Nucleic acids hydrogen bonding

Sponer J, Jurecka P, Hobza P. Accurate interaction energies of hydrogen-bonded nucleic acid base parrs. J Am Chem Soc 2004 126 10142-10151. 

Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers Complete basis set calculations at the MP2 and CCSD(T) levels ... 

Giese, T. J., Sherer, E. C., Cramer, C. J., and York, D. M. (2005]. A semiempirical quantum model for hydrogen-bonded nucleic acid base pairs,/. Chem. Theory Comput 1(6], 1275-1285. 

Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs. 

This article provides a survey of quantum chemical studies on the structure and properties of isolated DNA bases and their hydrogen-bonded and stacked pairs. Recent developments of computer hardware and software have allowed electron correlation to be considered even for very large systems, leading to a qualitative improvement in the accuracy of calculated properties. Experimental characterization of isolated bases and base pairs is very difficult, and only a limited number of reliable studies are available. There is still only one published gas phase experiment on the energetics of H-bonded nucleic acid bases, from the end of the 1970s, and experimental data on base stacking are absent the same is true for the structure of bases and base pairs. High-level quantum chemical calculations thus represent the only tool to obtain reference data on the structure, properties, and interactions of nucleic acid bases. These data help to properly understand the function and properties of nucleic acids and are exceptionally important for verification and/or parametrization of empirical potentials... 

When thinking about chemical reactivity, chemists usually focus their attention on bonds, the covalent interactions between atoms within individual molecules. Also important, hotvever, particularly in large biomolecules like proteins and nucleic acids, are a variety of interactions between molecules that strongly affect molecular properties. Collectively called either intermolecular forces, van der Waals forces, or noncovalent interactions, they are of several different types dipole-dipole forces, dispersion forces, and hydrogen bonds. 

A hypochromicity was observed between THPVP and APVP (or TPVP). Since theophylline is not a nucleic acid base and does not form hydrogen-bonding, these observations indicate that stacking-type hydrophobic forces are important. 

Poly A form a complex with a 4 1 stoichiometry. The apparent hypochromicities of various mixtures are listed in Table 4. The mixtures of A12 with Poly U and of T12 with Poly A showed large hypochromicities compared with other mixtures, which suggests the importance of the hydrogen-bonding formation between complementary nucleic acid bases such as A-U and T-A. 

Since these basic facts became known, a tremendous amount of research has been done on the structures and behaviors of these important substances. There has also been much research on the synthesis and study of other chain polyelectrolytes, containing hydrogen-bond-forming radicals (R) more-or-less like those in the natural nucleic acids. The primary aim of this research is, of course, to relate the behavior of the synthetic materials to the behavior of the natural ones. Okubo and Ise here present an excellent discussion on this research. 

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