Structural dynamics of propeller loop: towards folding of RNA G-quadruplex

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F18%3A00502419" target="_blank" >RIV/68081707:_____/18:00502419 - isvavai.cz</a>

Alternative codes found

RIV/61989592:15310/18:73590979

Result on the web

<a href="http://dx.doi.org/10.1093/nar/gky712" target="_blank" >http://dx.doi.org/10.1093/nar/gky712</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gky712" target="_blank" >10.1093/nar/gky712</a>

Result language

angličtina

Original language name

Structural dynamics of propeller loop: towards folding of RNA G-quadruplex

Original language description

We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 mu s) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged with the unfolded state via an ensemble of cross-like structures (CS) possessing mutually tilted or perpendicular G-strands interacting via guanine-guanine H-bonding. The oligonucleotides reach the PH conformation from the unfolded state via a conformational diffusion through the folding landscape, i.e. as a series of rearrangements of the H-bond interactions starting from compacted anti-parallel hairpin-like structures. Although isolated PHs do not appear to be thermodynamically stable we suggest that CS and PH-types of structures are sufficiently populated during RNA guanine quadruplex (GQ) folding within the context of complete GQ-forming sequences. These structures may participate in compact coil-like ensembles that involve all four G-strands and already some bound ions. Such ensembles can then rearrange into the fully folded parallel GQs via conformational diffusion. We propose that the basic atomistic folding mechanism of propeller loops suggested in this work may be common for their formation in RNA and DNA GQs.

Czech name

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Czech description

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Type

J_imp - 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

Project

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

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2018

Confidentiality

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

Name of the periodical

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

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Volume of the periodical

46

Issue of the periodical within the volume

17

Country of publishing house

GB - UNITED KINGDOM

Number of pages

18

Pages from-to

8754-8771

UT code for WoS article

000450952000015

EID of the result in the Scopus database

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