly stabilized by electrostatic/delocalization components and dispersion... 

The rare nucleic acid base tautomers, ordinarily present to the extent of 0.01% relative to the preferred tautomers, can be stabilized by metals via coordination of lone-pair electrons. For example, the 4-imino-2-oxo tautomer of cytosine has Pt + bound to its group, while the 4-hydroxy-2-oxo tautomer of U and T bases is platmated at N-3. ... 

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... 

The bases in nucleic acids can interact via hydrogen bonds. The standard Watson-Crick base pairs are G-C, A T (in DNA), and A U (in RNA). Base pairing stabilizes the native three-dimensional structures of DNA and RNA. 

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