Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch [PDF]
, 2006 Riboswitches are highly structured elements in the 50-untranslated regions (50-UTRs) of messenger RNA that control gene expression by specifically binding to small metabolite molecules. They consist of an aptamer domain responsible for ligand binding and
Wöhnert, Jens +5 more
core +1 more source
RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model. [PDF]
PLoS ONE, 2018 RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design.
Hosna Jabbari +2 more
doaj +1 more source
Hidden Structural Modules in a Cooperative RNA Folding Transition
Cell Reports, 2018 Summary: Large-scale, cooperative rearrangements underlie the functions of RNA in RNA-protein machines and gene regulation. To understand how such rearrangements are orchestrated, we used high-throughput chemical footprinting to dissect a seemingly ...
Brant Gracia +5 more
doaj +1 more source
The architecture of the SARS-CoV-2 RNA genome inside virion
Nature Communications, 2021 Secondary structures and long-range RNA interactions of the SARS-CoV-2 genome have been investigated by various sequencing methods. Here the authors use an RNA-RNA hybrid sequencing method to predict the secondary and tertiary structure of the SRAS-CoV-2
Changchang Cao +13 more
doaj +1 more source
Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain [PDF]
, 2011 Riboswitch RNAs fold into complex tertiary structures upon binding to their cognate ligand. Ligand recognition is accomplished by key residues in the binding pocket.
Julia Wirmer-Bartoschek +23 more
core +1 more source
Frontiers in Genetics, 2018 RNA molecules are essential players in many fundamental biological processes. Prokaryotes and eukaryotes have distinct RNA classes with specific structural features and functional roles.
Deborah Antunes +5 more
doaj +1 more source
Comparative analysis of RNA secondary structure accuracy on predicted RNA 3D models
PLoS ONE, 2023 RNA structure is conformationally dynamic, and accurate all-atom tertiary (3D) structure modeling of RNA remains challenging with the prevailing tools. Secondary structure (2D) information is the standard prerequisite for most RNA 3D modeling.
Mandar Kulkarni +3 more
doaj +3 more sources
Structure of a rare non-standard sequence k-turn bound by L7Ae protein [PDF]
, 2014 Kt-23 from Thelohania solenopsae is a rare RNA kink turn (k-turn) where an adenine replaces the normal guanine at the 2n position. L7Ae is a member of a strongly conserved family of proteins that bind a range of k-turn structures in the ribosome, box C/D
Huang, Lin, Lilley, David M J; id_orcid
core +1 more source
Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism [PDF]
, 2010 For a long time it has been assumed that the decay of RNA in eukaryotes is mainly carried out by exoribonucleases, which is in contrast to bacteria, where endoribonucleases are well documented to initiate RNA degradation.
Tomecki, Rafał, Dziembowski, Andrzej
core +3 more sources
Tertiary Hydrogen Bonds in the Solution Structure of Transfer RNA [PDF]
Proceedings of the National Academy of Sciences, 1975 The high resolution nuclear magnetic resonance (NMR) spectra of hydrogen-bonded protons in four tRNAs have been studied at 270 MHz. The relative intensity of the resonances between -11 ppm and -15 ppm of Escherichia coli tRNA 1 Val ...
Reid, B.R. +5 more
openaire +2 more sources