Opportunities in the design and application of RNA for gene expression control

In Vitro Screening and in Silico Modeling of RNA-Based Gene Expression Control

(2015) Maureen McKeague et al.   ACS Chemical Biology

Development of a fraction collection approach in capillary electrophoresis SELEX for aptamer selection

(2015) Zhaofeng Luo et al.   ANALYST

Combining capillary electrophoresis and next-generation sequencing for aptamer selection

(2015) Kathryn R. Riley et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Selection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencing

(2015) Rachel M. Eaton et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction

(2015) Tamaki Endoh et al.   ANALYTICAL CHEMISTRY

Comprehensive Analytical Comparison of Strategies Used for Small Molecule Aptamer Evaluation

(2015) Maureen McKeague et al.   ANALYTICAL CHEMISTRY

Current approaches in SELEX: An update to aptamer selection technology

(2015) Mariia Darmostuk et al.   BIOTECHNOLOGY ADVANCES

Hi-Fi SELEX: A high-fidelity digital-PCR based therapeutic aptamer discovery platform

(2015) Eric Ouellet et al.   BIOTECHNOLOGY AND BIOENGINEERING

RNA aptamers as genetic control devices: The potential of riboswitches as synthetic elements for regulating gene expression

(2015) Christian Berens et al.   Biotechnology Journal

A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future

(2015) James Chappell et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Computer-aided design of aptamers for cytochrome p450

(2015) Dmitrii S. Shcherbinin et al.   JOURNAL OF STRUCTURAL BIOLOGY

RNA-Based Fluorescent Biosensors for Live Cell Imaging of Second Messenger Cyclic di-AMP

(2015) Colleen A. Kellenberger et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae

(2015) Sang-Woo Lee et al.   METABOLIC ENGINEERING

A Highlight of Recent Advances in Aptamer Technology and Its Application

(2015) Hongguang Sun et al.   MOLECULES

Optimization of a whole-cell biocatalyst by employing genetically encoded product sensors inside nanolitre reactors

(2015) Andreas Meyer et al.   Nature Chemistry

High-throughput cellular RNA device engineering

(2015) Brent Townshend et al.   NATURE METHODS

Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment

(2015) Agata Levay et al.   NUCLEIC ACIDS RESEARCH

Characterisation of aptamer–target interactions by branched selection and high-throughput sequencing of SELEX pools

(2015) Daniel M. Dupont et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery

(2015) Jan Hoinka et al.   NUCLEIC ACIDS RESEARCH

Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq

(2015) Kyle E. Watters et al.   NUCLEIC ACIDS RESEARCH

Imaging metabolite dynamics in living cells using a Spinach-based riboswitch

(2015) Mingxu You et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A minimalist biosensor: Quantitation of cyclic di-GMP using the conformational change of a riboswitch aptamer

(2015) Colleen A Kellenberger et al.   RNA Biology

Control of alphavirus-based gene expression using engineered riboswitches

(2015) Christie L. Bell et al.   VIROLOGY

More DNA–Aptamers for Small Drugs: A Capture–SELEX Coupled with Surface Plasmon Resonance and High-Throughput Sequencing

(2015) Fabio M. Spiga et al.   ACS Combinatorial Science

Exploring Lysine Riboswitch for Metabolic Flux Control and Improvement of l-Lysine Synthesis in Corynebacterium glutamicum

(2015) Li-Bang Zhou et al.   ACS Synthetic Biology

RNA aptamers as genetic control devices: The potential of riboswitches as synthetic elements for regulating gene expression

(2015) Christian Berens et al.   Biotechnology Journal

FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections

(2015) Khalid K Alam et al.   Molecular Therapy-Nucleic Acids

RNA Mango Aptamer-Fluorophore: A Bright, High-Affinity Complex for RNA Labeling and Tracking

(2014) Elena V. Dolgosheina et al.   ACS Chemical Biology

Regulation of Gene Expression in Diverse Cyanobacterial Species by Using Theophylline-Responsive Riboswitches

(2014) Amy T. Ma et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Synthetic riboswitches — A tool comes of age

(2014) Florian Groher et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Themes and variations in riboswitch structure and function

(2014) Alla Peselis et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Modular Riboswitch Toolsets for Synthetic Genetic Control in Diverse Bacterial Species

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

Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution

(2014) Grigory S. Filonov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Plug-and-Play Fluorophores Extend the Spectral Properties of Spinach

(2014) Wenjiao Song et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Quantitative analysis of mammalian translation initiation sites by FACS-seq

(2014) W. L. Noderer et al.   Molecular Systems Biology

A quantitative framework for the forward design of synthetic miRNA circuits

(2014) Ryan J Bloom et al.   NATURE METHODS

A general design strategy for protein-responsive riboswitches in mammalian cells

(2014) Simon Ausländer et al.   NATURE METHODS

A versatile framework for microbial engineering using synthetic non-coding RNAs

(2014) Lei S. Qi et al.   NATURE REVIEWS MICROBIOLOGY

A family of synthetic riboswitches adopts a kinetic trapping mechanism

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

Synergetic regulation of translational reading-frame switch by ligand-responsive RNAs in mammalian cells

(2014) Hsiu-Ting Hsu et al.   NUCLEIC ACIDS RESEARCH

Protein-responsive ribozyme switches in eukaryotic cells

(2014) Andrew B. Kennedy et al.   NUCLEIC ACIDS RESEARCH

New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization

(2014) Abdullah Ozer et al.   Molecular Therapy-Nucleic Acids

Tracking the Emergence of High Affinity Aptamers for rhVEGF165 During Capillary Electrophoresis-Systematic Evolution of Ligands by Exponential Enrichment Using High Throughput Sequencing

(2013) Meng Jing et al.   ANALYTICAL CHEMISTRY

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

Fluorescent proteins for live-cell imaging with super-resolution

(2013) Karin Nienhaus et al.   CHEMICAL SOCIETY REVIEWS

Microfluidic Screening of Electrophoretic Mobility Shifts Elucidates Riboswitch Binding Function

(2013) Kelly Karns et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fluorescent activated cell sorting (FACS) combined with gene expression microarrays for transcription enrichment profiling of zebrafish lateral line cells

(2013) Viviana E. Gallardo et al.   METHODS

Engineering modular ‘ON’ RNA switches using biological components

(2013) Pablo Ceres 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

On the importance of cotranscriptional RNA structure formation

(2013) D. Lai et al.   RNA

Dynamically Reshaping Signaling Networks to Program Cell Fate via Genetic Controllers

(2013) K. E. Galloway et al.   SCIENCE

Synthetic Biology: Advancing the Design of Diverse Genetic Systems

(2013) Yen-Hsiang Wang et al.   Annual Review of Chemical and Biomolecular Engineering

Synthetic RNA devices to expedite the evolution of metabolite-producing microbes

(2013) Jina Yang et al.   Nature Communications

A Computationally Designed DNA Aptamer Template with Specific Binding to Phosphatidylserine

(2013) Md Ashrafuzzaman et al.   Nucleic Acid Therapeutics

Controlling Mammalian Gene Expression by Allosteric Hepatitis Delta Virus Ribozymes

(2013) Yoko Nomura et al.   ACS Synthetic Biology

Modularity of Select Riboswitch Expression Platforms Enables Facile Engineering of Novel Genetic Regulatory Devices

(2013) Pablo Ceres et al.   ACS Synthetic Biology

In vivo SELEX for Identification of Brain-penetrating Aptamers

(2013) Congsheng Cheng et al.   Molecular Therapy-Nucleic Acids

Engineered Allosteric Ribozymes That Sense the Bacterial Second Messenger Cyclic Diguanosyl 5′-Monophosphate

(2012) Hongzhou Gu et al.   ANALYTICAL CHEMISTRY

Synthetic mammalian riboswitches based on guanine aptazyme

(2012) Yoko Nomura et al.   CHEMICAL COMMUNICATIONS

Synthetic RNA switches as a tool for temporal and spatial control over gene expression

(2012) Andrew L Chang et al.   CURRENT OPINION IN BIOTECHNOLOGY

Engineered riboswitches: Expanding researchers' toolbox with synthetic RNA regulators

(2012) Alexander Wittmann et al.   FEBS LETTERS

High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch

(2012) Joshua K. Michener et al.   METABOLIC ENGINEERING

Engineering of ribozyme-based riboswitches for mammalian cells

(2012) Markus Wieland et al.   METHODS

De novo design of a synthetic riboswitch that regulates transcription termination

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

A versatile cis-blocking and trans-activation strategy for ribozyme characterization

(2012) Andrew B. Kennedy et al.   NUCLEIC ACIDS RESEARCH

Synthetic riboswitches for external regulation of genes transferred by replication-deficient and oncolytic adenoviruses

(2012) Patrick Ketzer et al.   NUCLEIC ACIDS RESEARCH

Engineering naturally occurring trans -acting non-coding RNAs to sense molecular signals

(2012) Lei Qi et al.   NUCLEIC ACIDS RESEARCH

A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity

(2012) Joe C. Liang et al.   NUCLEIC ACIDS RESEARCH

A Riboswitch-Based Inducible Gene Expression System for Mycobacteria

(2012) Jessica C. Seeliger et al.   PLoS One

Massively parallel measurements of molecular interaction kinetics on a microfluidic platform

(2012) M. Geertz 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

Genetic adaptation to high altitude in the Ethiopian highlands

(2012) Laura B Scheinfeldt et al.   GENOME BIOLOGY

Entropic Fragment-Based Approach to Aptamer Design

(2011) Chih-Yuan Tseng et al.   Chemical Biology & Drug Design

kinITC: A New Method for Obtaining Joint Thermodynamic and Kinetic Data by Isothermal Titration Calorimetry

(2011) Dominique Burnouf et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Selection of tetracycline inducible self-cleaving ribozymes as synthetic devices for gene regulation in yeast

(2011) Alexander Wittmann et al.   Molecular BioSystems

Engineering Biological Systems with Synthetic RNA Molecules

(2011) Joe C. Liang et al.   MOLECULAR CELL

Selective 2′-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA

(2011) Kady-Ann Steen et al.   Nature Protocols

Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy

(2011) Bin Chen et al.   NUCLEIC ACIDS RESEARCH

Probing the SELEX Process with Next-Generation Sequencing

(2011) Tatjana Schütze et al.   PLoS One

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

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

RNA Mimics of Green Fluorescent Protein

(2011) J. S. Paige et al.   SCIENCE

Applications of Aptamers as Sensors

(2010) Eun Jeong Cho et al.   Annual Review of Analytical Chemistry

A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression

(2010) Simon Ausländer et al.   Molecular BioSystems

Synthetic biology: applications come of age

(2010) Ahmad S. Khalil et al.   NATURE REVIEWS GENETICS

Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation

(2010) Simon Blouin et al.   NUCLEIC ACIDS RESEARCH

Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity

(2010) James M. Carothers et al.   NUCLEIC ACIDS RESEARCH

Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing

(2010) Chase L. Beisel et al.   NUCLEIC ACIDS RESEARCH

Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems

(2010) Y. Y. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing

(2010) M. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inducible gene expression from the plastid genome by a synthetic riboswitch

(2010) A. Verhounig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational approaches toward the design of pools for the in vitro selection of complex aptamers

(2010) X. Luo et al.   RNA

Frameworks for Programming Biological Function through RNA Parts and Devices

(2009) Maung Nyan Win et al.   CHEMISTRY & BIOLOGY

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

The second wave of synthetic biology: from modules to systems

(2009) Priscilla E. M. Purnick et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An efficient platform for genetic selection and screening of gene switches in Escherichia coli

(2009) Norihito Muranaka et al.   NUCLEIC ACIDS RESEARCH

In silico selection of RNA aptamers

(2009) Y. Chushak et al.   NUCLEIC ACIDS RESEARCH

Measuring the activity of BioBrick promoters using an in vivo reference standard

(2009) Jason R Kelly et al.   Journal of Biological Engineering

Engineering Complex Riboswitch Regulation by Dual Genetic Selection

(2008) Vandana Sharma et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Refinement and standardization of synthetic biological parts and devices

(2008) Barry Canton et al.   NATURE BIOTECHNOLOGY

A flow cytometry-based screen for synthetic riboswitches

(2008) Sean A. Lynch et al.   NUCLEIC ACIDS RESEARCH

Riboswitches in unexpected places--A synthetic riboswitch in a protein coding region

(2008) S. Topp et al.   RNA

Random Walks to Synthetic Riboswitches—A High-Throughput Selection Based on Cell Motility

(2007) Shana Topp et al.   CHEMBIOCHEM