Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes

J 2018

Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes

ŠPAČKOVÁ, Naděžda a Kamila RÉBLOVÁ

Základní údaje

Originální název

Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes

Autoři

ŠPAČKOVÁ, Naděžda (203 Česká republika, domácí) a Kamila RÉBLOVÁ (203 Česká republika, garant, domácí)

Vydání

GENES, BASEL, MDPI AG, 2018, 2073-4425

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

30101 Human genetics

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.331

Kód RIV

RIV/00216224:14740/18:00101215

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.3390/genes9070324

UT WoS

000445149700011

Klíčová slova anglicky

adenosine to inosine editing; dsRNA; molecular dynamics simulations; I-U base pairs

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 13. 3. 2019 16:52, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Adenosine to inosine (A-I) editing is the most common modification of double-stranded RNA (dsRNA). This change is mediated by adenosine deaminases acting on RNA (ADARs) enzymes with a preference of U>A>C>G for 5' neighbor and G>C=A>U or G>C>U=A for 3' neighbor. A-I editing occurs most frequently in the non-coding regions containing repetitive elements such as ALUs. It leads to disruption of RNA duplex structure, which prevents induction of innate immune response. We employed standard and biased molecular dynamics (MD) simulations to analyze the behavior of RNA duplexes with single and tandem inosine-uracil (I-U) base pairs in different sequence context. Our analysis showed that the I-U pairs induce changes in base pair and base pair step parameters and have different dynamics when compared with standard canonical base pairs. In particular, the first I-U pair from tandem I-U/I-U systems exhibited increased dynamics depending on its neighboring 5' base. We discovered that UII sequence, which is frequently edited, has lower flexibility compared with other sequences (AII, GII, CII), hence it only modestly disrupts dsRNA. This might indicate that the UAA motifs in ALUs do not have to be sufficiently effective in preventing immune signaling.

Návaznosti

GA16-11619S, projekt VaV

Název: Základní vlastnosti DNA mutačních coldspotů/hotspotů v genech asociovaných s dědičnými chorobami

Investor: Grantová agentura ČR, Základní vlastnosti DNA mutačních coldspotů/hotspotů v genech asociovaných s dědičnými chorobami

LM2015085, projekt VaV

Název: CERIT Scientific Cloud (Akronym: CERIT-SC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CERIT Scientific Cloud

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

ŠPAČKOVÁ, Naděžda a Kamila RÉBLOVÁ. Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes. GENES. BASEL: MDPI AG, 2018, roč. 9, č. 7, s. 324-337. ISSN 2073-4425. Dostupné z: https://dx.doi.org/10.3390/genes9070324.

@article{1442921,
   author = {Špačková, Naděžda and Réblová, Kamila},
   article_location = {BASEL},
   article_number = {7},
   doi = {http://dx.doi.org/10.3390/genes9070324},
   keywords = {adenosine to inosine editing; dsRNA; molecular dynamics simulations; I-U base pairs},
   language = {eng},
   issn = {2073-4425},
   journal = {GENES},
   title = {Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes},
   url = {https://www.mdpi.com/2073-4425/9/7/324},
   volume = {9},
   year = {2018}
}

TY  - JOUR
ID  - 1442921
AU  - Špačková, Naděžda - Réblová, Kamila
PY  - 2018
TI  - Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes
JF  - GENES
VL  - 9
IS  - 7
SP  - 324
EP  - 324
PB  - MDPI AG
SN  - 20734425
KW  - adenosine to inosine editing
KW  - dsRNA
KW  - molecular dynamics simulations
KW  - I-U base pairs
UR  - https://www.mdpi.com/2073-4425/9/7/324
N2  - Adenosine to inosine (A-I) editing is the most common modification of double-stranded RNA (dsRNA). This change is mediated by adenosine deaminases acting on RNA (ADARs) enzymes with a preference of U>A>C>G for 5' neighbor and G>C=A>U or G>C>U=A for 3' neighbor. A-I editing occurs most frequently in the non-coding regions containing repetitive elements such as ALUs. It leads to disruption of RNA duplex structure, which prevents induction of innate immune response. We employed standard and biased molecular dynamics (MD) simulations to analyze the behavior of RNA duplexes with single and tandem inosine-uracil (I-U) base pairs in different sequence context. Our analysis showed that the I-U pairs induce changes in base pair and base pair step parameters and have different dynamics when compared with standard canonical base pairs. In particular, the first I-U pair from tandem I-U/I-U systems exhibited increased dynamics depending on its neighboring 5' base. We discovered that UII sequence, which is frequently edited, has lower flexibility compared with other sequences (AII, GII, CII), hence it only modestly disrupts dsRNA. This might indicate that the UAA motifs in ALUs do not have to be sufficiently effective in preventing immune signaling.
ER  -

ŠPAČKOVÁ, Naděžda a Kamila RÉBLOVÁ. Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes. \textit{GENES}. BASEL: MDPI AG, 2018, roč.~9, č.~7, s.~324-337. ISSN~2073-4425. Dostupné z: https://dx.doi.org/10.3390/genes9070324.

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