Article
Biology
Martin Rieu, Jessica Valle-Orero, Bertrand Ducos, Jean-Francois Allemand, Vincent Croquette
Summary: The researchers introduced a single-molecule manipulation method called kinetic locking based on magnetic tweezers, which enables direct detection of biomolecular binding without the use of fluorescent probes. By measuring the dynamic interactions of E. coli RecQ helicase with its DNA substrate, they demonstrated the potential of this method for studying DNA-DNA and DNA-protein interactions while avoiding the need for labeling. This fluorescence-free micro-manipulation technique allows functional characterization of DNA/RNA processing proteins, without interference from labels.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemical Research Methods
Piero R. Bianco
Summary: This review discusses important aspects of studying DNA helicases, including the use of various assays, the contribution of single-molecule studies, and the correlation with bulk-phase studies.
Article
Biochemistry & Molecular Biology
Morgan L. Jones, Yasemin Baris, Martin R. G. Taylor, Joseph T. P. Yeeles
Summary: This study determined the structure of a human replisome containing multiple proteins, revealing their interactions and providing insights into the working mechanism of the replisome and how it maintains smooth replication progression.
Article
Multidisciplinary Sciences
Dillon B. Nye, Nathan A. Tanner
Summary: Recent advances in next generation sequencing technologies have made it possible to read DNA molecules hundreds of kilobases in length. This has motivated the development of DNA amplification methods capable of producing long amplicons. In this study, the researchers investigated strand-displacement amplification reactions using the T7 replisome, a multiprotein complex involved in DNA replication. They utilized Oxford Nanopore long-read sequencing technology to gain insight into the reaction mechanism. The results revealed chimeric DNA reads and a connection between template switching and polymerase exonuclease activity.
Article
Biochemistry & Molecular Biology
Yoshitami Hashimoto, Kota Sadano, Nene Miyata, Haruka Ito, Hirofumi Tanaka
Summary: DONSON is a novel initiator protein essential for CMG helicase assembly in vertebrates, as demonstrated by experiments in a Xenopus cell-free system. DONSON interacts with GINS and Pol ε to promote replisome assembly, and its chromatin association during replication initiation requires the pre-replicative complex, TopBP1, and kinase activities of S-CDK and DDK.
Article
Biochemistry & Molecular Biology
Dian Spakman, Julia A. M. Bakx, Andreas S. Biebricher, Erwin J. G. Peterman, Gijs J. L. Wuite, Graeme A. King
Summary: Type 1A topoisomerases are essential enzymes that require single-stranded DNA for activity, playing a crucial role in maintaining DNA structure and resolving entanglements during replication and repair. Recent advancements in single-molecule assays and biochemical studies have provided a deeper understanding of their gate opening dynamics, strand-passage mechanisms, and interactions with partner proteins like RecQ-family helicases. These assays have also shed new light on their functional roles in vivo and the potential for further enhancing our understanding of these enzymes through single-molecule technologies.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Holly M. M. Radford, Casey J. J. Toft, Alanna E. E. Sorenson, Patrick M. M. Schaeffer
Summary: Over 1.2 million deaths are caused by multi-drug-resistant bacteria each year, as a result of their fast replication and rapid evolution. The accumulation of resistance genes in pathogens has made current antibiotic treatments ineffective, leading to a decrease in reliable treatment options for MDR-associated diseases. This review provides a critical evaluation of DNA replication initiation in bacteria and highlights the potential of essential initiation proteins as emerging drug targets. It also examines the available methods to study and screen promising replication initiation proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Cell Biology
Muwen Kong, Eric C. Greene
Summary: DNA double strand breaks are highly deleterious forms of DNA damage that, if left unrepaired, can lead to a high risk of cancer. Homologous recombination and nonhomologous end joining are the two major mechanisms responsible for repairing DSBs, and single-molecule studies have provided detailed insights into the repair processes at each step.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
News Item
Optics
Xiaohe Zhang, Bing Gu, Cheng-Wei Qiu
Summary: Researchers have proposed a new method that can measure the weak force of a single microscopic particle.
LIGHT-SCIENCE & APPLICATIONS
(2021)
Article
Cell Biology
Lillian Campos, Sabrina X. Van Ravenstein, Emma J. Vontalge, Briana H. Greer, Darren R. Heintzman, Tamar Kavlashvili, W. Hayes McDonald, Kristie Lindsey Rose, Brandt F. Eichman, James M. Dewar
Summary: Topological stress can cause converging replication forks to stall during termination of vertebrate DNA synthesis. However, replication forks ultimately overcome fork stalling, suggesting that alternative mechanisms of termination exist. Using proteomics in Xenopus egg extracts, researchers found that the helicase RTEL1 and the replisome protein MCM10 play a general role in promoting progression of stalled forks, including when forks stall during termination. They discovered an alternative mechanism of termination involving RTEL1 and MCM10 that can be used to complete DNA synthesis under conditions of topological stress.
Article
Biochemistry & Molecular Biology
Sabrine Hedouin, Glennis A. Logsdon, Jason G. Underwood, Sue Biggins
Summary: This study used a targeted RNA isoform sequencing approach to identify the transcriptional landscape at and surrounding all centromeres in budding yeast. They found that most pericentromeres are transcribed throughout the cell cycle, but centromere accessibility to the transcription machinery is restricted to S-phase, which is controlled by the centromere-binding transcription factor Cbf1. Deletion of Cbf1 leads to an accumulation of cenRNAs at all phases of the cell cycle and increased chromosome mis-segregation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Cheng-Yu Li, Bei Zheng, Jiang-Tao Li, Jia-Ling Gao, Yu-Heng Liu, Dai-Wen Pang, Hong-Wu Tang
Summary: The CRISPR/Cas12a system offers an alternative opportunity for designing fluorescence biosensors with outstanding precision in target recognition. By utilizing collateral cleavage and representative transduction pathways, the system can extend sensing coverage and improve assay sensitivity. The developed biosensors not only exhibit ultrasensitive behavior towards non-nucleic acid analytes but also show practical application capacity in real samples.
Article
Multidisciplinary Sciences
Sarah Kono, Aafke van den Berg, Marco Simonetta, Ann Mukhortava, Elspeth F. Garman, Ingrid Tessmer
Summary: AGT is an important DNA repair protein that repairs highly mutagenic and cytotoxic alkylguanine lesions. Studies have revealed the interactions of AGT with alkyl lesions and its role in DNA repair mechanism. Surprisingly, AGT clusters do not enhance DNA translocation speed, suggesting a different role in AGT function.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Roman Renger, Jose A. Morin, Regis Lemaitre, Martine Ruer-Gruss, Frank Juelicher, Andreas Hermann, Stephan W. Grill
Summary: This study investigated the mechanism of how the FUS protein forms liquid-like assemblies by co-condensing with DNA molecules in vitro. It was found that the protein could adsorb onto DNA to generate a sticky FUS-DNA polymer, which then collapsed to form a liquid-like FUS-DNA co-condensate. The co-condensation mechanism mediated by protein adsorption on nucleic acids is suggested to be important for intracellular compartmentalization.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Nicholas A. W. Bell, Justin E. Molloy
Summary: The paper introduces a simple and fast technique for creating diverse DNA constructs by combining PCR amplicons and synthetic oligonucleotides using golden gate assembly rules. The method allows for high-yield fabrication of torsionally-constrained DNA and various DNA hairpin structures, as well as improving measurement lifetime.
NUCLEIC ACIDS RESEARCH
(2022)
