Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F86652036%3A_____%2F20%3A00540782" target="_blank" >RIV/86652036:_____/20:00540782 - isvavai.cz</a>

Alternative codes found

RIV/68407700:21340/20:00344563

Result on the web

<a href="https://scripts.iucr.org/cgi-bin/paper?S2059798320014151" target="_blank" >https://scripts.iucr.org/cgi-bin/paper?S2059798320014151</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1107/S2059798320014151" target="_blank" >10.1107/S2059798320014151</a>

Result language

angličtina

Original language name

Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches

Original language description

Solution and crystal data are reported for DNA 18-mers with sequences related to those of bacterial noncoding single-stranded DNA segments called repetitive extragenic palindromes (REPs). Solution CD and melting data showed that the CG-rich, near-palindromic REPs from various bacterial species exhibit dynamic temperature-dependent and concentration-dependent equilibria, including architectures compatible with not only hairpins, which are expected to be biologically relevant, but also antiparallel duplexes and bimolecular tetraplexes. Three 18-mer oligonucleotides named Hpar-18 (PDB entry 6rou), Chom-18 (PDB entry 6ros) and its brominated variant Chom-18Br (PDB entry 6ror) crystallized as isomorphic right-handed A-like duplexes. The low-resolution crystal structures were solved with the help of experimental phases for Chom-18Br. The center of the duplexes is formed by two successive T-T noncanonical base pairs (mismatches). They do not deform the double-helical geometry. The presence of T-T mismatches prompted an analysis of the geometries of these and other noncanonical pairs in other DNA crystals in terms of their fit to the experimental electron densities (RSCC) and their geometric fit to the NtC (dinucleotide conformational) classes (https://dnatco.datmos.org/). Throughout this work, knowledge of the NtC classes was used to refine and validate the crystal structures, and to analyze the mismatches.

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

10609 - Biochemical research methods

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2020

Confidentiality

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

Name of the periodical

Acta Crystallographica Section D-Structural Biology

ISSN

2059-7983

e-ISSN

—

Volume of the periodical

76

Issue of the periodical within the volume

DEC 1 2020

Country of publishing house

GB - UNITED KINGDOM

Number of pages

11

Pages from-to

1233-1243

UT code for WoS article

000596508400009

EID of the result in the Scopus database

2-s2.0-85097034095