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Rapid evolution of a highly efficient RNA polymerase by homologous recombination

Engineering polymerases to synthesize alternative genetic polymers remains a challenging problem in synthetic biology. Using DNA shuffling and droplet microfluidics, the current study provides a short evolutionary path from a DNA polymerase to one with robust RNA-synthesizing activity.

Esau L. Medina
Victoria A. Maola
John C. Chaput
Research07 Jan 2026
Nature Chemical Biology

P: 1-9
Directed evolution of a TNA polymerase identifies independent paths to fidelity and catalysis

Engineering polymerases to synthesize alternative genetic polymers remains a challenging problem in synthetic biology. The current study offers insights into the structural and biochemical changes responsible for improving the fidelity and catalytic activity of a laboratory evolved TNA polymerase.

Mohammad Hajjar
Victoria A. Maola
John C. Chaput
ResearchOpen Access19 Dec 2025
Nature Communications

Volume: 17, P: 1-14
Following replicative DNA synthesis by time-resolved X-ray crystallography

DNA polymerases are the key enzymes responsible for DNA replication and repair. Here the authors reveal through time-lapsed images of X-ray crystal structures that translocation precedes phosphodiester bond formation in the mechanism of DNA synthesis.

Nicholas Chim
Roman A. Meza
John C. Chaput
ResearchOpen Access11 May 2021
Nature Communications

Volume: 12, P: 1-8
Chronic Fluoxetine Reduces Serotonin Transporter mRNA and 5-HT_1B mRNA in a Sequential Manner in the Rat Dorsal Raphe Nucleus

John F Neumaier
Daniel C Root
Mark W Hamblin
Research01 Nov 1996
Neuropsychopharmacology

Volume: 15, P: 515-522
Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor

The pre-RNA-world hypothesis postulates that RNA was preceded in the evolution of life by a simpler genetic material. Here, Darwinian evolution methods were used to generate a threose nucleic acid (TNA) aptamer. This result provides evidence that TNA could have served as an ancestral genetic system during an early stage of life.

Hanyang Yu
Su Zhang
John C. Chaput
Research10 Jan 2012
Nature Chemistry

Volume: 4, P: 183-187
Analysis of aptamer discovery and technology

Aptamers are nucleic acid molecules that can be evolved to bind to specific molecular targets and have found applications in technologies such as sensors and actuators. This Review provides a critical analysis of the first 25 years of aptamer research.

Matthew R. Dunn
Randi M. Jimenez
John C. Chaput
Reviews04 Oct 2017
Nature Reviews Chemistry

Volume: 1, P: 1-16
Directed evolution of a highly efficient TNA polymerase achieved by homologous recombination

The catalytic power of DNA polymerases for artificial genetic polymer (XNA) synthesis remains underdeveloped. Now, the evolution and structure of an α-l-threofuranosyl nucleic acid polymerase is described that achieves XNA synthesis with ∼1 nt s⁻¹ and >99% template-copying fidelity.

Victoria A. Maola
Eric J. Yik
John C. Chaput
Research01 Oct 2024
Nature Catalysis

Volume: 7, P: 1173-1185
Genome-wide profiling of human cap-independent translation-enhancing elements

A method to identify genomic elements that promote cap-independent translation is described and is used to identify such elements in the human genome.

Brian P Wellensiek
Andrew C Larsen
John C Chaput
Research16 Jun 2013
Nature Methods

Volume: 10, P: 747-750
Reply to: On gene silencing by the X10-23 DNAzyme

Robert C. Spitale
John C. Chaput
Research18 Jul 2022
Nature Chemistry

Volume: 14, P: 859-861
Chemical evolution of an autonomous DNAzyme with allele-specific gene silencing activity

Low activity currently prevents the wider use of DNA enzymes (DNAzymes). Here the authors report the chemical evolution of a DNAzyme with high catalytic activity under near physiological conditions: the enzyme achieves ~65 turnovers in 30 minutes.

Kim Nguyen
Turnee N. Malik
John C. Chaput
ResearchOpen Access27 Apr 2023
Nature Communications

Volume: 14, P: 1-11
Evolution of a General RNA-Cleaving FANA Enzyme

Artificial genetic polymers (XNAs) have been explored for their nuclease activity, but XNAzymes have proven challenging to discover by in vitro selection. Here, the authors generate an efficient RNA-cleaving 2’-fluoroarabino nucleic acid enzyme (FANAzyme) by in vitro evolution using natural DNA polymerases.

Yajun Wang
Arlene K. Ngor
John C. Chaput
ResearchOpen Access29 Nov 2018
Nature Communications

Volume: 9, P: 1-10
A biologically stable DNAzyme that efficiently silences gene expression in cells

RNA-cleaving DNA enzymes (DNAzymes) have the potential to function as therapeutic agents by silencing the expression of disease-associated proteins. Xeno-nucleic acids were used to improve the catalytic activity and biological stability of a highly evolved DNAzyme known as 10–23. The enzyme exhibits a robust multiple-turnover activity in cultured mammalian cells.

Yajun Wang
Kim Nguyen
John C. Chaput
Research25 Mar 2021
Nature Chemistry

Volume: 13, P: 319-326
Structural basis for TNA synthesis by an engineered TNA polymerase

The laboratory-evolved polymerase Kod-RI catalyzes α-L-threose nucleic acid (TNA) synthesis. Here, the authors present Kod-RI crystal structures that give insights into how TNA triphosphates are selected and extended in a template-dependent manner, which will help to engineer improved TNA polymerases for synthetic genetics applications.

Nicholas Chim
Changhua Shi
John C. Chaput
ResearchOpen Access27 Nov 2017
Nature Communications

Volume: 8, P: 1-11
A general strategy for expanding polymerase function by droplet microfluidics

Droplet-based optical polymerase sorting employs a fluorescent sensor to monitor polymerase activity inside the microenvironment of uniform water-in-oil emulsions. Here, the authors use this technique to select and isolate single cells for evolution of an unnatural nucleic acid polymerase.

Andrew C. Larsen
Matthew R. Dunn
John C. Chaput
ResearchOpen Access05 Apr 2016
Nature Communications

Volume: 7, P: 1-9
Nod1 responds to peptidoglycan delivered by the Helicobacter pylori cag pathogenicity island

Jérôme Viala
Catherine Chaput
Richard L Ferrero
Research17 Oct 2004
Nature Immunology

Volume: 5, P: 1166-1174
Made in translation

Evolution of highly functionalized DNA could enable the discovery of artificial nucleic acid sequences with different properties to natural DNA. Now, an artificial translation system has been designed that can support the evolution of non-natural sequence-defined nucleic acid polymers carrying eight different functional groups on 32 codons.

John C. Chaput
News & Views22 Mar 2018
Nature Chemistry

Volume: 10, P: 379-381
The 5-HT1A Receptor: Signaling, Desensitization, and Gene Transcription

Paul R. Albert
Paola Lembo
Caroline Saucier
Research01 Jan 1996
Neuropsychopharmacology

Volume: 14, P: 19-25
Differential Occupancy of Somatodendritic and Postsynaptic 5HT_1A Receptors by Pindolol: A Dose-Occupancy Study with [¹¹C]WAY 100635 and Positron Emission Tomography in Humans

Diana Martinez
Dah-Ren Hwang
Marc Laruelle
Research01 Mar 2001
Neuropsychopharmacology

Volume: 24, P: 209-229
A Novel Small RNA-Cleaving Deoxyribozyme with a Short Binding Arm

Yueyao Wang
Jintao Yang
Hanyang Yu
ResearchOpen Access03 Jun 2019
Scientific Reports

Volume: 9, P: 1-12
An integrative investigation of sensory organ development and orientation behavior throughout the larval phase of a coral reef fish

John E. Majoris
Matthew A. Foretich
Peter M. Buston
ResearchOpen Access11 Jun 2021
Scientific Reports

Volume: 11, P: 1-13
Robo4 is constitutively shed by ADAMs from endothelial cells and the shed Robo4 functions to inhibit Slit3-induced angiogenesis

Wenyuan Xiao
Alejandro Pinilla-Baquero
Lianchun Wang
ResearchOpen Access14 Mar 2022
Scientific Reports

Volume: 12, P: 1-14
Dimethyl Sulfide is a Chemical Attractant for Reef Fish Larvae

Matthew A. Foretich
Claire B. Paris
Daniel D. Benetti
ResearchOpen Access31 May 2017
Scientific Reports

Volume: 7, P: 1-10
Relationships between active school transport and adiposity indicators in school-age children from low-, middle- and high-income countries

O L Sarmiento
P Lemoine
P T Katzmarzyk
Research08 Dec 2015
International Journal of Obesity Supplements

Volume: 5, P: S107-S114

Search

Rapid evolution of a highly efficient RNA polymerase by homologous recombination

Directed evolution of a TNA polymerase identifies independent paths to fidelity and catalysis

Following replicative DNA synthesis by time-resolved X-ray crystallography

Chronic Fluoxetine Reduces Serotonin Transporter mRNA and 5-HT_1B mRNA in a Sequential Manner in the Rat Dorsal Raphe Nucleus

Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor

Analysis of aptamer discovery and technology

Directed evolution of a highly efficient TNA polymerase achieved by homologous recombination

Genome-wide profiling of human cap-independent translation-enhancing elements

Reply to: On gene silencing by the X10-23 DNAzyme

Chemical evolution of an autonomous DNAzyme with allele-specific gene silencing activity

Evolution of a General RNA-Cleaving FANA Enzyme

A biologically stable DNAzyme that efficiently silences gene expression in cells

Structural basis for TNA synthesis by an engineered TNA polymerase

A general strategy for expanding polymerase function by droplet microfluidics

Nod1 responds to peptidoglycan delivered by the Helicobacter pylori cag pathogenicity island

Made in translation

The 5-HT1A Receptor: Signaling, Desensitization, and Gene Transcription

Differential Occupancy of Somatodendritic and Postsynaptic 5HT_1A Receptors by Pindolol: A Dose-Occupancy Study with [¹¹C]WAY 100635 and Positron Emission Tomography in Humans

A Novel Small RNA-Cleaving Deoxyribozyme with a Short Binding Arm

An integrative investigation of sensory organ development and orientation behavior throughout the larval phase of a coral reef fish

Robo4 is constitutively shed by ADAMs from endothelial cells and the shed Robo4 functions to inhibit Slit3-induced angiogenesis

Dimethyl Sulfide is a Chemical Attractant for Reef Fish Larvae

Relationships between active school transport and adiposity indicators in school-age children from low-, middle- and high-income countries

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