Results 11 to 20 of about 14,400 (274)
A steepest descent calculation of RNA pseudoknots [PDF]
Physical Review E, 2002 We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure.
A. Zee +3 more
arxiv +8 more sources
Inverse folding of RNA pseudoknot structures [PDF]
Algorithms for Molecular Biology, 2010 Background RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure) and additional cross-serial base pairs.
Li Linda YM +2 more
doaj +8 more sources
Nature Communications, 2021 The RNA pseudoknot of SARS-CoV-2 promotes -1 programmed ribosomal frameshifting. Here the authors use single molecule force spectroscopy to study the folding of this pseudoknot, showing that it forms at least two different pseudoknot conformers with ...
Krishna Neupane +8 more
doaj +2 more sources
Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement
Frontiers in Molecular Biosciences, 2021 Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional roles of ...
Chenjie Feng +4 more
doaj +2 more sources
Methods and Protocols, 2022 Obtaining valuable clues for noncoding RNA (ribonucleic acid) subsequences remains a significant challenge, acknowledging that most of the human genome transcribes into noncoding RNA parts related to unknown biological operations.
Christos Andrikos +5 more
doaj +2 more sources
Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.
PLoS Computational Biology, 2023 Multiple coronaviruses including MERS-CoV causing Middle East Respiratory Syndrome, SARS-CoV causing SARS, and SARS-CoV-2 causing COVID-19, use a mechanism known as -1 programmed ribosomal frameshifting (-1 PRF) to replicate.
Luke Trinity +4 more
doaj +2 more sources
Nature Communications, 2021 Exoribonuclease-resistant RNAs (xrRNAs) are RNA elements that block the exoribonucleolytic degradation of RNA. Here the authors show how a long-range pseudoknot length modulates the Mg2+-dependence of flaviviral xrRNA’s folding, conformational dynamics ...
Xiaolin Niu +6 more
doaj +2 more sources
The Topology of Pseudoknotted Homopolymers [PDF]
Physical Review E, 2005 We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The genus has been recently proposed for classifying pseudoknots (and their topological complexity) in the context of ...
Graziano Vernizzi +3 more
arxiv +6 more sources
Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot [PDF]
Proceedings of the National Academy of Sciences of the United States of America, 2017 The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics.
Ansari, Anjum +7 more
core +5 more sources
Possible involvement of three-stemmed pseudoknots in regulating translational initiation in human mRNAs. [PDF]
PLoS ONERNA pseudoknots play a crucial role in various cellular functions. Established pseudoknots show significant variation in both size and structural complexity. Specifically, three-stemmed pseudoknots are characterized by an additional stem-loop embedded in
Xiaolan Huang, Zhihua Du
doaj +2 more sources