Advances and opportunities in RNA structure experimental determination and computational modeling

J Zhang, Y Fei, L Sun, QC Zhang - Nature methods, 2022 - nature.com
Beyond transferring genetic information, RNAs are molecules with diverse functions that
include catalyzing biochemical reactions and regulating gene expression. Most of these …

Tailor made: the art of therapeutic mRNA design

M Metkar, CS Pepin, MJ Moore - Nature Reviews Drug Discovery, 2024 - nature.com
Abstract mRNA medicine is a new and rapidly developing field in which the delivery of
genetic information in the form of mRNA is used to direct therapeutic protein production in …

RNA methylation influences TDP43 binding and disease pathogenesis in models of amyotrophic lateral sclerosis and frontotemporal dementia

M McMillan, N Gomez, C Hsieh, M Bekier, X Li… - Molecular cell, 2023 - cell.com
RNA methylation at adenosine N6 (m6A) is one of the most common RNA modifications,
impacting RNA stability, transport, and translation. Previous studies uncovered RNA …

m6A readers, writers, erasers, and the m6A epitranscriptome in breast cancer

BJ Petri, CM Klinge - Journal of molecular endocrinology, 2023 - jme.bioscientifica.com
Epitranscriptomic modification of RNA regulates human development, health, and disease.
The true diversity of the transcriptome in breast cancer including chemical modification of …

Integrating experimental data with molecular simulations to investigate RNA structural dynamics

M Bernetti, G Bussi - Current Opinion in Structural Biology, 2023 - Elsevier
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as
nuclear magnetic resonance, cryo-electron microscopy, small-and wide-angle X-ray …

Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects

J Zuber, SJ Schroeder, H Sun, DH Turner… - Nucleic Acids …, 2022 - academic.oup.com
Nearest neighbor parameters for estimating the folding stability of RNA secondary structures
are in widespread use. For helices, current parameters penalize terminal AU base pairs …

Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations

WT Hsu, V Piomponi, PT Merz, G Bussi… - Journal of Chemical …, 2023 - ACS Publications
Performing alchemical transformations, in which one molecular system is nonphysically
changed to another system, is a popular approach adopted in performing free energy …

Advances in RNA 3D structure prediction

X Ou, Y Zhang, Y Xiong, Y Xiao - Journal of Chemical Information …, 2022 - ACS Publications
RNA molecules carry out various cellular functions, and understanding the mechanisms
behind their functions requires the knowledge of their 3D structures. Different types of …

Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions

S Ghosh, S Takahashi, D Banerjee… - Nucleic Acids …, 2023 - academic.oup.com
RNA performs various spatiotemporal functions in living cells. As the solution environments
significantly affect the stability of RNA duplexes, a stability prediction of the RNA duplexes in …

RNA levers and switches controlling viral gene expression

MF Allan, A Brivanlou, S Rouskin - Trends in Biochemical Sciences, 2023 - cell.com
RNA viruses are diverse and abundant pathogens that are responsible for numerous human
diseases. RNA viruses possess relatively compact genomes and have therefore evolved …