Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications

On universal coding events in protein biogenesis

(2018) Vladimir Kubyshkin et al.   BIOSYSTEMS

Exploring the parameters of post-segregational killing using heterologous expression of secreted toxin barnase and antitoxin barstar in an Escherichia coli case study

(2017) Dorien S Coray et al.   MICROBIOLOGY-SGM

Rational Design of Evolutionarily Stable Microbial Kill Switches

(2017) Finn Stirling et al.   MOLECULAR CELL

A semisynthetic organism engineered for the stable expansion of the genetic alphabet

(2017) Yorke Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Orthogonal Ribosome Biofirewall

(2017) Bin Jia et al.   ACS Synthetic Biology

Synthetic alienation of microbial organisms by using genetic code engineering: Why and how?

(2017) Vladimir Kubyshkin et al.   Biotechnology Journal

Pyrrolysyl-tRNA Synthetase, an Aminoacyl-tRNA Synthetase for Genetic Code Expansion

(2016) Ana Crnković et al.   CROATICA CHEMICA ACTA

Towards Reassignment of the Methionine Codon AUG to Two Different Noncanonical Amino Acids in Bacterial Translation

(2016) Alessandro De Simone et al.   CROATICA CHEMICA ACTA

Synthetic biology approaches to biological containment: pre-emptively tackling potential risks

(2016) Leticia Torres et al.   Essays in Biochemistry

Recent Progress in CRISPR/Cas9 Technology

(2016) Yue Mei et al.   Journal of Genetics and Genomics

Addicting diverse bacteria to a noncanonical amino acid

(2016) Drew S Tack et al.   Nature Chemical Biology

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

Combining Sense and Nonsense Codon Reassignment for Site-Selective Protein Modification with Unnatural Amino Acids

(2016) Zhenling Cui et al.   ACS Synthetic Biology

Chemical Evolution of a Bacterial Proteome

(2015) Michael Georg Hoesl et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Creating a completely “cell-free” system for protein synthesis

(2015) Mark Thomas Smith et al.   BIOTECHNOLOGY PROGRESS

A synthetic tRNA for EF-Tu mediated selenocysteine incorporationin vivoandin vitro

(2015) Corwin Miller et al.   FEBS LETTERS

Structural Basis for a Six Nucleotide Genetic Alphabet

(2015) Millie M. Georgiadis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium

(2015) M. Lluch-Senar et al.   Molecular Systems Biology

Recoded organisms engineered to depend on synthetic amino acids

(2015) Alexis J. Rovner et al.   NATURE

Biocontainment of genetically modified organisms by synthetic protein design

(2015) Daniel J. Mandell et al.   NATURE

'Deadman' and 'Passcode' microbial kill switches for bacterial containment

(2015) Clement T Y Chan et al.   Nature Chemical Biology

Reassignment of a rare sense codon to a non-canonical amino acid inEscherichia coli

(2015) Takahito Mukai et al.   NUCLEIC ACIDS RESEARCH

Multilayered genetic safeguards limit growth of microorganisms to defined environments

(2015) Ryan R. Gallagher et al.   NUCLEIC ACIDS RESEARCH

Viral bioterrorism: Learning the lesson of Ebola virus in West Africa 2013–2015

(2015) Orlando Cenciarelli et al.   VIRUS RESEARCH

Targeted DNA degradation using a CRISPR device stably carried in the host genome

(2015) Brian J. Caliando et al.   Nature Communications

High-throughput preparation methods of crude extract for robust cell-free protein synthesis

(2015) Yong-Chan Kwon et al.   Scientific Reports

A Barcoding Strategy Enabling Higher-Throughput Library Screening by Microscopy

(2015) Robert Chen et al.   ACS Synthetic Biology

Predicting the Genetic Stability of Engineered DNA Sequences with the EFM Calculator

(2015) Benjamin R. Jack et al.   ACS Synthetic Biology

BASIC: A New Biopart Assembly Standard for Idempotent Cloning Provides Accurate, Single-Tier DNA Assembly for Synthetic Biology

(2015) Marko Storch et al.   ACS Synthetic Biology

Synthetic Auxotrophs with Ligand-Dependent Essential Genes for a BL21(DE3) Biosafety Strain

(2015) Gabriel Lopez et al.   ACS Synthetic Biology

An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system

(2015) Yusuke Kato   PeerJ

Magnetically Recoverable, Thermostable, Hydrophobic DNA/Silica Encapsulates and Their Application as Invisible Oil Tags

(2014) Michela Puddu et al.   ACS Nano

Chassis organism fromCorynebacterium glutamicum- a top-down approach to identify and delete irrelevant gene clusters

(2014) Simon Unthan et al.   Biotechnology Journal

A semi-synthetic organism with an expanded genetic alphabet

(2014) Denis A. Malyshev et al.   NATURE

iGEM 2.0—refoundations for engineering biology

(2014) Cristina Vilanova et al.   NATURE BIOTECHNOLOGY

CRISPR-Cas systems for editing, regulating and targeting genomes

(2014) Jeffry D Sander et al.   NATURE BIOTECHNOLOGY

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

Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems

(2014) A. A. Gomaa et al.   mBio

Renewable resource-based polymeric microencapsulation of natural pesticide and its release study: an alternative green approach

(2014) Rahul Kishore Hedaoo et al.   RSC Advances

Transcription, Reverse Transcription, and Analysis of RNA Containing Artificial Genetic Components

(2014) Nicole A. Leal et al.   ACS Synthetic Biology

GeneGuard: A Modular Plasmid System Designed for Biosafety

(2014) Oliver Wright et al.   ACS Synthetic Biology

DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides

(2014) Roberto Laos et al.   Frontiers in Microbiology

High-Yield, Zero-Leakage Expression System with a Translational Switch Using Site-Specific Unnatural Amino Acid Incorporation

(2013) Masaomi Minaba et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biosafety Considerations of Synthetic Biology in the International Genetically Engineered Machine (iGEM) Competition

(2013) Zheng-jun Guan et al.   BIOSCIENCE

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

Building-in biosafety for synthetic biology

(2013) O. Wright et al.   MICROBIOLOGY-SGM

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases

(2013) O. Niewoehner et al.   NUCLEIC ACIDS RESEARCH

Development of a Biosafety Enhanced and Immunogenic Salmonella Enteritidis Ghost Using an Antibiotic Resistance Gene Free Plasmid Carrying a Bacteriophage Lysis System

(2013) Chetan V. Jawale et al.   PLoS One

DNA cloning: A personal view after 40 years

(2013) S. N. Cohen   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In defense of phage

(2013) Blake Wiedenheft   RNA Biology

Probing the Limits of Genetic Recoding in Essential Genes

(2013) M. J. Lajoie et al.   SCIENCE

Genomically Recoded Organisms Expand Biological Functions

(2013) M. J. Lajoie et al.   SCIENCE

The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis

(2013) Jara Radeck et al.   Journal of Biological Engineering

Metal-Mediated DNA Base Pairing: Alternatives to Hydrogen-Bonded Watson–Crick Base Pairs

(2012) Yusuke Takezawa et al.   ACCOUNTS OF CHEMICAL RESEARCH

Enhanced protein stability through minimally invasive, direct, covalent, and site-specific immobilization

(2012) Mark T. Smith et al.   BIOTECHNOLOGY PROGRESS

The XNA world: progress towards replication and evolution of synthetic genetic polymers

(2012) Vitor B Pinheiro et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Synthetic constructs in/for the environment: Managing the interplay between natural and engineered Biology

(2012) Markus Schmidt et al.   FEBS LETTERS

Novel Polyurea Microcapsules Using Dendritic Functional Monomer: Synthesis, Characterization, and Its Use in Self-healing and Anticorrosive Polyurethane Coatings

(2012) Pyus D. Tatiya et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

Efficient Decoding of the UAG Triplet as a Full-Fledged Sense Codon Enhances the Growth of a prfA-Deficient Strain of Escherichia coli

(2012) K. Ohtake et al.   JOURNAL OF BACTERIOLOGY

Microencapsulation of microbial cells

(2012) Sweta Rathore et al.   JOURNAL OF FOOD ENGINEERING

From Dusk till Dawn: One-Plasmid Systems for Light-Regulated Gene Expression

(2012) Robert Ohlendorf et al.   JOURNAL OF MOLECULAR BIOLOGY

Designing Allosteric Control into Enzymes by Chemical Rescue of Structure

(2012) Katelyn Deckert et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli

(2012) Hisako Masuda et al.   MOLECULAR MICROBIOLOGY

Structure and activity of AbiQ, a lactococcal endoribonuclease belonging to the type III toxin-antitoxin system

(2012) Julie E. Samson et al.   MOLECULAR MICROBIOLOGY

Chemical biology: DNA's new alphabet

(2012) Roberta Kwok   NATURE

RNA-guided genetic silencing systems in bacteria and archaea

(2012) Blake Wiedenheft et al.   NATURE

A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS

(2012) Xiaoxue Wang et al.   Nature Chemical Biology

An intermolecular disulfide-based light switch for chloroplastpsbDgene expression inChlamydomonas reinhardtii

(2012) Christian Schwarz et al.   PLANT JOURNAL

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

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

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Synthetic Genetic Polymers Capable of Heredity and Evolution

(2012) V. B. Pinheiro et al.   SCIENCE

Genetic engineering of a Lemna isoleucine auxotroph

(2012) Long V. Nguyen et al.   TRANSGENIC RESEARCH

From essential to persistent genes: a functional approach to constructing synthetic life

(2012) Carlos G. Acevedo-Rocha et al.   TRENDS IN GENETICS

Expanding the Product Profile of a Microbial Alkane Biosynthetic Pathway

(2012) Matthew Harger et al.   ACS Synthetic Biology

Synthetic biology: advancing biological frontiers by building synthetic systems

(2012) Yvonne Y Chen et al.   GENOME BIOLOGY

On the Road towards Chemically Modified Organisms Endowed with a Genetic Firewall

(2011) Carlos G. Acevedo-Rocha et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Chemical Evolution of a Bacterium’s Genome

(2011) Philippe Marlière et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

Toxins-antitoxins: diversity, evolution and function

(2011) Finbarr Hayes et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

CRISPR-based adaptive immune systems

(2011) Michael P Terns et al.   CURRENT OPINION IN MICROBIOLOGY

Encoding Phenotype in Bacteria with an Alternative Genetic Set

(2011) Andrew T. Krueger et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Amplification, Mutation, and Sequencing of a Six-Letter Synthetic Genetic System

(2011) Zunyi Yang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cell-free synthetic biology: Thinking outside the cell

(2011) C. Eric Hodgman et al.   METABOLIC ENGINEERING

Microbiology by numbers

(2011)   NATURE REVIEWS MICROBIOLOGY

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity

(2011) Fei Chen et al.   NUCLEIC ACIDS RESEARCH

Highly specific unnatural base pair systems as a third base pair for PCR amplification

(2011) Rie Yamashige et al.   NUCLEIC ACIDS RESEARCH

Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence

(2011) E. Semenova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement

(2011) Farren J. Isaacs et al.   SCIENCE

Essence of life: essential genes of minimal genomes

(2011) Mario Juhas et al.   TRENDS IN CELL BIOLOGY

Adding New Chemistries to the Genetic Code

(2010) Chang C. Liu et al.   Annual Review of Biochemistry

Novel Antibiotic-Free Plasmid Selection System Based on Complementation of Host Auxotrophy in the NAD De Novo Synthesis Pathway

(2010) W.-R. Dong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Xenobiology: A new form of life as the ultimate biosafety tool

(2010) Markus Schmidt   BIOESSAYS

Standard virtual biological parts: a repository of modular modeling components for synthetic biology

(2010) M. T. Cooling et al.   BIOINFORMATICS

Biosafety and biosecurity as essential pillars of international health security and cross-cutting elements of biological nonproliferation

(2010) Lela Bakanidze et al.   BMC PUBLIC HEALTH

Emerging knowledge of regulatory roles of d-amino acids in bacteria

(2010) Felipe Cava et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Bio-encapsulation of microbial cells for targeted agricultural delivery

(2010) Rojan P. John et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Update on designing and building minimal cells

(2010) Michael C Jewett et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genome-Wide Identification ofStreptococcus pneumoniaeGenes Essential for Bacterial Replication during Experimental Meningitis

(2010) T. E. Molzen et al.   INFECTION AND IMMUNITY

Oligonucleotide Duplexes and Multistrand Assemblies with 8-Aza-2′-deoxyisoguanosine: A Fluorescent isoGdShape Mimic Expanding the Genetic Alphabet and Forming Ionophores

(2010) Dawei Jiang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The cspA mRNA Is a Thermosensor that Modulates Translation of the Cold-Shock Protein CspA

(2010) Anna Maria Giuliodori et al.   MOLECULAR CELL

Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome

(2010) Heinz Neumann et al.   NATURE

Self versus non-self discrimination during CRISPR RNA-directed immunity

(2010) Luciano A. Marraffini et al.   NATURE

GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs

(2010) Yizhi Cai et al.   NUCLEIC ACIDS RESEARCH

Codon reassignment in the Escherichia coli genetic code

(2010) T. Mukai et al.   NUCLEIC ACIDS RESEARCH

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

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

Expanded Genetic Alphabets in the Polymerase Chain Reaction

(2009) Zunyi Yang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Structure and Replication of yDNA: A Novel Genetic Set Widened by Benzo-Homologation

(2009) Haige Lu et al.   CHEMBIOCHEM

Toward Safe Genetically Modified Organisms through the Chemical Diversification of Nucleic Acids

(2009) Piet Herdewijn et al.   CHEMISTRY & BIODIVERSITY

Mutagenesis and Functional Characterization of the RNA and Protein Components of the toxIN Abortive Infection and Toxin-Antitoxin Locus of Erwinia

(2009) T. R. Blower et al.   JOURNAL OF BACTERIOLOGY

Tracing Ancestors and Relatives of Escherichia coli B, and the Derivation of B Strains REL606 and BL21(DE3)

(2009) Patrick Daegelen et al.   JOURNAL OF MOLECULAR BIOLOGY

Transcription of an Expanded Genetic Alphabet

(2009) Young Jun Seo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

(2009)   MICROBIOLOGY-SGM

Building outside of the box: iGEM and the BioBricks Foundation

(2009) Christina D Smolke   NATURE BIOTECHNOLOGY

The phage abortive infection system, ToxIN, functions as a protein–RNA toxin–antitoxin pair

(2009) Peter C. Fineran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Toxin–Antitoxin Systems: More Than Selfish Entities?

(2009) Laurence Van Melderen et al.   PLoS Genetics

Brucella abortus Strain RB51 Leucine Auxotroph as an Environmentally Safe Vaccine for Plasmid Maintenance and Antigen Overexpression

(2008) P. Rajasekaran et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enzymatically Catalyzed DNA Synthesis UsingL-Asp-dGMP,L-Asp-dCMP, andL-Asp-dTMP

(2008) Montserrat Terrazas et al.   CHEMISTRY & BIODIVERSITY

Evidence-Based Biosafety: a Review of the Principles and Effectiveness of Microbiological Containment Measures

(2008) T. G. Kimman et al.   CLINICAL MICROBIOLOGY REVIEWS

Development of an antibiotic-free plasmid selection system based on glycine auxotrophy for recombinant protein overproduction in Escherichia coli

(2008) Luis Vidal et al.   JOURNAL OF BIOTECHNOLOGY

Design and Signaling Mechanism of Light-Regulated Histidine Kinases

(2008) Andreas Möglich et al.   JOURNAL OF MOLECULAR BIOLOGY

Bacterial DNA topology and infectious disease

(2008) C. J. Dorman et al.   NUCLEIC ACIDS RESEARCH

CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA

(2008) Luciano A. Marraffini et al.   SCIENCE

The effect of covalent cross-links between the membrane components of microcapsules on the dissemination of encapsulated malignant cells

(2007) J DUSSEAULT et al.   BIOMATERIALS

Engineering ingenuity at iGEM

(2007) Catherine Goodman   Nature Chemical Biology