Results 51 to 60 of about 12,203 (191)

Riboswitches: Structures and Mechanisms [PDF]

Cold Spring Harbor Perspectives in Biology, 2010
A critical feature of the hypothesized RNA world would have been the ability to control chemical processes in response to environmental cues. Riboswitches present themselves as viable candidates for a sophisticated mechanism of regulatory control in RNA-based life.
Andrew D, Garst, Andrea L, Edwards, Robert T, Batey   +2 more
openaire   +2 more sources

Bifidobacterium bifidum SAM-VI Riboswitch Conformation Change Requires Peripheral Helix Formation

Biomolecules
The Bifidobacterium bifidum SAM-VI riboswitch undergoes dynamic conformational changes that modulate downstream gene expression. Traditional structural methods such as crystallography capture the bound conformation at high resolution, and additional ...
Wenwen Xiao, Guangfeng Liu, Ting Chen, Yunlong Zhang, Changrui Lu   +4 more
doaj   +1 more source

Understanding the errors of SHAPE-directed RNA structure modeling

, 2011
Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms.
Aviran S., Brunel C., Butler E. B., Byrne R. T., Cate J. H., Christopher C. VanLang, Collins K., Correll C. C., Cruz J. A., Darty K., Das R., Das R., Deigan K. E., Efron B., Efron B., Felsenstein J., Gesteland R. F., Hickey D. R., Hofacker I. L., Kladwang W., Kladwang W., Kulshina N., Kwon M., Lemay J. F., Leontis N. B., Levitt M., Mandal M., Mandal M., Mathews D. H., Mathews D. H., Mills D. R., Mitra S., Mortimer S. A., Noller H. F., Pablo Cordero, Panning B., Pedersen J. S., Regulski E. E., Rhiju Das, Russell R., Russell R., Serganov A., Smith K. D., Staley J. P., Sudarsan N., Sussman J. L., Takamoto K., Vasa S. M., Watts J. M., Wilkinson K. A., Wilkinson K. A., Winkler W. C., Wipapat Kladwang, Yoon S.   +53 more
core   +1 more source

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
core   +3 more sources

An in vivo high-throughput screening for riboswitch ligands using a reverse reporter gene system

Scientific Reports, 2017
Riboswitches are bacterial RNA elements that regulate gene expression in response to metabolite or ion abundance and are considered as potential drug targets. In recent years a number of methods to find non-natural riboswitch ligands have been described.
Marion Kirchner, Kenji Schorpp, Kamyar Hadian, Sabine Schneider   +3 more
doaj   +1 more source

Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme. [PDF]

, 2020
Massively parallel, quantitative measurements of biomolecular activity across sequence space can greatly expand our understanding of RNA sequence-function relationships. We report the development of an RNA-array assay to perform such measurements and its
Andreasson, Johan OL, Block, Steven M, Greenleaf, William J, Savinov, Andrew   +3 more
core  

Expected degree for RNA secondary structure networks [PDF]

, 2014
Consider the network of all secondary structures of a given RNA sequence, where nodes are connected when the corresponding structures have base pair distance one. The expected degree of the network is the average number of neighbors, where average may be
Clote, Peter
core   +1 more source

Mix-and-Match Riboswitches [PDF]

ACS Chemical Biology, 2006
Riboswitches are noncoding RNA elements found in the 5'-untranslated region of messenger RNA (mRNA) that mediate gene expression in a cis fashion in the absence of protein. This common regulatory strategy in bacteria is achieved through the interplay of two distinct domains: an aptamer domain responsible for sensing intracellular concentrations of a ...
Colby D, Stoddard, Robert T, Batey
openaire   +2 more sources

Cobalamin Riboswitches Are Broadly Sensitive to Corrinoid Cofactors to Enable an Efficient Gene Regulatory Strategy

mBio, 2022
In bacteria, many essential metabolic processes are controlled by riboswitches, gene regulatory RNAs that directly bind and detect metabolites. Highly specific effector binding enables riboswitches to respond to a single biologically relevant metabolite.
Kristopher J. Kennedy, Florian J. Widner, Olga M. Sokolovskaya, Lina V. Innocent, Rebecca R. Procknow, Kenny C. Mok, Michiko E. Taga   +6 more
doaj   +1 more source

c-di-AMP: An essential molecule in the signaling pathways that regulate the viability and virulence of gram-positive bacteria [PDF]

, 2017
Signal transduction pathways enable organisms to monitor their external environment and adjust gene regulation to appropriately modify their cellular processes.
Cho, Kyu Hong, Fahmi, Tazin, Port, Gary C   +2 more
core   +2 more sources