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@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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