Conformation-based refinement of 18-mer DNA structures

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F86652036%3A_____%2F23%3A00574529" target="_blank" >RIV/86652036:_____/23:00574529 - isvavai.cz</a>

Result on the web

<a href="https://scripts.iucr.org/cgi-bin/paper?S2059798323004679" target="_blank" >https://scripts.iucr.org/cgi-bin/paper?S2059798323004679</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1107/S2059798323004679" target="_blank" >10.1107/S2059798323004679</a>

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

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10608 - Biochemistry and molecular biology

Project

<a href="/en/project/LTAUSA18197" target="_blank" >LTAUSA18197: Design, development, and testing of bioinformatic tools for validation of experimental and computer molecular models in structural biology, biotechnology and pharmacy</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Acta Crystallographica Section D-Biological Crystallography

ISSN

1399-0047

e-ISSN

2059-7983

Volume of the periodical

79

Issue of the periodical within the volume

JUL 2023

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