Automated physics-based design of synthetic riboswitches from diverse RNA aptamers

Riboswitch engineering — making the all-important second and third steps

(2015) Christian Berens et al.   CURRENT OPINION IN BIOTECHNOLOGY

A predictive biophysical model of translational coupling to coordinate and control protein expression in bacterial operons

(2015) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

Design criteria for synthetic riboswitches acting on transcription

(2015) Manja Wachsmuth et al.   RNA Biology

Toehold Switches: De-Novo-Designed Regulators of Gene Expression

(2014) Alexander A. Green et al.   CELL

Modular Riboswitch Toolsets for Synthetic Genetic Control in Diverse Bacterial Species

(2014) Christopher J. Robinson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

(2014) I. Farasat et al.   Molecular Systems Biology

A family of synthetic riboswitches adopts a kinetic trapping mechanism

(2014) Dennis M. Mishler et al.   NUCLEIC ACIDS RESEARCH

Artificial riboswitches for gene expression and replication control of DNA and RNA viruses

(2014) Patrick Ketzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stabilized Interleukin-6 receptor binding RNA aptamers

(2014) Cindy Meyer et al.   RNA Biology

A Synthetic Riboswitch that Operates using a Rationally Designed Ligand-RNA Pair

(2013) Chikara Dohno et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites

(2013) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Tuning a riboswitch response through structural extension of a pseudoknot

(2013) M. F. Souliere et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A new frontier in synthetic biology: automated design of small RNA devices in bacteria

(2013) Guillermo Rodrigo et al.   TRENDS IN GENETICS

Development of a 2,4-Dinitrotoluene-Responsive Synthetic Riboswitch in E. coli Cells

(2012) Molly E. Davidson et al.   ACS Chemical Biology

Metabolite Recognition Principles and Molecular Mechanisms Underlying Riboswitch Function

(2012) Alexander Serganov et al.   Annual Review of Biophysics

Rationally designed families of orthogonal RNA regulators of translation

(2012) Vivek K Mutalik et al.   Nature Chemical Biology

De novo design of a synthetic riboswitch that regulates transcription termination

(2012) M. Wachsmuth et al.   NUCLEIC ACIDS RESEARCH

De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells

(2012) G. Rodrigo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments

(2012) Jose Cruz-Toledo et al.   Database-The Journal of Biological Databases and Curation

Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways

(2011) Joshua K. Michener et al.   METABOLIC ENGINEERING

Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression

(2011) J. M. Carothers et al.   SCIENCE

Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride

(2011) J. L. Baker et al.   SCIENCE

DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model

(2010) Jana Sperschneider et al.   NUCLEIC ACIDS RESEARCH

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Characterization of RNA aptamers that disrupt the RUNX1–CBFβ/DNA complex

(2009) Jenny L. Barton et al.   NUCLEIC ACIDS RESEARCH

Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cells

(2009) Jiehua Zhou et al.   NUCLEIC ACIDS RESEARCH

Predicting structures and stabilities for H-type pseudoknots with interhelix loops

(2009) S. Cao et al.   RNA

Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes

(2009) Xi Chen et al.   PLoS Computational Biology

Design Principles for Riboswitch Function

(2009) Chase L. Beisel et al.   PLoS Computational Biology

Biosensor-based on-site explosives detection using aptamers as recognition elements

(2008) Eva Ehrentreich-Förster et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Riboswitches: Emerging Themes in RNA Structure and Function

(2008) Rebecca K. Montange et al.   Annual Review of Biophysics

Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

(2008) Huan-Xiang Zhou et al.   Annual Review of Biophysics

Riboswitches that Sense S-adenosylhomocysteine and Activate Genes Involved in Coenzyme Recycling

(2008) Joy Xin Wang et al.   MOLECULAR CELL