TY - JOUR
T1 - Automated physics-based design of synthetic riboswitches from diverse RNA aptamers
AU - Espah Borujeni, Amin
AU - Mishler, Dennis M.
AU - Wang, Jingzhi
AU - Huso, Walker
AU - Salis, Howard M.
N1 - Funding Information:
Author contributions: A.E.B. and H.M.S. developed the model, designed the DNA sequences, analyzed the results and wrote the manuscript. A.E.B., D.M.M., J.W. and W.H. performed the experiments. FUNDING Air Force Office of Scientific Research [FA9550-14-1-0089]; Office of Naval Research [N00014-13-1-0074]; NSF Career Award [CBET-1253641]; DARPA Young Faculty Award [N66001-10-1-4019 to H.M.S.]. Funding for open access charge: Air Force Office of Scientific Research [FA9550-14- 1-0089]. Conflict of interest statement. None declared.
Publisher Copyright:
© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2016/1/8
Y1 - 2016/1/8
N2 - Riboswitches are shape-changing regulatory RNAs that bind chemicals and regulate gene expression, directly coupling sensing to cellular actuation. However, it remains unclear how their sequence controls the physics of riboswitch switching and activation, particularly when changing the ligand-binding aptamer domain. We report the development of a statistical thermodynamic model that predicts the sequence-structure-function relationship for translation-regulating riboswitches that activate gene expression, characterized inside cells and within cell-free transcription-translation assays. Using the model, we carried out automated computational design of 62 synthetic riboswitches that used six different RNA aptamers to sense diverse chemicals (theophylline, tetramethylrosamine, fluoride, dopamine, thyroxine, 2,4-dinitrotoluene) and activated gene expression by up to 383-fold. The model explains how aptamer structure, ligand affinity, switching free energy and macromolecular crowding collectively control riboswitch activation. Our model-based approach for engineering riboswitches quantitatively confirms several physical mechanisms governing ligand-induced RNA shape-change and enables the development of cell-free and bacterial sensors for diverse applications.
AB - Riboswitches are shape-changing regulatory RNAs that bind chemicals and regulate gene expression, directly coupling sensing to cellular actuation. However, it remains unclear how their sequence controls the physics of riboswitch switching and activation, particularly when changing the ligand-binding aptamer domain. We report the development of a statistical thermodynamic model that predicts the sequence-structure-function relationship for translation-regulating riboswitches that activate gene expression, characterized inside cells and within cell-free transcription-translation assays. Using the model, we carried out automated computational design of 62 synthetic riboswitches that used six different RNA aptamers to sense diverse chemicals (theophylline, tetramethylrosamine, fluoride, dopamine, thyroxine, 2,4-dinitrotoluene) and activated gene expression by up to 383-fold. The model explains how aptamer structure, ligand affinity, switching free energy and macromolecular crowding collectively control riboswitch activation. Our model-based approach for engineering riboswitches quantitatively confirms several physical mechanisms governing ligand-induced RNA shape-change and enables the development of cell-free and bacterial sensors for diverse applications.
UR - http://www.scopus.com/inward/record.url?scp=84959368267&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84959368267&partnerID=8YFLogxK
U2 - 10.1093/nar/gkv1289
DO - 10.1093/nar/gkv1289
M3 - Article
C2 - 26621913
AN - SCOPUS:84959368267
SN - 0305-1048
VL - 44
SP - 1
EP - 13
JO - Nucleic acids research
JF - Nucleic acids research
IS - 1
ER -