Article
Multidisciplinary Sciences
Georgii Pobegalov, Lee-Ya Chu, Jan-Michael Peters, Maxim I. Molodtsov
Summary: The spatial organization of DNA is facilitated by cohesin protein complexes, which move on DNA and extrude DNA loops. However, the mechanistic functioning of cohesin as a molecular machine is not well understood. In this study, we measured the mechanical forces generated by conformational changes in single cohesin molecules and found that bending of SMC coiled coils is driven by random thermal fluctuations, while ATPase head engagement occurs through an ATP dependent head-head movement. Our findings shed light on the force-generating mechanisms of cohesin and provide insights into the cohesin-DNA interaction.
NATURE COMMUNICATIONS
(2023)
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)
Article
Biochemistry & Molecular Biology
Charlotte Cockram, Agnes Thierry, Aurore Gorlas, Roxane Lestini, Romain Koszul
Summary: This study developed a cost-effective Hi-C protocol for exploring chromosome conformations in prokaryotes and archaea. By validating and applying this method in different microorganisms, the research found that these euryarchaeota lack compartment-like structures and their genomes are mainly composed of self-interacting domains and chromatin loops.
Article
Biochemistry & Molecular Biology
Paul Batty, Christoph C. H. Langer, Zsuzsanna Takacs, Wen Tang, Claudia Blaukopf, Jan-Michael Peters, Daniel W. Gerlich
Summary: Genetic information is stored in folded linear DNA molecules inside cells. During cell division, sister chromatids need to be disentangled and condensed into separate bodies for proper separation. In human cells, sister chromatids are extensively resolved during interphase, depending on the loop-extruding activity of cohesin. Increasing cohesin's looping capability can further enhance sister DNA resolution, even in the absence of mitosis-specific activities.
Article
Biochemistry & Molecular Biology
Belen Martinez-Garcia, Silvia Dyson, Joana Segura, Alba Ayats, Erin E. Cutts, Pilar Gutierrez-Escribano, Luis Aragon, Joaquim Roca
Summary: Condensin, an SMC protein complex, alters DNA topology by extruding loops using an ATP-dependent mechanism. High concentrations of condensin restrain positive supercoils, but restrain negative supercoils during DNA loop extrusion. ATP binding causes a short DNA domain to form a negatively supercoiled loop, which may be merged with an extruding loop, with the involvement of Ycg1.
Article
Biochemistry & Molecular Biology
Sumitabha Brahmachari, Vinicius G. Contessoto, Michele Di Pierro, Jose N. Onuchic
Summary: This article explores the link between genomic structure and function, highlighting the crucial role of physical manipulation of the genome by various proteins. By constructing a coarse-grained polymer model of the genome, the authors demonstrate how interactions among different classes of genomic interactions can drive predictable changes in global genome architecture and make testable predictions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Eddy I. Jimenez, Clementine Gibard, Ramanarayanan Krishnamurthy
Summary: Recent demonstrations have shown that RNA-DNA chimeras and diamidophosphate can facilitate DNA synthesis under conditions similar to those of ribonucleosides, supporting the hypothesis of co-emergence of RNA and DNA. This provides a basis for further systematic investigation of a systems chemistry approach of RNA-DNA coevolution.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Microbiology
Nora Halgasova, Rachel Javorova, Lucia Bocanova, Daniela Krajcikova, Jacob A. Bauer, Gabriela Bukovska
Summary: The bacteriophage phiBP contains putative replisome organizer, helicase loader, and beta clamp that may play a role in DNA replication. Bioinformatics analysis found that the phiBP replisome organizer belongs to a newly identified family of initiator proteins. Recombinant proteins gpRO-HC and gpRO-HCK8A, with a lysine to alanine substitution at position 8, were prepared and studied. gpRO-HC showed low ATPase activity, regardless of DNA presence, while the mutant demonstrated significantly higher ATPase activity. gpRO-HC bound to both single- and double-stranded DNA substrates, forming higher oligomers composed of about 12 subunits. This study provides valuable information on phage initiator proteins involved in DNA replication in low GC Gram-positive bacteria.
MICROBIOLOGICAL RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Yuchen Wu, Jin Huang, Hui He, Meixia Wang, Guanyu Yin, Lanlin Qi, Xiaoxiao He, Hong-Hui Wang, Kemin Wang
Summary: The reprogramming of cell signaling and behavior through the artificial control of cell surface receptor oligomerization shows promise in biomedical research and cell-based therapy. However, achieving combinatorial recognition in a complicated environment and logical regulation of receptors remains challenging. In this study, a logic-gated DNA nanodevice was developed to assemble heterogeneous receptors and modulate signaling in response to multiple environmental inputs. This strategy has potential applications in precision therapeutics and cancer treatment.
Article
Cell Biology
Emily Weyburne, Giovanni Bosco
Summary: The study focused on specific mutations of the CAPH2 subunit in condensin II, which are enriched in human cancer patients. These mutations were found to cause genomic instability by inducing DNA damage, anaphase defects, micronuclei, and chromosomal instability. They also decreased the binding of CAPH2 to other subunits of the condensin II complex and reduced the amount of CAPH2 protein bound to chromatin, potentially impairing condensin II complex formation and activity during mitosis and interphase, leading to genetic heterogeneity in cell populations.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Biology
Makoto M. Yoshida, Kazuhisa Kinoshita, Yuuki Aizawa, Shoji Tane, Daisuke Yamashita, Keishi Shintomi, Tatsuya Hirano
Summary: In vertebrates, condensin I and condensin II work together to assemble chromosomes during mitosis. However, our understanding of condensin II is limited. Through experiments, we discovered that one of the two HEAT subunits, CAP-D3, plays a crucial role in condensin II-mediated chromosome assembly, while the other HEAT subunit, CAP-G2, has a negative impact on this process. The ATPase protein and basic amino acid clusters of the kleisin subunit CAP-H2 are also essential. Deleting the C-terminal tail of CAP-D3 enhances the ability of condensin II to assemble chromosomes and reveals a hidden function of CAP-G2 in chromosome compaction.
Article
Chemistry, Multidisciplinary
Eric S. S. Yang, Daniel W. N. Wilson, Jose M. M. Goicoechea
Summary: The cyaphide anion, CP-, can undergo three different oligomerization reactions in the coordination sphere of metals. These reactions result in the formation of tetra-metallic, asymmetric bimetallic, and trimetallic complexes containing various phosphorus-containing fragments. The study highlights the instability of cyaphido transition metal complexes towards further oligomerization processes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Polymer Science
Rongyan Zhang, Yanwei Wang, Guangcan Yang
Summary: The interaction between DNA and proteins is important for both basic research in biology and potential applications in nanotechnology. This study investigated the complexes formed by lambda DNA and lysozyme in a dilute aqueous solution. It was found that lysozyme effectively neutralizes the positive charge of DNA, inducing charge inversion. The compact and positively charged structure of lysozyme contributes to its high efficiency in charge neutralization. Increasing the concentration of lysozyme leads to changes in both DNA mobility and condensing force, as well as the morphology of the DNA-lysozyme complex.
Article
Chemistry, Physical
Chuan Jie Tan, Rajib Basak, Indresh Yadav, Jeroen A. van Kan, Veronique Arluison, Johan R. C. van der Maarel
Summary: The study investigates the impact of DNA binding and DNA segmental fluctuation on the mobility of the bacterial Hfq master regulator. The results demonstrate the subtle role of DNA internal motion in controlling the mobility of a nucleoid associated protein.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biophysics
Marc Joyeux
Summary: This study investigates the impact of self-association of nucleoid proteins on their architectural properties, demonstrating that self-association greatly enhances their ability to shape the DNA coil. Different forms of self-association lead to significant changes in the organization of the DNA coil.
BIOPHYSICAL JOURNAL
(2021)
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)
Review
Cell Biology
Andrew D. Stephens, Edward J. Banigan, John F. Marko
CURRENT OPINION IN CELL BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
John F. Marko, Paolo De Los Rios, Alessandro Barducci, Stephan Gruber
NUCLEIC ACIDS RESEARCH
(2019)
Article
Multidisciplinary Sciences
J. P. Renn, S. Bhattacharyya, H. Bai, C. He, H. Li, A. F. Oberhauser, J. F. Marko, D. E. Makarov, A. Matouschek
SCIENTIFIC REPORTS
(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
Biophysics
Tetiana Zaichuk, John F. Marko
Summary: The study using single-molecule magnetic force spectroscopy techniques found that cytosine methylation increases DNA flexibility and results in longer contour length. Under physiological conditions, DNA tends to form plectonemes rather than unwound single-stranded bubbles. The flexibility and high structural stability of methylated DNA are likely to have significant consequences on protein recognition and DNA packaging.
BIOPHYSICAL JOURNAL
(2021)
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)