Feb 03 2022 Cyclization studies of Japanese encephalitis virus non-coding RNA terminal regions

Japanese encephalitis virus genome cyclization is kinetically driven (PREPRINT)

Abstract

Many flaviviruses such as Dengue and West Nile virus undergo essential long-range interactions of their 5’ and 3’ terminal regions (TRs), mediated by a conserved complementary cyclization sequence. However, we lack insights into such long-range interactions for the Japanese Encephalitis virus (JEV). Here, we utilized an extensive, multi-faceted approach involving computational and biophysical tools. We performed multi-angle light scattering (SEC-MALS) to determine absolute molecular weights of JEV TRs, and their complex concluding they form a 1:1 complex and corroborated this interaction using analytical ultracentrifugation (AUC). The microscale thermophoresis (MST) experiments demonstrated that the 5’ and 3’ TR of JEV interact with nM affinity, which is significantly reduced without the conserved cyclization sequence. To our knowledge, this is the first study representing the application of three key biophysical methods (AUC, MST and SEC-MALS) to study RNA-RNA interactions. Furthermore, we performed computational kinetic analyses corroborating our MST studies showing the essential role of the cyclization sequence in the RNA-RNA interaction. The binding affinity of this biologically critical event is a vital pharmacological feature that can influence potential competitive inhibition by therapeutics. This evidence can also influence pharmaceutical interventions aimed at inhibiting the conserved flavivirus cyclization, thus, interrupting replication across the flavivirus family.

Jan 20 2022 Biophysical Characterisation of Human LincRNA-p21 Sense and Antisense Alu Inverted Repeats

LincRNA-p21 structure determined with biophysical and computational approaches (PREPRINT)

Dec 17 2021 Pervasive non-coding RNA structure conservation and molecular epidemiology of TBEV

RNA structure conservation and molecular epidemiology of Tick-borne encephalitis virus (PREPRINT)

Dec 16 2021 Caveats to deep learning approaches to RNA secondary structure prediction

How good are modern machine learning approaches in predicting the pairing potential of RNA (PREPRINT)

Sep 02 2021 Functional RNA Structures in the 3’UTR of Mosquito-Borne Flaviviruses

You might have heard of Zika virus, Dengue virus, West Nile virus, or Japanese encephalitis virus

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