Computational Analysis of Co-Transcriptional Riboswitch Folding
نویسندگان
چکیده
منابع مشابه
Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers
To function as gene regulatory elements in response to environmental signals, riboswitches must adopt specific secondary structures on appropriate time scales. We employ kinetic Monte Carlo simulation to model the time-dependent folding during transcription of TPP riboswitch expression platforms. According to our simulations, riboswitch transcriptional terminators, which must adopt a specific h...
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Early attempts include Pipas & McMahon (1975), who simply summed over all possible secondary structures and evaluated them with respect to free-energy functions. Biological and thermodynamical principles were then used to advanced free-energy functions to get more accurate predictions, which have been used to great effect in algorithms such as UNAFold (Markham et al. 2008) and RNAfold (Hofacker...
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Riboswitches are cis-acting elements that regulate gene expression by affecting transcriptional termination or translational initiation in response to binding of a metabolite. A typical riboswitch is made of an upstream aptamer domain and a downstream expression platform. Both domains participate in the folding and structural rearrangement in the absence or presence of its cognate metabolite. R...
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7-Aminomethyl-7-deazaguanine (preQ(1)) sensitive mRNA domains belong to the smallest riboswitches known to date. Although recent efforts have revealed the three-dimensional architecture of the ligand-aptamer complex less is known about the molecular details of the ligand-induced response mechanism that modulates gene expression. We present an in vitro investigation on the ligand-induced folding...
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The Bacillus subtilis lysC lysine riboswitch modulates its own gene expression upon lysine binding through a transcription attenuation mechanism. The riboswitch aptamer is organized around a single five-way junction that provides the scaffold for two long-range tertiary interactions (loop L2-loop L3 and helix P2-loop L4)--all of this for the creation of a specific lysine binding site. We have d...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2014
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2013.11.1660