Cargando…
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...
Autores principales: | , , , , , , |
---|---|
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 |
_version_ | 1785065861865799680 |
---|---|
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. |
format | Online Article Text |
id | pubmed-10306069 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT svobodajakub conformationbasedrefinementof18merdnastructures AT berdardaniel conformationbasedrefinementof18merdnastructures AT kolenkopetr conformationbasedrefinementof18merdnastructures AT cernyjiri conformationbasedrefinementof18merdnastructures AT novakovazora conformationbasedrefinementof18merdnastructures AT pavlicekjiri conformationbasedrefinementof18merdnastructures AT schneiderbohdan conformationbasedrefinementof18merdnastructures |