TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences
BMC Bioinformatics, 2011 Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence.
Sharma Gaurav +2 more
doaj +1 more source
RNA base-pairing complexity in living cells visualized by correlated chemical probing
Proceedings of the National Academy of Sciences of the United States of America, 2019 Significance How do we determine the structure of an RNA, particularly in cells? Chemical probing is a broadly applicable strategy for mapping RNA structure. However, chemical probing experiments do not observe base pairs directly and hence are unable to
Anthony M Mustoe +4 more
semanticscholar +1 more source
Identification of the base-pairing requirements for repression of hctA translation by the small RNA IhtA leads to the discovery of a new mRNA target in Chlamydia trachomatis. [PDF]
PLoS ONE, 2015 The non-coding small RNA, IhtA expressed by the obligate intracellular human pathogen Chlamydia trachomatis modulates the translation of HctA, a key protein involved in replicative to infectious cell type differentiation.
Nicole A Grieshaber +5 more
doaj +1 more source
Enzyme-free genetic copying of DNA and RNA sequences
Beilstein Journal of Organic Chemistry, 2018 The copying of short DNA or RNA sequences in the absence of enzymes is a fascinating reaction that has been studied in the context of prebiotic chemistry.
Marilyne Sosson, Clemens Richert
doaj +1 more source
Evaluation of RNA secondary structure prediction for both base-pairing and topology
Biophysics Reports, 2018 Graphical abstractAbstractSecondary structures of RNAs are crucial to the understanding of their tertiary structures and functions. At present, many theoretical methods are widely used to predict RNA secondary structures. The performance of these methods
Yunjie Zhao +3 more
semanticscholar +1 more source
Base-pairing of uracil and 2,6-diaminopurine: from cocrystals to photoreactivity. [PDF]
iScienceSummary: We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U
Stolar T +12 more
europepmc +2 more sources
Life, 2019 A mixture of sugar diphosphates is produced in reactions between small aldehyde phosphates catalysed by layered double hydroxide (LDH) clays under plausibly prebiotic conditions.
Harold S. Bernhardt
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Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position
Molecules, 2017 Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon University of California base ...
Wei Liu +5 more
doaj +1 more source
Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation
eLife, 2020 By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and ...
Ira Alexandra Iosub +8 more
doaj +1 more source
Guide-substrate base-pairing requirement for box H/ACA RNA-guided RNA pseudouridylation
RNA: A publication of the RNA Society, 2018 Box H/ACA RNAs are a group of small RNAs found in abundance in eukaryotes (as well as in archaea). Although their sequences differ, eukaryotic box H/ACA RNAs all share the same unique hairpin-hinge-hairpin-tail structure.
Meemanage D De Zoysa +3 more
semanticscholar +1 more source