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Conformation-based refinement of 18-mer DNA structures

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 behav...

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Autores principales: Svoboda, Jakub, Berdár, Daniel, Kolenko, Petr, Černý, Jiří, Nováková, Zora, Pavlíček, Jiří, Schneider, Bohdan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10306069/
https://www.ncbi.nlm.nih.gov/pubmed/37338420
http://dx.doi.org/10.1107/S2059798323004679
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author Svoboda, Jakub
Berdár, Daniel
Kolenko, Petr
Černý, Jiří
Nováková, Zora
Pavlíček, Jiří
Schneider, Bohdan
author_facet Svoboda, Jakub
Berdár, Daniel
Kolenko, Petr
Černý, Jiří
Nováková, Zora
Pavlíček, Jiří
Schneider, Bohdan
author_sort Svoboda, Jakub
collection PubMed
description 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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spelling pubmed-103060692023-06-29 Conformation-based refinement of 18-mer DNA structures Svoboda, Jakub Berdár, Daniel Kolenko, Petr Černý, Jiří Nováková, Zora Pavlíček, Jiří Schneider, Bohdan Acta Crystallogr D Struct Biol Research Papers 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. International Union of Crystallography 2023-06-20 /pmc/articles/PMC10306069/ /pubmed/37338420 http://dx.doi.org/10.1107/S2059798323004679 Text en © Jakub Svoboda et al. 2023 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Research Papers
Svoboda, Jakub
Berdár, Daniel
Kolenko, Petr
Černý, Jiří
Nováková, Zora
Pavlíček, Jiří
Schneider, Bohdan
Conformation-based refinement of 18-mer DNA structures
title Conformation-based refinement of 18-mer DNA structures
title_full Conformation-based refinement of 18-mer DNA structures
title_fullStr Conformation-based refinement of 18-mer DNA structures
title_full_unstemmed Conformation-based refinement of 18-mer DNA structures
title_short Conformation-based refinement of 18-mer DNA structures
title_sort conformation-based refinement of 18-mer dna structures
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10306069/
https://www.ncbi.nlm.nih.gov/pubmed/37338420
http://dx.doi.org/10.1107/S2059798323004679
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