Sequence-dependent folding landscapes of adenine riboswitch aptamers
نویسندگان
چکیده
منابع مشابه
Sequence-dependent folding landscapes of adenine riboswitch aptamers.
Expression of a large fraction of genes in bacteria is controlled by riboswitches, which are found in the untranslated region of mRNA. Structurally riboswitches have a conserved aptamer domain to which a metabolite binds, resulting in a conformational change in the downstream expression platform. Prediction of the functions of riboswitches requires a quantitative description of the folding land...
متن کاملRelative stability of helices determines the folding landscape of adenine riboswitch aptamers.
Riboswitches, whose folding is controlled by binding of metabolites to the aptamer domain, regulate downstream gene expression. Folding properties of the aptamer strongly influence the conformation of the downstream expression platform, which controls transcription termination or translation initiation. We have characterized the energy landscape of the add riboswitch aptamer quantitatively by u...
متن کاملDirect observation of hierarchical folding in single riboswitch aptamers.
Riboswitches regulate genes through structural changes in ligand-binding RNA aptamers. With the use of an optical-trapping assay based on in situ transcription by a molecule of RNA polymerase, single nascent RNAs containing pbuE adenine riboswitch aptamers were unfolded and refolded. Multiple folding states were characterized by means of both force-extension curves and folding trajectories unde...
متن کاملSequence-dependent base-stacking stabilities guide tRNA folding energy landscapes.
The folding of bacterial tRNAs with disparate sequences has been observed to proceed in distinct folding mechanisms despite their structural similarity. To explore the folding landscapes of tRNA, we performed ion concentration-dependent coarse-grained TIS model MD simulations of several E. coli tRNAs to compare their thermodynamic melting profiles to the classical absorbance spectra of Crothers...
متن کاملSingle-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism
Riboswitches regulate gene expression via ligand binding to an aptamer domain which induces conformational changes in a regulatory expression platform. By unfolding and refolding single add adenine riboswitch molecules in an optical trap, an integrated picture of the folding was developed and related to the regulatory mechanism. Force-extension curves (FECs) and constant-force folding trajector...
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ژورنال
عنوان ژورنال: Phys. Chem. Chem. Phys.
سال: 2014
ISSN: 1463-9076,1463-9084
DOI: 10.1039/c3cp53932f