Publication Date:
2008-01-05
Description:
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 under constant force by measuring the molecular contour length, kinetics, and energetics with and without adenine. Distinct folding steps correlated with the formation of key secondary or tertiary structures and with ligand binding. Adenine-induced stabilization of the weakest helix in the aptamer, the mechanical switch underlying regulatory action, was observed directly. These results provide an integrated view of hierarchical folding in an aptamer, demonstrating how complex folding can be resolved into constituent parts, and supply further insights into tertiary structure formation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640945/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640945/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greenleaf, William J -- Frieda, Kirsten L -- Foster, Daniel A N -- Woodside, Michael T -- Block, Steven M -- GM057035/GM/NIGMS NIH HHS/ -- GM066275/GM/NIGMS NIH HHS/ -- R01 GM057035/GM/NIGMS NIH HHS/ -- R01 GM057035-12/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Feb 1;319(5863):630-3. doi: 10.1126/science.1151298. Epub 2008 Jan 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18174398" target="_blank"〉PubMed〈/a〉
Keywords:
Adenine/chemistry/metabolism
;
Aptamers, Nucleotide/*chemistry/metabolism
;
Base Pairing
;
DNA-Directed RNA Polymerases/metabolism
;
Ligands
;
*Nucleic Acid Conformation
;
Optical Tweezers
;
RNA, Messenger/*chemistry/metabolism
;
Thermodynamics
Print ISSN:
0036-8075
Electronic ISSN:
1095-9203
Topics:
Biology
,
Chemistry and Pharmacology
,
Computer Science
,
Medicine
,
Natural Sciences in General
,
Physics
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