Article
Biochemistry & Molecular Biology
Roberto Fabian, Santosh Gaire, Christopher Tyson, Raghabendra Adhikari, Ian Pegg, Abhijit Sarkar
Summary: In this study, single molecule studies were conducted on the interaction between single DNA molecules and core histones using custom-designed horizontal magnetic tweezers. The assembly and disassembly of histone octamers from DNA tethers were observed to occur in approximately 50 nm increments. The findings provide valuable insights into the force-mediated DNA-core histone processes.
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)
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
Biochemistry & Molecular Biology
Wonje Heo, Jeonghwan Seo, Yoonhee Lee, Yoori Kim
Summary: This paper reviews the advances in single-molecule tools for imaging long genomic DNA and studying dynamic protein interactions. It focuses on three representative techniques: molecular combing, nanochannel confinement, and DNA curtain assays, which elongate individual DNA using fluid-driven force. The paper provides an integrated perspective and direction for future use in dissecting protein function.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Santosh Gaire, Roberto L. L. Fabian Jr, Raghabendra Adhikari, Pamela L. Tuma, Ian L. Pegg, Abhijit Sarkar
Summary: Nucleosomes are stable complexes of DNA and histone proteins that are essential for genome function. Histone post-translational modifications play a role in regulating nucleosome structure, but the mechanisms are unclear. This study used transverse magnetic tweezers to investigate DNA-protein complexes with hyperacetylated histones. The experiments showed that hyperacetylated nucleosomes require a similar unbinding force to native histones and have different dissociation behaviors at higher forces.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Chemistry, Multidisciplinary
Biao-Feng Zeng, Yu-Ling Zou, Gan Wang, Wenjing Hong, Zhong-Qun Tian, Yang Yang
Summary: Recent advances in single-molecule electronics have opened up new opportunities to investigate single-molecule chemistry. The focus has shifted towards quantitative analysis of the physical and chemical behavior of single molecules, including dynamic molecular configurations, redox states, single-molecule reactions, single-molecule sensing, and molecular adsorption behaviors.
Review
Biochemistry & Molecular Biology
Longfu Xu, Matthew T. J. Halma, Gijs J. L. Wuite
Summary: Single-stranded DNA-binding proteins (SSBs) are essential for DNA metabolism and play crucial roles in maintaining genome integrity and coordinating with other proteins involved in DNA replication, recombination, and repair. Recent advances in single-molecule techniques and structural methods have greatly improved our understanding of the binding dynamics and interaction of SSBs with ssDNA and other protein partners. We highlight the central coordination role of SSBs in directly modulating the activities of other proteins and discuss the various modes of interaction between SSBs and their protein partners, providing a comprehensive view of the interaction network shaped by SSBs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Piero R. Bianco
Summary: Visual biochemistry is a powerful technique that allows the observation of stochastic properties in single enzymes or enzyme complexes. By using dual optical tweezers and microfluidic devices, the visualization of DNA molecules is achieved. This method enhances the understanding of enzyme reactions.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Physics, Fluids & Plasmas
Ting Liang, Chao Yang, Xiaoya Song, Yuyu Feng, Yanhui Liu, Hu Chen
Summary: This study systematically investigated the kinetics and thermodynamics of the folding-unfolding transition of an individual DNA hairpin in a crowded environment using a combination of high-resolution magnetic tweezers and an extended crowder-oxDNA model. The results demonstrated a linear dependence of the critical force of the DNA hairpin on the polyethylene glycol (PEG) concentration, highlighting the importance of excluded volume effects in the interaction between PEG and the DNA hairpin. The method provides insights into accurately mimicking cytosolic environments using mixtures of different inert molecules. Overall rating: 9/10.
Article
Multidisciplinary Sciences
Johannes P. P. Suwita, Calvin K. K. Voong, Elina Ly, James A. A. Goodrich, Jennifer F. F. Kugel
Summary: p53 is a transcriptional activator that controls cellular pathways important for cell fate decisions. It binds to specific DNA sequences known as response elements to control transcription. Using a single molecule fluorescence approach, we have quantified the dynamic binding of p53 to response elements and found that there are two kinetically distinct populations of p53/response element complexes.
Article
Chemistry, Multidisciplinary
Yufeng Pei, Tianyuan Bian, Yonglin Liu, Yan Liu, Yujie Xie, Jie Song
Summary: This study developed a real-time, label-free, and force-controlled single-molecule DNA computing method. By using stretching forces and tracking real-time signals, Boolean logic computing was achieved at the single-molecule level with output determined at a single base-pair resolution.
Article
Chemistry, Analytical
Yongyao Wang, Xiao Hu, Jiangang Long, Jiajie Diao
Summary: Researchers have developed a chemical labeling-based single-molecule imaging method, known as SMEL, which enables the detection and study of epigenetic modifications, specifically 5-hydroxymethylcytosine. They successfully applied this method to mouse embryonic stem cell genomic DNA and demonstrated its potential clinical applications.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Chemistry, Multidisciplinary
Aleksandra K. Adamczyk, Teun A. P. M. Huijben, Miguel Sison, Andrea Di Luca, Stefano Vanni, Sophie Brasselet, Kim I. Mortensen, Fernando D. Stefani, Mauricio Pilo-Pais, Guillermo P. Acuna
Summary: This study demonstrates a controlled orientation of single molecules in DNA origami by linking them to oligonucleotide strands and leaving unpaired bases. The number of unpaired bases affects the stretching and orientation of the fluorophore linkers. These findings expand the application of DNA origami in the fabrication of nanodevices involving orientation-dependent molecular interactions.
Article
Chemistry, Multidisciplinary
Mike Filius, Sung Hyun Kim, Ivo Severins, Chirlmin Joo
Summary: The research team introduced a new method that allows for determining multiple distances between FRET pairs in a single object by resolving the FRET efficiency of multiple fluorophore pairs through transient binding of short DNA strands. This FRET X technology is expected to be a tool for high-resolution analysis of biomolecules and nanostructures.
Article
Chemistry, Multidisciplinary
Shui Yu, Chuying Chen, Yuzhen Zhang, Yuning Liang, Huan-Cheng Hu, Hua-Hong Zou, Dongcheng Liu, Fupei Liang, Zilu Chen
Summary: Two tetranuclear Dy(III) complexes with different substitution groups and coordinated solvent molecules were synthesized and found to exhibit field-induced single-molecule magnet properties. The magnetic investigation revealed the tuning effect of coordinated solvent molecules and substitution groups on the single-molecule magnet performance. The assembling mechanisms of these complexes were elucidated through time-dependent high-resolution electrospray ionization mass spectrometry.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Cell Biology
Ronald Biggs, Patrick Z. Liu, Andrew D. Stephens, John F. Marko
MOLECULAR BIOLOGY OF THE CELL
(2019)
Article
Biophysics
Aykut Erbas, Monica Olvera de la Cruz, John F. Marko
BIOPHYSICAL JOURNAL
(2019)
Article
Multidisciplinary Sciences
Scott Gladstein, Luay M. Almassalha, Lusik Cherkezyan, John E. Chandler, Adam Eshein, Aya Eid, Di Zhang, Wenli Wu, Greta M. Bauer, Andrew D. Stephens, Simona Morochnik, Hariharan Subramanian, John F. Marko, Guillermo A. Ameer, Igal Szleifer, Vadim Backman
NATURE COMMUNICATIONS
(2019)
Article
Multidisciplinary Sciences
Sumitabha Brahmachari, John F. Marko
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Review
Biochemistry & Molecular Biology
Aykut Erbas, John F. Marko
CURRENT OPINION IN CHEMICAL BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
John F. Marko
JOURNAL OF MOLECULAR BIOLOGY
(2020)
Article
Biology
Edward J. Banigan, Aafke A. van den Berg, Hugo B. Brandao, John F. Marko, Leonid A. Mirny
Article
Biochemistry & Molecular Biology
Parth Rakesh Desai, Sumitabha Brahmachari, John F. Marko, Siddhartha Das, Keir C. Neuman
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biology
Ronald J. Biggs, Ning Liu, Yiheng Peng, John F. Marko, Huanyu Qiao
COMMUNICATIONS BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Diego Serrano, Gustavo Cordero, Ryo Kawamura, Aleksandr Sverzhinsky, Muzaddid Sarker, Shamayita Roy, Catherine Malo, John M. Pascal, John F. Marko, Damien D'Amours
Article
Genetics & Heredity
Houda Belaghzal, Tyler Borrman, Andrew D. Stephens, Denis L. Lafontaine, Sergey V. Venev, Zhiping Weng, John F. Marko, Job Dekker
Summary: Liquid chromatin Hi-C technique reveals the stability of interactions between chromatin loci, showing that compartmentalization is stabilized when fragments are larger than 10-25 kb and smaller chromatin fragments can lead to gradual loss of genome organization. Lamin-associated domains are more stable compared to speckle- and polycomb-associated loci, and cohesin-mediated loops dissolve after fragmentation. This technique provides a genome-wide view of chromosome interaction dynamics.
Article
Biology
Monica S. Guo, Ryo Kawamura, Megan L. Littlehale, John F. Marko, Michael T. Laub
Summary: The GapR-seq method allows high-resolution mapping of positive supercoiling in genomes, revealing its widespread presence, association with transcription, and enrichment between certain genes. This approach provides new insights into chromosome structure and organization that are not accessible with existing methods like Hi-C.
Article
Biology
Amy R. Strom, Ronald J. Biggs, Edward J. Banigan, Xiaotao Wang, Katherine Chiu, Cameron Herman, Jimena Collado, Feng Yue, Joan C. Ritland Politz, Leah J. Tait, David Scalzo, Agnes Telling, Mark Groudine, Clifford P. Brangwynne, John F. Marko, Andrew D. Stephens
Summary: HP1 alpha plays a critical role in chromatin-based mechanics by maintaining chromatin stiffness and nuclear morphology, supporting cellular functions.
Article
Biochemistry & Molecular Biology
Stefanos K. Nomidis, Enrico Carlon, Stephan Gruber, John F. Marko
Summary: Structural Maintenance of Chromosomes (SMC) complexes play critical roles in genome organization. Researchers developed a molecular dynamics model to investigate the control of SMC complex activities by ATP binding and hydrolysis. The model revealed the sensitivity of this process to DNA tension and the ability of the SMC complex to perform loop extrusion by tethering DNA to an additional binding site.
NUCLEIC ACIDS RESEARCH
(2022)