Conformation-based refinement of 18-mer DNA structures

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

Conformation-based refinement of 18-mer DNA structures

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Conformation-based refinement of 18-mer DNA structures

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

<a href="/cs/project/LTAUSA18197" target="_blank" >LTAUSA18197: Návrh, vývoj a testování bioinformatických nástrojů pro hodnocení kvality experimentálních a počítačových molekulárních modelů ve strukturní biologii, biotechnologii a farmacii</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2023

Kód důvěrnosti údajů

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

Název periodika

Acta Crystallographica Section D-Biological Crystallography

ISSN

1399-0047

e-ISSN

2059-7983

Svazek periodika

79

Číslo periodika v rámci svazku

JUL 2023

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

11

Strana od-do

655-665

Kód UT WoS článku

001020462200010

EID výsledku v databázi Scopus

2-s2.0-85164062188