Hydroxypyridone and pyridopurine homo- and hetero-base pairs have been investigated in the context of duplex GNA (glycol nucleic acid). Phosphoramidites for automated GNA solid phase synthesis were synthesized economically in a few steps starting from commercially available enantiopure glycidol. Similar to their behavior in DNA, the hydroxypyridone and pyridopurine homo-base pairs display a met...

Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. The study presents reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from -5 to -47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc-pVTZ basis set of ato...

This survey focuses on recent developments in the radiation chemistry of purine bases in nucleic acids and related model compounds. Both direct and indirect effects of ionizing radiation are investigated with special emphasis on the structural characterization of the final decomposition products of nucleic acid components. Available assays for monitoring radiation-induced base lesions are criti...

Nucleosides and nucleotides are powerful building units for creating functional molecules with novel properties. The structural and functional variations of these biomolecules have caused a renaissance of nucleic acid chemistry and biology, and paved the way for fresh avenues in nucleic acid research, including therapeutics, nucleic acid biology, structure-function studies, catalytic and mechan...

The description of the nonbonded contact terms used in simulated annealing refinement can have a major impact on nucleic acid structures generated from NMR data. Using complete dipolar coupling cross-validation, we demonstrate that substantial improvements in coordinate accuracy of NMR structures of RNA can be obtained by making use of two conformational database potentials of mean force: a nuc...

Randall, Charles C. (University of Mississippi School of Medicine, Jackson), Lanelle G. Gafford, and Robert W. Darlington. Bases of the nucleic acid of fowlpox virus and host deoxyribonucleic acid. J. Bacteriol. 83:1037-1041. 1962.-The nucleic acid of fowlpox virus obtained from purified inclusions was identified as deoxyribonucleic acid (DNA). The base ratios determined on whole virus and on i...

We have simulated ionization of purine nucleic acid components in the gas phase and in a water environment. The vertical and adiabatic ionization processes were calculated at the PMP2/aug-cc-pVDZ level with the TDDFT method applied to obtain ionization from the deeper lying orbitals. The water environment was modeled via microsolvation approach and using a nonequilibrium polarizable continuum m...

Structured as a data base and associated with data analysis tools, ACNUC allows both on-line access to a central computer and local exploitation of published nucleotide sequences. Its data retrieval capabilities seem to be presently the most powerful available.

The crystal structure of the duplex formed by oligo(2',3'-dideoxy-beta-d-glucopyranosyl)nucleotides (homo-DNA) revealed strongly inclined backbone and base-pair axes [Egli,M., Pallan,P.S., Pattanayek,R., Wilds,C.J., Lubini,P., Minasov,G., Dobler,M., Leumann,C.J. and Eschenmoser,A. (2006) Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J. Am. Chem....

We present NAFlex, a new web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server allows the user to incorporate structures from protein data banks, completing gaps and removing structural inconsistencies. It is also possible to define canonical (average or sequence-adapted) nucleic acid structures using a variety of predefined internal librari...