Nine new crystal structures of CG-rich DNA 18-mers with the sequence 5'-GGTGGGGGC-XZ-GCCCCACC-3', which are related to the bacterial repetitive extragenic palindromes, are reported. 18-mer oligonucleotides with the central XZ dinucleotide systematically mutated to all 16 sequences show complex behavior in solution, but all ten so far successfully crystallized 18-mers crystallized as A-form duplexes. The refinement protocol benefited from the recurrent use of geometries of the dinucleotide conformer (NtC) classes as refinement restraints in regions of poor electron density. The restraints are automatically generated at the dnatco.datmos.org web service and are available for download. This NtC-driven protocol significantly helped to stabilize the structure refinement. The NtC-driven refinement protocol can be adapted to other low-resolution data such as cryo-EM maps. To test the quality of the final structural models, a novel validation method based on comparison of the electron density and conformational similarity to the NtC classes was employed.

• Keywords
• DNA structure, base pairing, dnatco.datmos.org, structure refinement, structure validation,
• MeSH
• DNA * chemistry   MeSH
• Cryoelectron Microscopy methods   MeSH
• Nucleic Acid Conformation MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA * MeSH

A detailed description of the dnatco.datmos.org web server implementing the universal structural alphabet of nucleic acids is presented. It is capable of processing any mmCIF- or PDB-formatted files containing DNA or RNA molecules; these can either be uploaded by the user or supplied as the wwPDB or PDB-REDO structural database access code. The web server performs an assignment of the nucleic acid conformations and presents the results for the intuitive annotation, validation, modeling and refinement of nucleic acids.

• Keywords
• annotation, nucleic acids, refinement, structural alphabets, validation,
• MeSH
• Databases, Nucleic Acid MeSH
• DNA chemistry   MeSH
• Internet MeSH
• Nucleic Acid Conformation MeSH
• Models, Molecular MeSH
• RNA chemistry   MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA MeSH
• RNA MeSH