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Biochemistry x Science and Mathematics x Enzymology x clear all

Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes

Lucia Greenough, Kelly M. Schermerhorn, Laurie Mazzola, Joanna Bybee, Danielle Rivizzigno, Elizabeth Cantin, Barton E. Slatko and Andrew F. Gardner.

in Nucleic Acids Research

January 2016; p ublished online September 2015 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics. 6454 words.

Detailed biochemical characterization of nucleic acid enzymes is fundamental to understanding nucleic acid metabolism, genome replication and repair. We report the development of a rapid,...

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The catalytic efficiency of yeast ribonuclease III depends on substrate specific product release rate

Marc-Andre Comeau, Daniel A. Lafontaine and Sherif Abou Elela.

in Nucleic Acids Research

September 2016; p ublished online June 2016 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics. 7172 words.

Members of the ribonuclease III (RNase III) family regulate gene expression by triggering the degradation of double stranded RNA (dsRNA). Hundreds of RNase III cleavage targets have been...

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Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes

Alexandre Melnikov, Peter Rogov, Li Wang, Andreas Gnirke and Tarjei S. Mikkelsen.

in Nucleic Acids Research

August 2014; p ublished online June 2014 .

Journal Article. Subjects: Research Methods in Life Sciences; Enzymology; Molecular Biology and Genetics. 4829 words.

Deep mutational scanning has emerged as a promising tool for mapping sequence–activity relationships in proteins, ribonucleic acid and deoxyribonucleic acid. In this approach, diverse...

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The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility

Kyle T Powers, Adrian H Elcock and M Todd Washington.

in Nucleic Acids Research

February 2018; p ublished online January 2018 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 9555 words.

Abstract

Eukaryotic DNA polymerase η catalyzes translesion synthesis of thymine dimers and 8-oxoguanines. It is comprised of a polymerase domain and a...

De novo assembly of genuine replication forks on an immobilized circular plasmid in Xenopus egg extracts

Akiko Zembutsu and Shou Waga.

in Nucleic Acids Research

August 2006; p ublished online August 2006 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics. 5952 words.

We describe an improved model of DNA replication in Xenopus egg extracts, in which a circular plasmid immobilized on paramagnetic beads is used as a template. DNA synthesis occurred on...

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Design and synthesis of fluorescent substrates for human tyrosyl-DNA phosphodiesterase I

Marc C. Rideout, Amy C. Raymond and Alex B. Burgin.

in Nucleic Acids Research

January 2004; p ublished online January 2004 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics. 4942 words.

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that acts upon protein–DNA covalent complexes. Tdp1 hydrolyzes 3′-phosphotyrosyl bonds to generate 3′-phosphate DNA and free...

A fluorescence-based helicase assay: application to the screening of G-quadruplex ligands

Oscar Mendoza, Nassima Meriem Gueddouda, Jean-Baptiste Boulé, Anne Bourdoncle and Jean-Louis Mergny.

in Nucleic Acids Research

June 2015; p ublished online March 2015 .

Journal Article. Subjects: Research Methods in Life Sciences; Enzymology; Molecular Biology and Genetics; Proteins. 6241 words.

Helicases, enzymes that unwind DNA or RNA structure, are present in the cell nucleus and in the mitochondrion. Although the majority of the helicases unwind DNA or RNA duplexes, some of...

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FRET-based assay to screen inhibitors of HIV-1 reverse transcriptase and nucleocapsid protein

Kamal K. Sharma, Frédéric Przybilla, Tobias Restle, Julien Godet and Yves Mély.

in Nucleic Acids Research

May 2016; p ublished online January 2016 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics. 6566 words.

During HIV-1 reverse transcription, the single-stranded RNA genome is converted into proviral double stranded DNA by Reverse Transcriptase (RT) within a reverse transcription complex...

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High-temperature single-molecule kinetic analysis of thermophilic archaeal MCM helicases

Kelly M. Schermerhorn, Nathan Tanner, Zvi Kelman and Andrew F. Gardner.

in Nucleic Acids Research

October 2016; p ublished online July 2016 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics; Proteins. 5625 words.

The minichromosome maintenance (MCM) complex is the replicative helicase responsible for unwinding DNA during archaeal and eukaryal genome replication. To mimic long helicase events in the...

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High-throughput assay and engineering of self-cleaving ribozymes by sequencing

Shungo Kobori, Yoko Nomura, Anh Miu and Yohei Yokobayashi.

in Nucleic Acids Research

July 2015; p ublished online March 2015 .

Journal Article. Subjects: Enzymology; Research Methods in Life Sciences; Molecular Biology and Genetics. 5349 words.

Self-cleaving ribozymes are found in all domains of life and are believed to play important roles in biology. Additionally, self-cleaving ribozymes have been the subject of extensive...

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A high-throughput assay for the comprehensive profiling of DNA ligase fidelity

Gregory J. S. Lohman, Robert J. Bauer, Nicole M. Nichols, Laurie Mazzola, Joanna Bybee, Danielle Rivizzigno, Elizabeth Cantin and Thomas C. Evans.

in Nucleic Acids Research

January 2016; p ublished online September 2015 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics. 8044 words.

DNA ligases have broad application in molecular biology, from traditional cloning methods to modern synthetic biology and molecular diagnostics protocols. Ligation-based detection of...

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A high-throughput assay for Tn5 Tnp-induced DNA cleavage

Brandon Ason and William S. Reznikoff.

in Nucleic Acids Research

January 2004; p ublished online January 2004 .

Journal Article. Subjects: Enzymology; Molecular and Cell Biology; Molecular Biology and Genetics. 3431 words.

Transposition causes genomic instability by mobilizing DNA elements. This phenomenon is mechanistically related to other DNA rearrangements, such as V(D)J recombination and retroviral DNA...

Identification of human telomerase assembly inhibitors enabled by a novel method to produce hTERT

Guillaume Kellermann, Markus Kaiser, Florent Dingli, Olivier Lahuna, Delphine Naud-Martin, Florence Mahuteau-Betzer, Damarys Loew, Evelyne Ségal-Bendirdjian, Marie-Paule Teulade-Fichou and Sophie Bombard.

in Nucleic Acids Research

September 2015; p ublished online May 2015 .

Journal Article. Subjects: Proteins; Enzymology; Molecular and Cell Biology; Molecular Biology and Genetics. 7197 words.

Telomerase is the enzyme that maintains the length of telomeres. It is minimally constituted of two components: a core reverse transcriptase protein (hTERT) and an RNA (hTR). Despite its...

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In vitro selection of restriction endonucleases by in vitro compartmentalization

Nobuhide Doi, Shin Kumadaki, Yuko Oishi, Nobutaka Matsumura and Hiroshi Yanagawa.

in Nucleic Acids Research

January 2004; p ublished online January 2004 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics. 4368 words.

Restriction endonucleases are widely used in laboratory applications from recombinant DNA technology to diagnostics, but engineering of restriction enzymes by structure-guided design and in...

Ligase‐mediated construction of branched DNA strands: a novel DNA joining activity catalyzed by T4 DNA ligase

Maritha Mendel‐Hartvig, Anil Kumar and Ulf Landegren.

in Nucleic Acids Research

January 2004; p ublished online January 2004 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics. 3641 words.

Branched nucleic acid strands exist as intermediates in certain biological reactions, and bifurcating DNA also presents interesting opportunities in biotechnological applications. We...

Massively parallel determination and modeling of endonuclease substrate specificity

Summer B. Thyme, Yifan Song, T. J. Brunette, Mindy D. Szeto, Lara Kusak, Philip Bradley and David Baker.

in Nucleic Acids Research

December 2014; p ublished online November 2014 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics; Proteins; Research Methods in Life Sciences. 8116 words.

We describe the identification and characterization of novel homing endonucleases using genome database mining to identify putative target sites, followed by high throughput activity...

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Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase

Zhong Ren.

in Nucleic Acids Research

September 2016; p ublished online June 2016 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 12316 words.

DNA polymerases in family B are workhorses of DNA replication that carry out the bulk of the job at a high speed with high accuracy. A polymerase in this family relies on a built-in...

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A novel high-throughput activity assay for the Trypanosoma brucei editosome enzyme REL1 and other RNA ligases

Stephan Zimmermann, Laurence Hall, Sean Riley, Jesper Sørensen, Rommie E. Amaro and Achim Schnaufer.

in Nucleic Acids Research

February 2016; p ublished online September 2015 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics; Research Methods in Life Sciences. 7890 words.

The protist parasite Trypanosoma brucei causes Human African trypanosomiasis (HAT), which threatens millions of people in sub-Saharan Africa. Without treatment the infection is almost...

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Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq

Michael J Guertin, Amy E Cullen, Florian Markowetz and Andrew N Holding.

in Nucleic Acids Research

July 2018; p ublished online April 2018 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics; Proteins. 8747 words.

Abstract

A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide...

Polyadenylation-dependent screening assay for respiratory syncytial virus RNA transcriptase activity and identification of an inhibitor

Stephen W. Mason, Carol Lawetz, Yvon Gaudette, Florence Dô, Erika Scouten, Lisette Lagacé, Bruno Simoneau and Michel Liuzzi.

in Nucleic Acids Research

September 2004; p ublished online September 2004 .

Journal Article. Subjects: Enzymology; Molecular Biology and Genetics. 6964 words.

RNA-dependent RNA polymerase from respiratory syncytial virus (RSV) is a multi-subunit ribonucleoprotein (RNP) complex that, in addition to synthesizing the full 15 222 nt viral genomic RNA,...