Hydrogen bonding nucleic acid base pairs

Sponer J, Jurecka P, Hobza P (2004) Accurate interaction energies of hydrogen-bonded nucleic acid base pairs, J Am Chem Soc, 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. 

The nucleic acids known as deoxyribonucleic acid (DNA) are the molecules that store genetic information. This information is carried as a sequence of bases in the polymeric molecule. Remarkably, the interpretation of this sequence depends upon simple hydrogen bonding interactions between base pairs. Hydrogen bonding is fundamental to the double helix arrangement of the DNA molecule, and the translation and transcription via ribonucleic acid (RNA) of the genetic information present in the DNA molecule. 

Where nucleic acids are concerned, the enhanced hydrophobicity of abiotic polyfluorinated aromatic bases (e.g., tetrafluorobenzene or tetrafluoroindole deoxyribose derivatives) was exploited as an alternative to natural hydrogen bonding to achieve selective and stable nucleic acid base pairing in duplex DNA [85], The DNA replication was examined using polyfluorinated-nucleotide analogs as substrates. A DNA polymerase active site was able to process the polyfluorinated base pairs more effectively than the analogous hydrocarbon pairs, demonstrating hydrophobic selectivity of polyfluorinated bases for other polyfluorinated bases [86]. 

Hartree-Fock study of hydrogen-bonded systems in the absence of basis-set superposition error the nucleic-acid base pairs 313... 

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)... 

M. Elstner, P. Hobza, T. Frauenheim, S. Suhai, E. Kaxiras, Hydrogen bonding and stacking interactions of nucleic acid base pairs A density-functional-theory based treatment. J. Chem. Phys. 114, 5149-5155 (2001)... 

The structure of the DNA molecule is basically determined by nucleic acid base interactions. Although the three-dimensional double helix structure of DNA is influenced by various contributions, the hydrogen bonding in DNA base pairs is of particuar importance. Because it is difficult to obtain gas phase experimental data for isolated base pair characterisation (only a limited number of experimental studies are available [21]) quantum chemical calculations can represent a useful tool to obtain reference data on the structure, properties and interactions of nucleic acid pairs. Theoretical studies can help us to understand the properties of nucleic acids and they are fundamental for verification... 

In all these events, the hydrogen-bonded Watson-Crick base pair is operative and is responsible for DNA reduplication, transcription, and translation. Since mispairing can occur, all these processes are checked for fidelity by several enzymes which can correct for errors [6521. At this and all other levels of DNA reduplication and protein biosynthesis, intermolecular hydrogen bonds between nucleic acids and between nucleic acids and proteins are responsible for recognition, interaction, and, finally, for information transfer. 

Turner DH, Sugimoto N, Kierzek R, Dreiker SD. Free energy increments for hydrogen bonds in nucleic acid base pairs. J. Am. 

In related work, Riley and Hobza have provided an assessment of the MP2 method in conjunction with several medium and extended basis sets in the study of various hydrogen bonded and dispersion bound complexes of biological relevance. They report that the MP2/cc-pVTZ method supports the most well balanced description of noncovalent interactions. However, the MP2 method does not provide reliable results for the cyclic hydrogen bonds found in nucleic acid base pairs in combination with any of the basis sets considered by these authors. 

Some experimental evidence for a DPT process in the excited state leading to tautomerization not observed in the ground state has been reported (Chang et al., 1980 Sepiol and Wild, 1982) for solutions of 1-azacarbazole in 3-methylpentane and mixed l-azacarbazole/7-azaindol solutions in the same solvent. For these systems the tautomeric forms that are unstable in the ground state are formed adiabatically from the excited state hydrogen-bonded dimers via a DPT and detected in the fluorescence spectra. These results are especially relevant to excited state DPT processes possible for nucleic acid base pairs. Clearly, further experimental and theoretical studies on heterocyclic dimer systems are needed. 

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... 

---