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Showing 1–8 of 8 results
Advanced filters: Author: Martin Depken Clear advanced filters

  • 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

  • Argonaute protein is loaded with small RNA and scans long stretch of sequences to find complementary target sites. Here, using single-molecule FRET and kinetic modelling, the authors showed that prokaryotic Argonaute protein binds target DNA loosely and slides along the DNA during target search.

    • Tao Ju Cui
    • Misha Klein
    • Chirlmin Joo
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-11

  • Eukaryotic Argonaute proteins participate in RNA-guided RNA silencing pathways and are divided into AGO and PIWI clades, with functional and mechanistic differences. Here, the authors show that a deep-branching PIWI protein from Asgard archaea (the closest prokaryotic relatives of eukaryotes) displays hybrid features and may reflect an ancestral molecular architecture that preceded the divergence of eukaryotic AGOs and PIWIs.

    • Carolien Bastiaanssen
    • Pilar Bobadilla Ugarte
    • Fabai Wu
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-14

  • The sequence determinants governing CRISPR/Cas9 specificity are not fully understood. Here, the authors devise a high-throughput dual-target synthetic system to explore the sequence features associated with CRISPR/Cas9 off-target effect, reveal a set of sequence-dependent rules, and develop an off-target prediction model and a strategy for Cas9-based allele-specific editing.

    • Rongjie Fu
    • Wei He
    • Han Xu
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-15

  • RNA synthesis by bacterial RNA polymerase is interrupted by pauses but their role in RNA synthesis is poorly understood. Here the authors use single-molecule FRET and biochemical analysis to show that pausing regulates branching between the abortive and productive outcomes of initial transcription.

    • David Dulin
    • David L. V. Bauer
    • Achillefs N. Kapanidis
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-12

  • DNA replication is accomplished by the replisome, a multi-protein complex that comprises the sliding clamp. Here, Moolman et al. present quantitative and dynamic measurements of the number of β2-sliding clamps at the single-cell level in live E. colicells to shed light on key aspects of DNA replication.

    • M. Charl Moolman
    • Sriram Tiruvadi Krishnan
    • Nynke H. Dekker
    ResearchOpen Access
    Nature Communications
    Volume: 5, P: 1-11

  • In the one-cell Caenorhabditis elegans embryo, anteroposterior polarization is facilitated by large-scale flow of the actomyosin cortex, which segregates cortical polarity proteins into anterior and posterior domains. The underlying forces and physical principles behind long-range flow are unclear. Here, a new method is described by which to measure cortical tension. The results identify two prerequisites for large-scale cortical flow: a gradient in actomyosin contractility and a sufficiently large viscosity of the cortex.

    • Mirjam Mayer
    • Martin Depken
    • Stephan W. Grill
    Research
    Nature
    Volume: 467, P: 617-621

  • Tus protein bound to Ter sites on circular bacterial chromosomes provides a way to avoid random crashes of opposing replication forks. DNA-unzipping experiments show that the Tus–Ter–induced lock during unzipping at the nonpermissive face requires only DNA-strand separation.

    • Bojk A Berghuis
    • David Dulin
    • Nynke H Dekker
    Research
    Nature Chemical Biology
    Volume: 11, P: 579-585