keyword
https://read.qxmd.com/read/37821038/method-to-generate-holliday-junction-recombination-intermediates-via-reca-mediated-four-strand-exchange
#21
JOURNAL ARTICLE
Han Ngoc Ho, Stephen C West
DNA molecules that contain single Holliday junctions have served as model substrates to investigate the pathway in which homologous recombination intermediates are processed. However, the preparation of DNA containing Holliday junctions in high yield remains a challenge. In this work, we used a nicking endonuclease to generate gapped DNA, from which α-structured DNA or figure-8 DNA were created via RecA-mediated reactions. The resulting DNA molecules were found to serve as good substrates for Holliday junction resolvases...
October 9, 2023: Analytical Biochemistry
https://read.qxmd.com/read/37759442/protein-phosphatase-4-is-required-for-centrobin-function-in-dna-damage-repair
#22
JOURNAL ARTICLE
Zsuzsánna Réthi-Nagy, Edit Ábrahám, Rita Sinka, Szilvia Juhász, Zoltán Lipinszki
Genome stability in human cells relies on the efficient repair of double-stranded DNA breaks, which is mainly achieved by homologous recombination (HR). Among the regulators of various cellular functions, Protein phosphatase 4 (PP4) plays a pivotal role in coordinating cellular response to DNA damage. Meanwhile, Centrobin (CNTRB), initially recognized for its association with centrosomal function and microtubule dynamics, has sparked interest due to its potential contribution to DNA repair processes. In this study, we investigate the involvement of PP4 and its interaction with CNTRB in HR-mediated DNA repair in human cells...
September 6, 2023: Cells
https://read.qxmd.com/read/37756637/plant-organellar-msh1-is-a-displacement-loop-specific-endonuclease
#23
JOURNAL ARTICLE
Alejandro Peñafiel-Ayala, Antolin Peralta-Castro, Josue Mora-Garduño, Paola García-Medel, Angie G Zambrano-Pereira, Corina Díaz-Quezada, María Jazmín Abraham-Juárez, Claudia G Benítez-Cardoza, Daniel B Sloan, Luis G Brieba
MSH1 is an organellar targeted protein that obstructs ectopic recombination and the accumulation of mutations in plant organellar genomes. MSH1 also modulates the epigenetic status of nuclear DNA, and its absence induces a variety of phenotypic responses. MSH1 is a member of the MutS family of DNA mismatch repair proteins but harbors an additional GIY-YIG nuclease domain that distinguishes it from the rest of this family. How MSH1 hampers recombination and promotes fidelity in organellar DNA inheritance is unknown...
September 26, 2023: Plant & Cell Physiology
https://read.qxmd.com/read/37690737/analysis-of-non-canonical-three-and-four-way-dna-junctions
#24
JOURNAL ARTICLE
Bríonna McGorman, Simon Poole, Miguel Vázquez López, Andrew Kellett
The development of compounds that can selectively bind with non-canonical DNA structures has expanded in recent years. Junction DNA, including three-way junctions (3WJs) and four-way Holliday junctions (HJs), offer an intriguing target for developmental therapeutics as both 3WJs and HJs are involved in DNA replication and repair processes. However, there are a limited number of assays available for the analysis of junction DNA binding. Here, we describe the design and execution of multiplex fluorescent polyacrylamide gel electrophoresis (PAGE) and microscale thermophoresis (MST) assays that enable evaluation of junction-binding compounds...
September 8, 2023: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/37604043/holliday-junction-branch-migration-driven-by-aaa-atpase-motors
#25
REVIEW
Jiri Wald, Thomas C Marlovits
Holliday junctions are key intermediate DNA structures during genetic recombination. One of the first Holliday junction-processing protein complexes to be discovered was the well conserved RuvAB branch migration complex present in bacteria that mediates an ATP-dependent movement of the Holliday junction (branch migration). Although the RuvAB complex served as a paradigm for the processing of the Holliday junction, due to technical limitations the detailed structure and underlying mechanism of the RuvAB branch migration complex has until now remained unclear...
August 18, 2023: Current Opinion in Structural Biology
https://read.qxmd.com/read/37595556/genetic-dissection-of-crossover-mutants-defines-discrete-intermediates-in-mouse-meiosis
#26
JOURNAL ARTICLE
Tolkappiyan Premkumar, Lakshmi Paniker, Rhea Kang, Mathilde Biot, Ericka Humphrey, Honorine Destain, Isabella Ferranti, Iyinyeoluwa Okulate, Holly Nguyen, Vindhya Kilaru, Melissa Frasca, Parijat Chakraborty, Francesca Cole
Crossovers (COs), the exchange of homolog arms, are required for accurate chromosome segregation during meiosis. Studies in yeast have described the single-end invasion (SEI) intermediate: a stabilized 3' end annealed with the homolog as the first detectible CO precursor. SEIs are thought to differentiate into double Holliday junctions (dHJs) that are resolved by MutLgamma (MLH1/MLH3) into COs. Currently, we lack knowledge of early steps of mammalian CO recombination or how intermediates are differentiated in any organism...
August 17, 2023: Molecular Cell
https://read.qxmd.com/read/37563161/in-vitro-transcription-of-self-assembling-dna-nanoparticles
#27
JOURNAL ARTICLE
Chang Yong Oh, Eric R Henderson
Nucleic acid nanoparticles are playing an increasingly important role in biomolecular diagnostics and therapeutics as well as a variety of other areas. The unique attributes of self-assembling DNA nanoparticles provide a potentially valuable addition or alternative to the lipid-based nanoparticles that are currently used to ferry nucleic acids in living systems. To explore this possibility, we have assessed the ability of self-assembling DNA nanoparticles to be constructed from complete gene cassettes that are capable of gene expression in vitro...
August 10, 2023: Scientific Reports
https://read.qxmd.com/read/37433388/new-insights-into-the-antimicrobial-action-and-protective-therapeutic-effect-of-tirapazamine-towards-escherichia-coli-infected-mice
#28
JOURNAL ARTICLE
Zhouhui Wu, Yu Wang, Lei Li, Sihui Zhen, Heng Du, Zhiwen Wang, Shuang Xiao, Jinliang Wu, Lifei Zhu, Jiachen Shen, Zhen Wang
Escherichia coli is an important pathogen responsible for numerous cases of diarrhea worldwide. The bioreductive agent tirapazamine (TPZ), which was clinically used to treat various types of cancers, has obvious antibacterial activity against E. coli strains. In the present study, we aimed to evaluate the protective therapeutic effects of TPZ in E. coli-infected mice and provide insights into its antimicrobial action mechanism. Interestingly, TPZ-induced the reversal of drug resistance in E. coli by regulating the expression of resistance-related genes, which may have an auxiliary role in the clinical treatment of drug-resistant bacterial infections...
July 9, 2023: International Journal of Antimicrobial Agents
https://read.qxmd.com/read/37430391/rad51c-rad51d-interplays-with-msh5-and-regulates-crossover-maturation-in-rice-meiosis
#29
JOURNAL ARTICLE
Fanfan Zhang, Wenqing Shi, Yue Zhou, Lijun Ma, Yongjie Miao, Na Mu, Haiyun Ren, Zhukuan Cheng
Meiotic crossovers ensure accurate chromosome segregation and increase genetic diversity. RAD51C and RAD51D play an early role in facilitating RAD51 during homologous recombination. However, their later function in meiosis is largely unknown in plants. Here, through targeted disruption of RAD51C and RAD51D, we generated three new mutants and revealed their later meiotic role in crossover maturation. The rad51c-3 and rad51d-4 mutants showed a mixture of bivalents and univalents and no chromosomal entanglements, whereas rad51d-5 exhibited an intermediate phenotype with reduced chromosomal entanglements and increased bivalent formation compared with knockout alleles...
July 10, 2023: New Phytologist
https://read.qxmd.com/read/37358447/the-ruvabc-holliday-junction-processing-system-is-not-required-for-is-26-mediated-targeted-conservative-cointegrate-formation
#30
JOURNAL ARTICLE
Carol H Pong, Jade E Peace, Christopher J Harmer, Ruth M Hall
The insertion sequence IS 26 plays a key role in the spread of antibiotic resistance genes in Gram-negative bacteria. IS 26 and members of the IS 26 family are able to use two distinct mechanisms to form cointegrates made up of two DNA molecules linked via directly oriented copies of the IS. The well-known copy-in (formerly replicative) reaction occurs at very low frequency, and the more recently discovered targeted conservative reaction, which joins two molecules that already include an IS, is substantially more efficient...
June 26, 2023: Microbiology Spectrum
https://read.qxmd.com/read/37322069/molecular-mechanisms-of-holliday-junction-branch-migration-catalyzed-by-an-asymmetric-ruvb-hexamer
#31
JOURNAL ARTICLE
Anthony D Rish, Zhangfei Shen, Zhenhang Chen, Nan Zhang, Qingfei Zheng, Tian-Min Fu
The Holliday junction (HJ) is a DNA intermediate of homologous recombination, involved in many fundamental physiological processes. RuvB, an ATPase motor protein, drives branch migration of the Holliday junction with a mechanism that had yet to be elucidated. Here we report two cryo-EM structures of RuvB, providing a comprehensive understanding of HJ branch migration. RuvB assembles into a spiral staircase, ring-like hexamer, encircling dsDNA. Four protomers of RuvB contact the DNA backbone with a translocation step size of 2 nucleotides...
June 15, 2023: Nature Communications
https://read.qxmd.com/read/37318835/organometallic-pillarplexes-that-bind-dna-4-way-holliday-junctions-and-forks
#32
JOURNAL ARTICLE
James S Craig, Larry Melidis, Hugo D Williams, Samuel J Dettmer, Alexandra A Heidecker, Philipp J Altmann, Shengyang Guan, Callum Campbell, Douglas F Browning, Roland K O Sigel, Silke Johannsen, Ross T Egan, Brech Aikman, Angela Casini, Alexander Pöthig, Michael J Hannon
Holliday 4-way junctions are key to important biological DNA processes (insertion, recombination, and repair) and are dynamic structures that adopt either open or closed conformations, the open conformation being the biologically active form. Tetracationic metallo-supramolecular pillarplexes display aryl faces about a cylindrical core, an ideal structure to interact with open DNA junction cavities. Combining experimental studies and MD simulations, we show that an Au pillarplex can bind DNA 4-way (Holliday) junctions in their open form, a binding mode not accessed by synthetic agents before...
June 15, 2023: Journal of the American Chemical Society
https://read.qxmd.com/read/37309220/conformational-dynamics-and-mechanical-properties-of-biomimetic-rna-dna-and-rna-dna-hybrid-nanotubes-an-atomistic-molecular-dynamics-study
#33
JOURNAL ARTICLE
Ehsan Torkan, Mehdi Salmani-Tehrani
With the nanotechnology boom, artificially designed nucleic acid nanotubes have aroused interest due to their practical applications in nanorobotics, vaccine design, membrane channels, drug delivery, and force sensing. In this paper, computational study was performed to investigate the structural dynamics and mechanical properties of RNA nanotubes (RNTs), DNA nanotubes (DNTs), and RNA-DNA hybrid nanotubes (RDHNTs). So far, the structural and mechanical properties of RDHNTs have not been examined in experiments or theoretical calculations, and there is limited knowledge regarding these properties for RNTs...
June 21, 2023: Physical Chemistry Chemical Physics: PCCP
https://read.qxmd.com/read/37267626/the-scientific-revolution-that-unraveled-the-astonishing-dna-repair-capacity-of-the-deinococcaceae-forty-years-on
#34
JOURNAL ARTICLE
Michael Daly
The Deinococcaceae family exhibits exceptional radiation resistance and possesses all the necessary traits for surviving in radiation-exposed environments. Their survival strategy involves the coupling of metabolic and DNA repair functions, resulting in an extraordinarily efficient homologous repair of DNA double-strand breaks (DSBs) caused by radiation or desiccation. The keys to their survival lie in the hyperaccumulation of manganous (Mn2+)-metabolite antioxidants that protect their DNA repair proteins under extreme oxidative stress, and the persistent structural linkage by Holliday junctions of their multiple genome copies per cell that facilitates DSB repair...
June 2, 2023: Canadian Journal of Microbiology
https://read.qxmd.com/read/37187699/self-assembly-of-dna-origami-for-nanofabrication-biosensing-drug-delivery-and-computational-storage
#35
REVIEW
Zhimei He, Kejun Shi, Jinggang Li, Jie Chao
Since the pioneering work of immobile DNA Holliday junction by Ned Seeman in the early 1980s, the past few decades have witnessed the development of DNA nanotechnology. In particular, DNA origami has pushed the field of DNA nanotechnology to a new level. It obeys the strict Watson-Crick base pairing principle to create intricate structures with nanoscale accuracy, which greatly enriches the complexity, dimension, and functionality of DNA nanostructures. Benefiting from its high programmability and addressability, DNA origami has emerged as versatile nanomachines for transportation, sensing, and computing...
May 19, 2023: IScience
https://read.qxmd.com/read/37185609/a-rapid-and-highly-sensitive-immunosorbent-assay-to-monitor-helicases-unwinding-diverse-nucleic-acid-structures
#36
JOURNAL ARTICLE
Jia-En Wang, Ying-Chen Zhou, Bi-Han Wu, Xiu-Cai Chen, Junqiu Zhai, Jia-Heng Tan, Zhi-Shu Huang, Shuo-Bin Chen
Helicases are crucial enzymes in DNA and RNA metabolism and function by unwinding particular nucleic acid structures. However, most convenient and high-throughput helicase assays are limited to the typical duplex DNA. Herein, we developed an immunosorbent assay to monitor the Werner syndrome (WRN) helicase unwinding a wide range of DNA structures, such as a replication fork, a bubble, Holliday junction, G-quadruplex and hairpin. This assay could sensitively detect the unwinding of DNA structures with detection limits around 0...
April 26, 2023: Analyst
https://read.qxmd.com/read/37126365/atomistic-picture-of-opening-closing-dynamics-of-dna-holliday-junction-obtained-by-molecular-simulations
#37
JOURNAL ARTICLE
Zhengyue Zhang, Jiří Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Šulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Holliday junction (HJ) is a noncanonical four-way DNA structure with a prominent role in DNA repair, recombination, and DNA nanotechnology. By rearranging its four arms, HJ can adopt either closed or open state. With enzymes typically recognizing only a single state, acquiring detailed knowledge of the rearrangement process is an important step toward fully understanding the biological function of HJs. Here, we carried out standard all-atom molecular dynamics (MD) simulations of the spontaneous opening-closing transitions, which revealed complex conformational transitions of HJs with an involvement of previously unconsidered "half-closed" intermediates...
April 26, 2023: Journal of Chemical Information and Modeling
https://read.qxmd.com/read/37079643/exo1-protects-dna-nicks-from-ligation-to-promote-crossover-formation-during-meiosis
#38
JOURNAL ARTICLE
Michael Gioia, Lisette Payero, Sagar Salim, Ghanim Fajish V, Amamah F Farnaz, Gianno Pannafino, Jun Jie Chen, V P Ajith, Sherikat Momoh, Michelle Scotland, Vandana Raghavan, Carol M Manhart, Akira Shinohara, K T Nishant, Eric Alani
In most sexually reproducing organisms crossing over between chromosome homologs during meiosis is essential to produce haploid gametes. Most crossovers that form in meiosis in budding yeast result from the biased resolution of double Holliday junction (dHJ) intermediates. This dHJ resolution step involves the actions of Rad2/XPG family nuclease Exo1 and the Mlh1-Mlh3 mismatch repair endonuclease. Here, we provide genetic evidence in baker's yeast that Exo1 promotes meiotic crossing over by protecting DNA nicks from ligation...
April 2023: PLoS Biology
https://read.qxmd.com/read/37043705/bleaching-resistant-near-continuous-single-molecule-fluorescence-and-fret-based-on-fluorogenic-and-transient-dna-binding
#39
JOURNAL ARTICLE
Mirjam Kümmerlin, Abhishek Mazumder, Achillefs N Kapanidis
Photobleaching of fluorescent probes limits the observation span of typical single-molecule fluorescence measurements and hinders observation of dynamics at long timescales. Here, we present a general strategy to circumvent photobleaching by replenishing fluorescent probes via transient binding of fluorogenic DNAs to complementary DNA strands attached to a target molecule. Our strategy allows observation of near-continuous single-molecule fluorescence for more than an hour, a timescale two orders of magnitude longer than the typical photobleaching time of single fluorophores under our conditions...
April 12, 2023: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://read.qxmd.com/read/37025176/advances-in-holliday-junction-recognition-protein-hjurp-structure-molecular-functions-and-roles-in-cancer
#40
REVIEW
Lin Li, Qiang Yuan, Yue-Ming Chu, Hang-Yu Jiang, Ju-Hua Zhao, Qiang Su, Dan-Qun Huo, Xiao-Fen Zhang
Oncogenes are increasingly recognized as important factors in the development and progression of cancer. Holliday Junction Recognition Protein (HJURP) is a highly specialized mitogenic protein that is a chaperone protein of histone H3. The HJURP gene is located on chromosome 2q37.1 and is involved in nucleosome composition in the mitotic region, forming a three-dimensional crystal structure with Centromere Protein A (CENP-A) and the histone 4 complex. HJURP is involved in the recruitment and assembly of centromere and kinetochore and plays a key role in stabilizing the chromosome structure of tumor cells, and its dysfunction may contribute to tumorigenesis...
2023: Frontiers in Cell and Developmental Biology
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