Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3′-UTR of the SARS-CoV-2 genomic RNA
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F24%3A00587348" target="_blank" >RIV/68081707:_____/24:00587348 - isvavai.cz</a>
Result on the web
<a href="https://academic.oup.com/nar/article/52/11/6687/7680630?login=true" target="_blank" >https://academic.oup.com/nar/article/52/11/6687/7680630?login=true</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/nar/gkae349" target="_blank" >10.1093/nar/gkae349</a>
Alternative languages
Result language
angličtina
Original language name
Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3′-UTR of the SARS-CoV-2 genomic RNA
Original language description
The single-stranded RNA genome of SARS-CoV-2 is highly structured. Numerous helical stem-loop structures interrupted by mismatch motifs are present in the functionally important 5 '- and 3 '-UTRs. These mismatches modulate local helical geometries and feature unusual arrays of hydrogen bonding donor and acceptor groups. However, their conformational and dynamical properties cannot be directly inferred from chemical probing and are difficult to predict theoretically. A mismatch motif (SL1-motif) consisting of three consecutive U center dot U base pairs is located in stem-loop 1 of the 3 '-UTR. We combined NMR-spectroscopy and MD-simulations to investigate its structure and dynamics. All three U center dot U base pairs feature two direct hydrogen bonds and are as stable as Watson-Crick A:U base pairs. Plasmodium falciparum 25S rRNA contains a triple U center dot U mismatch motif (Pf-motif) differing from SL1-motif only with respect to the orientation of the two closing base pairs. Interestingly, while the geometry of the outer two U center dot U mismatches was identical in both motifs the preferred orientation of the central U center dot U mismatch was different. MD simulations and potassium ion titrations revealed that the potassium ion-binding mode to the major groove is connected to the different preferred geometries of the central base pair in the two motifs.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10608 - Biochemistry and molecular biology
Result continuities
Project
<a href="/en/project/GA23-05639S" target="_blank" >GA23-05639S: Molecular dynamics simulations of RNA: from static structures to molecular ensembles</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Nucleic Acids Research
ISSN
0305-1048
e-ISSN
1362-4962
Volume of the periodical
52
Issue of the periodical within the volume
11
Country of publishing house
US - UNITED STATES
Number of pages
20
Pages from-to
6687-6706
UT code for WoS article
001230005600001
EID of the result in the Scopus database
2-s2.0-85196836622