Results 1 to 10 of about 492,946 (224)

Viral RNA as a branched polymer [PDF]

Chapter 1 in: Comas-Garcia, M., Rosales-Mendoza, S. (eds) Physical Virology. Springer Series in Biophysics, vol 24. Springer, Cham (2023), 2022
Myriad viruses use positive-strand RNA molecules as their genomes. Far from being only a repository of genetic material, viral RNA performs numerous other functions mediated by its physical structure and chemical properties. In this chapter, we focus on its structure and discuss how long RNA molecules can be treated as branched polymers through planar ...
arxiv   +1 more source

Stem-loop formation drives RNA folding in mechanical unzipping experiments [PDF]

PNAS 119 (3), 2022, 2022
Accurate knowledge of RNA hybridization is essential for understanding RNA structure and function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 nearest-neighbor base pair (NNBP) RNA free energies in sodium and magnesium with 0.1 kcal/mol precision using optical tweezers. Notably, force-distance curves (FDCs) exhibit strong
arxiv   +1 more source

Interplay between single-stranded binding proteins on RNA secondary structure [PDF]

Phys. Rev. E 88, 052707 (2013), 2013
RNA protein interactions control the fate of cellular RNAs and play an important role in gene regulation. An interdependency between such interactions allows for the implementation of logic functions in gene regulation. We investigate the interplay between RNA binding partners in the context of the statistical physics of RNA secondary structure, and ...
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Probing complex RNA structures by mechanical force [PDF]

European Physical Journal E 12 (2003) 605-615, 2003
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by solely invoking successive openings of native helices.
arxiv   +1 more source

Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations [PDF]

Proceedings of the National Academy of Sciences USA 100 (2003) 15310-15315, 2003
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA folding simulations, which follow the stochastic closing and opening of individual RNA helices.
arxiv   +1 more source

Computational prediction of RNA tertiary structures using machine learning methods [PDF]

Chinese Physics B, Sept. 2020, 2020
RNAs play crucial and versatile roles in biological processes. Computational prediction approaches can help to understand RNA structures and their stabilizing factors, thus providing information on their functions, and facilitating the design of new RNAs.
arxiv   +1 more source

Network Representation of Large-Scale Heterogeneous RNA Sequences with Integration of Diverse Multi-omics, Interactions, and Annotations Data [PDF]

Pacific Symposium on Biocomputing, Vol 25, 2020, 2019
Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes is essential in order to uncover the functional role of individual RNA transcripts, especially for unannotated ...
arxiv   +1 more source

The effect of RNA stiffness on the self-assembly of virus particles [PDF]

, 2018
Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between a ssRNA with no ...
arxiv   +1 more source

PLIT: An alignment-free computational tool for identification of long non-coding RNAs in plant transcriptomic datasets [PDF]

Computers in Biology and Medicine, 105, pp. 169 - 181, Elevier, 2019, 2019
Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate identification of lncRNAs in RNA-seq datasets is crucial for exploring their characteristic functions in the genome
arxiv   +1 more source

Kinetics of viral self-assembly: the role of ss RNA antenna [PDF]

Phys. Rev. E 75, 051901 (2007), 2006
A big class of viruses self-assemble from a large number of identical capsid proteins with long flexible N-terminal tails and ss RNA. We study the role of the strong Coulomb interaction of positive N-terminal tails with ss RNA in the kinetics of the in vitro virus self-assembly.
arxiv   +1 more source