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Showing 1–9 of 9 results
Advanced filters: Author: "David Rueda" Clear advanced filters

  • DEAD-box helicases use ATP hydrolysis to unwind duplex RNA and facilitate RNA or RNA–protein remodelling. One such helicase is Mss116, which targets a particular group II intron in RNA. Here, single-molecule fluorescence was used to monitor the effect of Mss16 on a minimal construct containing this intron. The data show that Mss16 stimulates the sampling of different folded states of the RNA. Moreover, the helicase promotes RNA folding through discrete ATP-independent and ATP-dependent steps.

    • Krishanthi S. Karunatilaka
    • Amanda Solem
    • David Rueda
    Research
    Nature
    Volume: 467, P: 935-939

  • Activation-induced deoxycytidine deaminase (AID) induces somatic hypermutation and class-switch recombination during transcription of immunoglobulin genes. Here the authors use single-molecule FRET to show that AID translocates together with RNA polymerase and scans within stalled transcription bubbles.

    • Gayan Senavirathne
    • Jeffrey G. Bertram
    • David Rueda
    ResearchOpen Access
    Nature Communications
    Volume: 6, P: 1-11

  • Locating a four-way junction in a high background of genomic DNA is likely to be the rate-limiting step of the resolution process. This study captures the entire reaction trajectory of a nuclease targeting and resolving a DNA junction at single-molecule level.

    • Artur P. Kaczmarczyk
    • Anne-Cécile Déclais
    • David S. Rueda
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-13

  • Many aptamer-fluorophore complexes suffer from low quantum yield and low extinction coefficients limiting their usability. Here the authors isolate new Mango aptamers with improved fluorescent properties for both fixed and live-cell imaging by using competitive ligand binding microfluidic selection.

    • Alexis Autour
    • Sunny C. Y. Jeng
    • Peter J. Unrau
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-12

  • Fluorogenic RNA aptamers have been used for RNA imaging, but folding and fluorescence stability often limited their use in high resolution applications. Here the authors present an array of stably folding Mango II aptamers for imaging of coding and non-coding RNAs at single-molecule resolution, in both live and fixed cells.

    • Adam D. Cawte
    • Peter J. Unrau
    • David S. Rueda
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-11

  • Retroviral integrases catalyze the insertion of viral DNA into the host cell DNA and can use nucleosomes as substrates for integration. Here the authors present the 3.9 Å cryo-EM structure of prototype foamy virus integrase after strand transfer into nucleosomal DNA, which together with single-molecule FRET measurements provides evidence for a DNA looping and sliding mechanism of integrases.

    • Marcus D. Wilson
    • Ludovic Renault
    • Alessandro Costa
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-10

  • Mechanical distortion of DNA structure induces off-target binding and cleavage by SpyCas9 at sites with up to ten mismatches, a potential mechanism that exposes cryptic off-target sites in cells during transcription or replication.

    • Matthew D. Newton
    • Benjamin J. Taylor
    • David S. Rueda
    Research
    Nature Structural & Molecular Biology
    Volume: 26, P: 185-192