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A DNA structural alphabet provides new insight into DNA flexibility
DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786007/ https://www.ncbi.nlm.nih.gov/pubmed/29372899 http://dx.doi.org/10.1107/S2059798318000050 |
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author | Schneider, Bohdan Božíková, Paulína Nečasová, Iva Čech, Petr Svozil, Daniel Černý, Jiří |
author_facet | Schneider, Bohdan Božíková, Paulína Nečasová, Iva Čech, Petr Svozil, Daniel Černý, Jiří |
author_sort | Schneider, Bohdan |
collection | PubMed |
description | DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson–Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website https://dnatco.org, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:2. |
format | Online Article Text |
id | pubmed-5786007 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-57860072018-02-07 A DNA structural alphabet provides new insight into DNA flexibility Schneider, Bohdan Božíková, Paulína Nečasová, Iva Čech, Petr Svozil, Daniel Černý, Jiří Acta Crystallogr D Struct Biol Research Papers DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson–Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website https://dnatco.org, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:2. International Union of Crystallography 2018-01-01 /pmc/articles/PMC5786007/ /pubmed/29372899 http://dx.doi.org/10.1107/S2059798318000050 Text en © Schneider et al. 2018 http://creativecommons.org/licenses/by/2.0/uk/ 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.http://creativecommons.org/licenses/by/2.0/uk/ |
spellingShingle | Research Papers Schneider, Bohdan Božíková, Paulína Nečasová, Iva Čech, Petr Svozil, Daniel Černý, Jiří A DNA structural alphabet provides new insight into DNA flexibility |
title | A DNA structural alphabet provides new insight into DNA flexibility |
title_full | A DNA structural alphabet provides new insight into DNA flexibility |
title_fullStr | A DNA structural alphabet provides new insight into DNA flexibility |
title_full_unstemmed | A DNA structural alphabet provides new insight into DNA flexibility |
title_short | A DNA structural alphabet provides new insight into DNA flexibility |
title_sort | dna structural alphabet provides new insight into dna flexibility |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786007/ https://www.ncbi.nlm.nih.gov/pubmed/29372899 http://dx.doi.org/10.1107/S2059798318000050 |
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