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Updated: Jul 26, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Conformation-based refinement of 18-mer DNA structures
Jakub Svoboda1, Daniel Berdár1, Petr Kolenko1
1Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic.
Abstract:
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.
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