Conformation-based refinement of 18-mer DNA structures
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68407700%3A21340%2F23%3A00367358" target="_blank" >RIV/68407700:21340/23:00367358 - isvavai.cz</a>
Result on the web
<a href="https://doi.org/10.1107/S2059798323004679" target="_blank" >https://doi.org/10.1107/S2059798323004679</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1107/S2059798323004679" target="_blank" >10.1107/S2059798323004679</a>
Alternative languages
Result language
angličtina
Original language name
Conformation-based refinement of 18-mer DNA structures
Original language 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.
Czech name
—
Czech description
—
Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10610 - Biophysics
Result continuities
Project
—
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Acta Crystallographica Section D: Structural Biology
ISSN
2059-7983
e-ISSN
—
Volume of the periodical
79
Issue of the periodical within the volume
7
Country of publishing house
GB - UNITED KINGDOM
Number of pages
11
Pages from-to
655-665
UT code for WoS article
001020462200010
EID of the result in the Scopus database
2-s2.0-85164062188