The iron-sulfur (FeS) cluster helicase DDX11 is associated with a human disorder termed Warsaw Breakage Syndrome. Interestingly, one disease-associated mutation affects the highly conserved arginine-263 in the FeS cluster-binding motif. Here, we demonstrate that the FeS cluster in DDX11 is required for DNA binding, ATP hydrolysis, and DNA helicase activity, and that arginine-263 affects FeS cluster binding, most likely because of its positive charge. We further show that DDX11 interacts with the replication factors DNA polymerase delta and WDHD1. In vitro, DDX11 can remove DNA obstacles ahead of Pol δ in an ATPase- and FeS domain-dependent manner, and hence generate single-stranded DNA. Accordingly, depletion of DDX11 causes reduced levels of single-stranded DNA, a reduction of chromatin-bound replication protein A, and impaired CHK1 phosphorylation at serine-345. Taken together, we propose that DDX11 plays a role in dismantling secondary structures during DNA replication, thereby promoting CHK1 activation.
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http://dx.doi.org/10.26508/lsa.201900547 | DOI Listing |
Adv Sci (Weinh)
January 2025
Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 43150, Sweden.
Targeted delivery of therapeutic agents is a persistent challenge in modern medicine. Recent efforts in this area have highlighted the utility of extracellular vesicles (EVs) as drug carriers, given that they naturally occur in bloodstream and tissues, and can be loaded with a wide range of therapeutic molecules. However, biodistribution and tissue tropism of EVs remain difficult to study systematically.
View Article and Find Full Text PDFJ Med Virol
January 2025
State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
Coronaviruses (CoVs) pose a significant threat to human health, as demonstrated by the COVID-19 pandemic. The large size of the CoV genome (around 30 kb) represents a major obstacle to the development of reverse genetics systems, which are invaluable for basic research and antiviral drug screening. In this study, we established a rapid and convenient method for generating reverse genetic systems for various CoVs using a bacterial artificial chromosome (BAC) vector and Gibson DNA assembly.
View Article and Find Full Text PDFACS Nano
January 2025
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, United States.
Most traditional optical biosensors operate through molecular recognition, where ligand binding causes conformational changes that lead to optical perturbations in the emitting motif. Optical sensors developed from single-stranded DNA-functionalized single-walled carbon nanotubes (ssDNA-SWCNTs) have started to make useful contributions to biological research. However, the mechanisms underlying their function have remained poorly understood.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic.
Molecular dynamics (MD) simulations are an important and well-established tool for investigating RNA structural dynamics, but their accuracy relies heavily on the quality of the employed force field (). In this work, we present a comprehensive evaluation of widely used pair-additive and polarizable RNA s using the challenging UUCG tetraloop (TL) benchmark system. Extensive standard MD simulations, initiated from the NMR structure of the 14-mer UUCG TL, revealed that most s did not maintain the native state, instead favoring alternative loop conformations.
View Article and Find Full Text PDFArch Microbiol
January 2025
Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, K K Birla Goa Campus, NH17B, Zuarinagar, Goa, 403726, India.
The gene gp13 in bacteriophage Phi11 has been annotated as a Single-Stranded DNA binding protein (SSB protein, GenBank accession no. NC_004615.1).
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