The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics

Structure–Activity Relationships of Anti-microRNA Oligonucleotides Containing Cationic Guanidine-Modified Nucleic Acids

(2022) Tomo Takegawa-Araki et al.   JOURNAL OF MEDICINAL CHEMISTRY

On gene silencing by the X10-23 DNAzyme

(2022) Alexander I. Taylor et al.   Nature Chemistry

A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing

(2022) Alexander I. Taylor et al.   Nature Chemistry

A two-residue nascent-strand steric gate controls synthesis of 2′-O-methyl- and 2′-O-(2-methoxyethyl)-RNA

(2022) Niklas Freund et al.   Nature Chemistry

Ribonucleotide incorporation into DNA during DNA replication and its consequences

(2021) Zhi-Xiong Zhou et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

A biologically stable DNAzyme that efficiently silences gene expression in cells

(2021) Yajun Wang et al.   Nature Chemistry

Bioorthogonal information storage in l-DNA with a high-fidelity mirror-image Pfu DNA polymerase

(2021) Chuyao Fan et al.   NATURE BIOTECHNOLOGY

Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II

(2021) Juntaek Oh et al.   Nature Chemical Biology

A 68-codon genetic code to incorporate four distinct non-canonical amino acids enabled by automated orthogonal mRNA design

(2021) Daniel L. Dunkelmann et al.   Nature Chemistry

Sense codon reassignment enables viral resistance and encoded polymer synthesis

(2021) Wesley E. Robertson et al.   SCIENCE

Structure and hybridization properties of phosphoryl guanidine oligonucleotides under crowding conditions

(2021) Maria A. Kanarskaya et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Toward synthetic life: Biomimetic synthetic cell communication

(2021) Abbey O. Robinson et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Time-resolved structural analysis of an RNA-cleaving DNA catalyst

(2021) Jan Borggräfe et al.   NATURE

An RNA-cleaving threose nucleic acid enzyme capable of single point mutation discrimination

(2021) Yueyao Wang et al.   Nature Chemistry

Xeno-Nucleic Acid (XNA) 2’-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor-Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding

(2021) Irani Alves Ferreira-Bravo et al.   Viruses-Basel

Multiplex suppression of four quadruplet codons via tRNA directed evolution

(2021) Erika A. DeBenedictis et al.   Nature Communications

New chemistries and enzymes for synthetic genetics

(2021) Niklas Freund et al.   CURRENT OPINION IN BIOTECHNOLOGY

Generating Biologically Stable TNA Aptamers that Function with High Affinity and Thermal Stability

(2020) Matthew R. Dunn et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform

(2020) Tran Thi Nhu Thao et al.   NATURE

New codons for efficient production of unnatural proteins in a semisynthetic organism

(2020) Emil C. Fischer et al.   Nature Chemical Biology

Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis

(2020) Daisuke Kawaguchi et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Discovery and evolution of RNA and XNA reverse transcriptase function and fidelity

(2020) Gillian Houlihan et al.   Nature Chemistry

Programmed Allelic Mutagenesis of a DNA Polymerase with Single Amino Acid Resolution

(2020) Ali Nikoomanzar et al.   ACS Synthetic Biology

Modified nucleic acids: replication, evolution, and next-generation therapeutics

(2020) Karen Duffy et al.   BMC BIOLOGY

In Vitro Selection of an ATP-Binding TNA Aptamer

(2020) Li Zhang et al.   MOLECULES

Addicting Escherichia coli to New-to-Nature Reactions

(2020) Rudy Rubini et al.   ACS Chemical Biology

DNA Polymerase Variants with High Processivity and Accuracy for Encoding and Decoding Locked Nucleic Acid Sequences

(2020) Hidekazu Hoshino et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA 2’-O-Methylation (Nm) Modification in Human Diseases

(2019) Dilyana G. Dimitrova et al.   Genes

Hachimoji DNA and RNA: A genetic system with eight building blocks

(2019) Shuichi Hoshika et al.   SCIENCE

Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes

(2019) Christopher D. Reinkemeier et al.   SCIENCE

Total synthesis of Escherichia coli with a recoded genome

(2019) Julius Fredens et al.   NATURE

A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids

(2019) Sebastian Arangundy-Franklin et al.   Nature Chemistry

Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor

(2019) Elena Eremeeva et al.   NUCLEIC ACIDS RESEARCH

Beyond DNA and RNA: The Expanding Toolbox of Synthetic Genetics

(2019) Alexander I. Taylor et al.   Cold Spring Harbor Perspectives in Biology

The structural basis for processing of unnatural base pairs by DNA polymerases

(2019) Andreas Marx et al.   CHEMISTRY-A EUROPEAN JOURNAL

Dual Mechanisms of Action of Self-Delivering, Anti-HIV-1 FANA Oligonucleotides as a Potential New Approach to HIV Therapy

(2019) Mayumi Takahashi et al.   Molecular Therapy-Nucleic Acids

A metric space for semantic containment: Towards the implementation of genetic firewalls

(2019) Markus Schmidt   BIOSYSTEMS

Orthogonal Genetic Systems

(2019) John C. Chaput et al.   CHEMBIOCHEM

Mercury-Free Automated Synthesis of Guanidinium Backbone Oligonucleotides

(2019) Kacper Skakuj et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Synthesis and Evolution of a Threose Nucleic Acid Aptamer Bearing 7-Deaza-7-Substituted Guanosine Residues

(2018) Hui Mei et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reprograming the Replisome of a Semisynthetic Organism for the Expansion of the Genetic Alphabet

(2018) Michael P. Ledbetter et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Next-generation biocontainment systems for engineered organisms

(2018) Jeong Wook Lee et al.   Nature Chemical Biology

Toward an orthogonal central dogma

(2018) Chang C Liu et al.   Nature Chemical Biology

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome

(2018) B. A. Blount et al.   Nature Communications

Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods

(2018) Wei Liu et al.   Nature Communications

Metabolic Recruitment and Directed Evolution of Nucleoside Triphosphate Uptake in Escherichia coli

(2018) Valérie Pezo et al.   ACS Synthetic Biology

“Skinny” and “Fat” DNA: Two New Double Helices

(2018) Shuichi Hoshika et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Creating a functional single-chromosome yeast

(2018) Yangyang Shao et al.   NATURE

Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds

(2018) Arjun Ravikumar et al.   CELL

Evolution of a General RNA-Cleaving FANA Enzyme

(2018) Yajun Wang et al.   Nature Communications

Chemical Stabilization of Unnatural Nucleotide Triphosphates for the in Vivo Expansion of the Genetic Alphabet

(2017) Aaron W. Feldman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Expanding and reprogramming the genetic code

(2017) Jason W. Chin   NATURE

A semi-synthetic organism that stores and retrieves increased genetic information

(2017) Yorke Zhang et al.   NATURE

Biological phosphorylation of an Unnatural Base Pair (UBP) using a Drosophila melanogaster deoxynucleoside kinase (DmdNK) mutant

(2017) Fei Chen et al.   PLoS One

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

Design of a synthetic yeast genome

(2017) Sarah M. Richardson et al.   SCIENCE

Reverse Transcription of Threose Nucleic Acid by a Naturally Occurring DNA Polymerase

(2016) Matthew R. Dunn et al.   CHEMBIOCHEM

Nanostructures from Synthetic Genetic Polymers

(2016) Alexander I. Taylor et al.   CHEMBIOCHEM

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

(2016) Leticia Torres et al.   Essays in Biochemistry

The Medicinal Chemistry of Therapeutic Oligonucleotides

(2016) W. Brad Wan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Defining synonymous codon compression schemes by genome recoding

(2016) Kaihang Wang et al.   NATURE

Engineering genetic circuit interactions within and between synthetic minimal cells

(2016) Katarzyna P. Adamala et al.   Nature Chemistry

Design and synthesis of a minimal bacterial genome

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

The Genome Project-Write

(2016) J. D. Boeke et al.   SCIENCE

Alternative Watson–Crick Synthetic Genetic Systems

(2016) Steven A. Benner et al.   Cold Spring Harbor Perspectives in Biology

Assays To Detect the Formation of Triphosphates of Unnatural Nucleotides: Application to Escherichia coli Nucleoside Diphosphate Kinase

(2016) Mariko F. Matsuura et al.   ACS Synthetic Biology

Biocontainment through Reengineered Genetic Codes

(2015) Arjun Ravikumar et al.   CHEMBIOCHEM

Structural Basis for a Six Nucleotide Genetic Alphabet

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

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

Directed evolution of artificial enzymes (XNAzymes) from diverse repertoires of synthetic genetic polymers

(2015) Alexander I Taylor et al.   Nature Protocols

Efficient Multisite Unnatural Amino Acid Incorporation in Mammalian Cells via Optimized Pyrrolysyl tRNA Synthetase/tRNA Expression and Engineered eRF1

(2014) Wolfgang H. Schmied et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A semi-synthetic organism with an expanded genetic alphabet

(2014) Denis A. Malyshev et al.   NATURE

Catalysts from synthetic genetic polymers

(2014) Alexander I. Taylor et al.   NATURE

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

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

Natural-like Replication of an Unnatural Base Pair for the Expansion of the Genetic Alphabet and Biotechnology Applications

(2013) Lingjun Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Binding of a Structured d-RNA Molecule by an l-RNA Aptamer

(2013) Jonathan T. Sczepanski et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Natural versus Artificial Creation of Base Pairs in DNA: Origin of Nucleobases from the Perspectives of Unnatural Base Pair Studies

(2012) Ichiro Hirao et al.   ACCOUNTS OF CHEMICAL RESEARCH

Redesigning the leaving group in nucleic acid polymerization

(2012) P. Herdewijn et al.   FEBS LETTERS

KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry

(2012) Karin Betz et al.   Nature Chemical Biology

Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet

(2012) Denis A. Malyshev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic Genetic Polymers Capable of Heredity and Evolution

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

Chemical Evolution of a Bacterium’s Genome

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

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

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

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

(2011) Jessica S. Dymond et al.   NATURE

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

(2011) Rie Yamashige et al.   NUCLEIC ACIDS RESEARCH

Aptamer-Based Multiplexed Proteomic Technology for Biomarker Discovery

(2011) Larry Gold et al.   PLoS One

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

(2011) Farren J. Isaacs et al.   SCIENCE

Synthesis and evaluation of 2′-O-allyl substituted dinucleotide cap analog for mRNA translation

(2010) Anilkumar R. Kore et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Solution Structure, Mechanism of Replication, and Optimization of an Unnatural Base Pair

(2010) Denis A. Malyshev et al.   CHEMISTRY-A EUROPEAN JOURNAL

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

(2010) Heinz Neumann et al.   NATURE

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

PCR with an Expanded Genetic Alphabet

(2009) Denis A. Malyshev et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Transcription of an Expanded Genetic Alphabet

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

Optimization of an Unnatural Base Pair toward Natural-Like Replication

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

An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules

(2008) Michiko Kimoto et al.   NUCLEIC ACIDS RESEARCH