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Showing 1–21 of 21 results
Advanced filters: Author: Daniel Herschlag Clear advanced filters

  • Short-lived RNA folding intermediates have important roles in the folding of RNA. Here, the authors combine 15N relaxation dispersion NMR with chemical probing to visualise one of these intermediates, and are able to show it is a secondary structural switch, that might help with folding.

    • Yi Xue
    • Brant Gracia
    • Hashim M. Al-Hashimi
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-11

  • Automated 3D design produces rapid and near-atomically accurate predictions of RNA tertiary structure as well as the ability to generate complex RNA machines such as functional single-stranded tethered ribosomes, and enhancement of the binding properties of small-molecule RNA aptamers.

    • Joseph D. Yesselman
    • Daniel Eiler
    • Rhiju Das
    Research
    Nature Nanotechnology
    Volume: 14, P: 866-873

  • Cooperativity is a universal property of biological macromolecules that is widely exploited in their regulation and function. Simulations and single-molecule FRET studies demonstrate that molecular heterogeneity lowers the cooperativity of ligand binding, suggesting that it is crucial to determine the cooperativity of individual molecules and the extent of heterogeneity in order to derive accurate molecular models.

    • Sergey V Solomatin
    • Max Greenfeld
    • Daniel Herschlag
    Research
    Nature Structural & Molecular Biology
    Volume: 18, P: 732-734

  • XSI analysis of two RNA kink-turn motifs, KtA and KtB, in a range of solution concentrations and in the presence of the kink-turn protein partner L7Ae reveals a restricted conformational ensemble that is regulated by ions and protein binding.

    • Xuesong Shi
    • Lin Huang
    • Daniel Herschlag
    Research
    Nature Chemical Biology
    Volume: 12, P: 146-152

  • Determining dynamic ensembles of biomolecules is still challenging. Here the authors present an approach for rapid RNA ensemble determination that combines RNA structure prediction tools and NMR residual dipolar coupling data and use it to determine atomistic ensemble models for a variety of RNAs.

    • Honglue Shi
    • Atul Rangadurai
    • Hashim M. Al-Hashimi
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-14

  • Systematic alteration of HIV-1 TAR RNA and quantitative determination of its propensity to bind to the Tat protein establish a key role role for a rare and short-lived RNA state in Tat-dependent transactivation in cells.

    • Megan L. Ken
    • Rohit Roy
    • Hashim M. Al-Hashimi
    Research
    Nature
    Volume: 617, P: 835-841

  • Dimethyl sulfate mutational profiling with sequencing, combined with the newly developed DREEM algorithm, reveals that heterogeneity of RNA structure in HIV-1 regulates the use of splice sites and expression of viral genes.

    • Phillip J. Tomezsko
    • Vincent D. A. Corbin
    • Silvi Rouskin
    Research
    Nature
    Volume: 582, P: 438-442

  • A new technology platform called μSCALE combines the use of a microcapillary array with laser-based extraction to enable high-throughput biochemical and biophysical analysis and isolation of protein variants for protein-engineering applications.

    • Bob Chen
    • Sungwon Lim
    • Jennifer R Cochran
    Research
    Nature Chemical Biology
    Volume: 12, P: 76-81

  • The 'thermodynamic hypothesis' proposes that the sequence of a biological macromolecule defines its folded, active structure as a global energy minimum in the folding landscape; however, it is not clear whether there is only one global minimum or several local minima corresponding to active conformations. Here, using single-molecule experiments, an RNA enzyme is shown to fold into multiple distinct native states that interconvert.

    • Sergey V. Solomatin
    • Max Greenfeld
    • Daniel Herschlag
    Research
    Nature
    Volume: 463, P: 681-684

  • After waiting almost 15 years since the first ribozyme (catalytic RNA molecule) was crystallized, the RNA community finds that such structures are a bit like buses, with two coming at once. One is the high-resolution structure of the hepatitis delta helper virus ribozyme, and the other, at slightly lower resolution, is the group I intron fromTetrahymena thermophila.

    • Daniel Herschlag
    News & Views
    Nature
    Volume: 395, P: 548-549

  • The scope of enzymology has expanded rapidly over the last century, from an early focus on the chemical and catalytic mechanisms of individual enzymes to more recent efforts to understand enzyme action in the context of dynamic, functional biological systems consisting of many interacting enzymes and proteins. Continuing progress in probing the link between molecular structure and function now promises to pave the way for a deeper understanding of the evolution and behavior of the complex biological systems that govern cellular behavior.

    • Jesse G Zalatan
    • Daniel Herschlag
    Comments & Opinion
    Nature Chemical Biology
    Volume: 5, P: 516-520

  • The functions of many regulatory RNAs depend on how their 3D structure changes in response to cellular conditions. Recent studies have revealed that RNA exists as a dynamic ensemble of conformations, which form with different probabilities in different cellular conditions and thus modulate RNA function.

    • Laura R. Ganser
    • Megan L. Kelly
    • Hashim M. Al-Hashimi
    Reviews
    Nature Reviews Molecular Cell Biology
    Volume: 20, P: 474-489

  • A cryo-EM structure of an initiation complex of HIV-1 reverse transcriptase sheds light on the initiation of reverse transcription of viral RNA.

    • Kevin P. Larsen
    • Yamuna Kalyani Mathiharan
    • Elisabetta Viani Puglisi
    Research
    Nature
    Volume: 557, P: 118-122