Results 131 to 140 of about 14,400 (274)
The block spectrum of RNA pseudoknot structures [PDF]
Journal of Mathematical Biology, 2019 In this paper we analyze the length-spectrum of blocks in $ $-structures. $ $-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time RNA folding. A $ $-structure is constructed by nesting and concatenating specific building components having topological genus at most $ $.
Christina S. Burris +2 more
openaire +4 more sources
Automatic generation of pseudoknotted RNAs taxonomy
BMC Bioinformatics, 2023 Background The ability to compare RNA secondary structures is important in understanding their biological function and for grouping similar organisms into families by looking at evolutionarily conserved sequences such as 16S rRNA. Most comparison methods
Michela Quadrini +2 more
doaj +1 more source
The Signed Weighted Resolution Set is Not a Complete Pseudoknot Invariant [PDF]
arXiv, 2014 When the signed weighted resolution set was defined as an invariant of pseudoknots, it was unknown whether this invariant was complete. Using the Gauss-diagrammatic invariants of pseudoknots introduced by Dorais et al, we show that the signed were-set cannot distinguish all non-equivalent pseudoknots.
arxiv
Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs
Genes, 2018 RNA molecules are composed of modular architectural units that define their unique structural and functional properties. Characterization of these building blocks can help interpret RNA structure/function relationships.
Swati Jain +3 more
semanticscholar +1 more source
A Modular Engineered DNA Nanodevice for Precise Profiling of Telomerase RNA Location and Activity
Advanced Science, Volume 12, Issue 7, February 17, 2025.Telomerase is a key cancer biomarker vital for cellular processes. A modular DNA nanodevice is designed to profile hTR location and telomerase activity, enabled in situ co‐imaging in cytoplasm and nucleus. A logic imaging method distinguished colocalized from non‐colocalized subcellular regions, aiding statistical analysis of hTR/active telomerase ...
Shi‐Yi Zhang +6 more
wiley +1 more source
PseudoBase: structural information on RNA pseudoknots [PDF]
Nucleic Acids Research, 2001 PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo-knots. It can be reached at http://wwwbio.LeidenUniv.nl/ approximately Batenburg/PKB.html. For each pseudoknot, thirteen items are stored, for example the relevant sequence, the stem positions of the pseudoknot, the EMBL accession number of the sequence ...
Cornelis W. A. Pleij +2 more
openaire +2 more sources
Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot
Nucleic Acids Research, 2017 Frameshifting is an essential process that regulates protein synthesis in many viruses. The ribosome may slip backward when encountering a frameshift motif on the messenger RNA, which usually contains a pseudoknot structure involving tertiary base pair ...
Yu-Ting Chen +8 more
semanticscholar +1 more source
Effects of lipid membranes on RNA catalytic activity and stability
Biology of the Cell, Volume 117, Issue 2, February 2025.This study explores how lipid membranes influence the activity and stability of natural ribozymes. We found that lipid membranes can both decrease and enhance ribozyme activity. We also observed that lipid membranes promote RNA degradation, depending on lipid composition and membrane fluidity.
Tomasz Czerniak, James P. Saenz
wiley +1 more source
A Graph Grammar for Modelling RNA Folding
, 2016 We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the global behaviour ...
Mamuye, Adane Letta +2 more
core +2 more sources
Tangle Insertion Invariants for Pseudoknots, Singular Knots, and Rigid Vertex Spatial Graphs [PDF]
arXiv, 2016 The notion of a pseudoknot is defined as an equivalence class of knot diagrams that may be missing some crossing information. We provide here a topological invariant schema for pseudoknots and their relatives, 4-valent rigid vertex spatial graphs and singular knots, that is obtained by replacing unknown crossings or vertices by rational tangles.
arxiv