In this paper we study properties of topological RNA structures, i.e. RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological structures having genus zero. We derive a new bivariate generating function whose singular expansion allows us to analyze the distributions of arcs, stacks, hairpin- , interior- and multi-loops. We then extend this analysis to H-type pseudoknots, kissing hairpins as well as 3-knots and compute their respective expectation values. Finally we discuss our results and put them into context with data obtained by uniform sampling structures of fixed genus.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1007/s00285-016-1078-1 | DOI Listing |
Sci Rep
January 2025
College of Information Science Technology, Hainan Normal University, Haikou, 571158, China.
MiRNAs and lncRNAs are two essential noncoding RNAs. Predicting associations between noncoding RNAs and diseases can significantly improve the accuracy of early diagnosis.With the continuous breakthroughs in artificial intelligence, researchers increasingly use deep learning methods to predict associations.
View Article and Find Full Text PDFBiosystems
December 2024
Departamento de Estado Sólido, Instituto de Física, Universidad Nacional Autónoma de México, Circuito de la Investigación Científica, Ciudad Universitaria, Ciudad de México, 04510, Mexico.
A prebiotic model, based in the framework of thermodynamic efficiency loss from small dissipative eukaryote organisms is developed to describe the maximum possible concentration of solar power to be dissipated on topological circular molecules structures encapsulated in lipid-walled vacuoles, which floated in the Archean oceans. By considering previously, the analysis of 71 species examined by covering 18 orders of mass magnitude from the Megapteranovaeangliae to Saccharomyces cerevisiae suggest that in molecular structures of smaller masses than any living being known nowadays, the power dissipation must be directly proportional to the power of the photons of solar origin that impinge them to give rise to the formation of more complex self-assembled molecular structures at the prebiotic stage by a quantum mechanics model of resonant photon wavelength excitation. The analysis of 12 circular molecules (encapsulated in lipid-walled vacuoles) relevant to the evolution of life on planet Earth such as the five nucleobases, and some aromatic molecules as pyrimidine, porphyrin, chlorin, coumarin, xanthine, etc.
View Article and Find Full Text PDFNature
December 2024
Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
Much of the human genome is transcribed into RNAs, many of which contain structural elements that are important for their function. Such RNA molecules-including those that are structured and well-folded-are conformationally heterogeneous and flexible, which is a prerequisite for function, but this limits the applicability of methods such as NMR, crystallography and cryo-electron microscopy for structure elucidation. Moreover, owing to the lack of a large RNA structure database, and no clear correlation between sequence and structure, approaches such as AlphaFold for protein structure prediction do not apply to RNA.
View Article and Find Full Text PDFNAR Genom Bioinform
December 2024
Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Sector 14, Chandigarh 160014, India.
Water is essential for the formation, stability and function of RNA-protein complexes. To delineate the structural role of water molecules in shaping the interactions between RNA and proteins, we comprehensively analyzed a dataset of 329 crystal structures of these complexes to identify water-mediated hydrogen-bonded contacts at RNA-protein interface. Our survey identified a total of 4963 water bridges.
View Article and Find Full Text PDFThe COVID-19 mRNA vaccines demonstrated the power of mRNA medicines. Despite advancements in sequence design, evidence regarding the preferential use of synonymous codons on cellular stress and innate immune responses is lacking. To this end, we developed a proprietary codon optimality matrix to re-engineer the coding sequences of three luciferase reporters.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!