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Showing 1–14 of 14 results
Advanced filters: Author: Ilya J Finkelstein Clear advanced filters
  • Systematic understanding of CRISPR enzyme RNA binding specificity and cleavage is lacking. Here the authors report RNA chip-hybridised association-mapping platform (RNA-CHAMP), a workflow that repurposes next generation DNA sequencing chips to measure the binding affinity for RNA targets.

    • Hung-Che Kuo
    • Joshua Prupes
    • Ilya J. Finkelstein
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-13
  • Protein machineries that move along the DNA, such as DNA polymerases and helicases, will necessarily encounter other bound proteins interacting with specific sites. Using 'curtains' of labelled DNA, this study measured whether such bound proteins interfere with the activity of the bacterial DNA translocase RecBCD. The translocase is able to push the proteins over nonspecific sites for thousands of base pairs before they are displaced.

    • Ilya J. Finkelstein
    • Mari-Liis Visnapuu
    • Eric C. Greene
    Research
    Nature
    Volume: 468, P: 983-987
  • Bacteria possess many types of antiviral immune systems, some of which are present also in eukaryotes. Here, Leão et al. explore the diversity and distribution of antiviral defense systems in archaea and their evolutionary relationships with bacterial and eukaryotic immune systems, supporting that Asgard archaea played important roles in the origin of eukaryotic innate immunity.

    • Pedro Leão
    • Mary E. Little
    • Brett J. Baker
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-9
  • CRISPR-Cas9 is a powerful tool, but the strict requirement for an “NGG” protospacer-adjacent motif (PAM) sequence limits the number of editable genes. Here the authors combine enzyme kinetics, cryo-EM, and single-molecule imaging to determine how SpRY interrogates DNA and recognises target sites for cleavage.

    • Grace N. Hibshman
    • Jack P. K. Bravo
    • David W. Taylor
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-15
  • DNA-binding proteins need to scan the genome to find their targets though how this occurs in the crowded nuclear environment is poorly understood. Here the authors use single-molecular fluorescence to show the repair complex Msh2-Msh3 can hop over blocks that impede the sliding complex Msh2-Msh6.

    • Maxwell W. Brown
    • Yoori Kim
    • Ilya J. Finkelstein
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-12
  • Cas9 off-target sites can be predicted by many bioinformatics tools. Here the authors present low complexity mechanistic model that characterizes SpCas9 kinetics in free-energy terms, allowing quantitative prediction of off-target activity in bulk-biochemistry, single molecule, and whole-genome profiling experiments.

    • Behrouz Eslami-Mossallam
    • Misha Klein
    • Martin Depken
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-10
  • Poly(ADP-ribose) polymerase-1 (PARP-1) facilitates local chromatin relaxation and the recruitment of DNA repair factors at double strand breaks site (DSBs). Here the authors reveal that PARP-1 acts as a critical regulator of DNA end resection of DSBs.

    • Marie-Christine Caron
    • Ajit K. Sharma
    • Jean-Yves Masson
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-16
  • The transcription machinery must locate specific promoter sequences among a vast excess of nonspecific DNA. Real-time single-molecule experiments with E. coli RNA polymerase, combined with theoretical calculations, suggest that facilitated diffusion does not contribute to promoter targeting at physiologically relevant protein concentrations but that instead the promoter search is dominated by three-dimensional diffusion.

    • Feng Wang
    • Sy Redding
    • Eric C Greene
    Research
    Nature Structural & Molecular Biology
    Volume: 20, P: 174-181
  • The authors present a protocol for expressing and biophysically characterizing rationally engineered SARS-CoV-2 spike proteins in Freestyle 293 and ExpiCHO cell lines.

    • Jeffrey M. Schaub
    • Chia-Wei Chou
    • Ilya J. Finkelstein
    Protocols
    Nature Protocols
    Volume: 16, P: 5339-5356