Results 131 to 140 of about 14,795 (267)

Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation

Scientific Reports, 2016
Minus-one ribosomal frameshifting is a translational recoding mechanism widely utilized by many RNA viruses to generate accurate ratios of structural and catalytic proteins. An RNA pseudoknot structure located in the overlapping region of the gag and pro
Zhensheng Zhong, Lixia Yang, Haiping Zhang, Jiahao Shi, J. J. Vandana, Do Thuy Uyen Ha Lam, R. Olsthoorn, Lanyuan Lu, Gang Chen   +8 more
semanticscholar   +1 more source

Exploring the Potential and Advancements of Circular RNA Therapeutics

Exploration, Volume 5, Issue 4, August 2025.
Given the remarkable advantages in terms of stability, sustained expression profile, safety, wide range of druggable targets, scalable and cost‐effective manufacturing capabilities, circRNA is currently undergoing intensive investigation for various therapeutic applications such as vaccines, protein replacement, genetic disease treatment, gene therapy,
Lei Wang, Lianqing Wang, Chunbo Dong, Jialong Liu, Guoxin Cui, Shan Gao, Zhida Liu   +6 more
wiley   +1 more source

An Ancient Pseudoknot in TNF-α Pre-mRNA Activates PKR, Inducing eIF2α Phosphorylation that Potently Enhances Splicing

Cell Reports, 2017
Tumor necrosis factor alpha (TNF-α) is expressed promptly during inflammatory responses. Efficient TNF-α mRNA splicing is achieved through a 3′ UTR element that activates RNA-dependent eIF2α protein kinase (PKR).
Lise Sarah Namer, Farhat Osman, Yona Banai, Benoît Masquida, Rodrigo Jung, Raymond Kaempfer   +5 more
doaj   +1 more source

Ab initio RNA folding

, 2014
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray crystallography and
Cragnolini, Tristan, Derreumaux, Philippe, Pasquali, Samuela   +2 more
core   +1 more source

Machine Learning‐Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands

Angewandte Chemie, Volume 137, Issue 31, July 28, 2025.
This study combines computational and experimental approaches to study how natural and synthetic small molecules interact with the ZTP riboswitch, a bacterial RNA element that regulates gene expression. Using chemical synthesis, biochemical approaches, and artificial intelligence augmented MD simulations, we analyze both ligand binding and riboswitch ...
Christopher R. Fullenkamp, Shams Mehdi, Christopher P. Jones, Logan Tenney, Patricio Pichling, Peri R. Prestwood, Adrian R. Ferré‐D'Amaré, Pratyush Tiwary, John S. Schneekloth   +8 more
wiley   +1 more source

Pseudoknot Identification through Learning TAGRNA [PDF]

, 2008
Studying the structure of RNA sequences is an important problem that helps in understanding the functional properties of RNA. Pseudoknot is one type of RNA structures that cannot be modeled with Context Free Grammars (CFG) because it exhibits crossing dependencies.
Seesi, Sahar Al, Rajasekaran, Sanguthevar, Ammar, Reda   +2 more
openaire   +1 more source

Use of RNA secondary structure for evolutionary relationships : investigating RNase P and RNase MRP : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University, New Zealand [PDF]

, 1998
Bioinformatics is applied here to examine whether RNA secondary structure data can reflect distant evolutionary relationships. This is important when there is little confidence in sequence data such as when looking at the evolution of RNase MRP (MRP ...
Collins, Lesley Joan
core  

Translocation of structured polynucleotides through nanopores

, 2004
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic barriers for the ...
Akeson M, Bates M, Cate J H, Cech T R, Chuang J, Flomenbom O, Gerland U, Gerland U, Gutell R R, Hofacker I L, Karlin S, Koch S J, Lubensky D K, McCaskill J S, Meller A, Metzler R, Ralf Bundschuh, Terence Hwa, Ulrich Gerland, Walter A E, Zuker M   +20 more
core   +1 more source

Slip of grip of a molecular motor on a crowded track: Modeling shift of reading frame of ribosome on RNA template

, 2016
We develop a stochastic model for the programmed frameshift of ribosomes synthesizing a protein while moving along a mRNA template. Normally the reading frame of a ribosome decodes successive triplets of nucleotides on the mRNA in a step-by-step manner ...
Chowdhury, Debashish, Mishra, Bhavya, Schütz, Gunter M.   +2 more
core   +1 more source

The DEAH-box Helicase Dhr1 Dissociates U3 from the Pre-rRNA to Promote Formation of the Central Pseudoknot

PLoS Biology, 2015
In eukaryotes, the highly conserved U3 small nucleolar RNA (snoRNA) base-pairs to multiple sites in the pre-ribosomal RNA (pre-rRNA) to promote early cleavage and folding events.
Richa Sardana, Xin Liu, S. Granneman, Jieyi Zhu, Michael Gill, Ophelia Papoulas, E. Marcotte, D. Tollervey, C. C. Correll, Arlen W. Johnson   +9 more
semanticscholar   +1 more source