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  1. Article ; Online: 3D RNA-scaffolded wireframe origami

    Molly F. Parsons / Matthew F. Allan / Shanshan Li / Tyson R. Shepherd / Sakul Ratanalert / Kaiming Zhang / Krista M. Pullen / Wah Chiu / Silvi Rouskin / Mark Bathe

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 14

    Abstract: Hybrid nucleic acid origami has potential for biomedical delivery of mRNA and fabrication of artificial ribozymes. Here, the authors use chemical footprinting and cryo-electron microscopy to reveal insights into nucleic acid origami used to fold ... ...

    Abstract Hybrid nucleic acid origami has potential for biomedical delivery of mRNA and fabrication of artificial ribozymes. Here, the authors use chemical footprinting and cryo-electron microscopy to reveal insights into nucleic acid origami used to fold messenger and ribosomal RNA into 3D polyhedral structures.
    Keywords Science ; Q
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells

    Tammy C. T. Lan / Matty F. Allan / Lauren E. Malsick / Jia Z. Woo / Chi Zhu / Fengrui Zhang / Stuti Khandwala / Sherry S. Y. Nyeo / Yu Sun / Junjie U. Guo / Mark Bathe / Anders Näär / Anthony Griffiths / Silvi Rouskin

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 14

    Abstract: Lan et al. report RNA structure ensembles across the entire SARSCoV-2 genome in infected human cells at single nucleotide resolution. They find alternative RNA conformations critical for promoting near-native frameshifting rates in ORF1ab. ...

    Abstract Lan et al. report RNA structure ensembles across the entire SARSCoV-2 genome in infected human cells at single nucleotide resolution. They find alternative RNA conformations critical for promoting near-native frameshifting rates in ORF1ab.
    Keywords Science ; Q
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: An intranasal ASO therapeutic targeting SARS-CoV-2

    Chi Zhu / Justin Y. Lee / Jia Z. Woo / Lei Xu / Xammy Nguyenla / Livia H. Yamashiro / Fei Ji / Scott B. Biering / Erik Van Dis / Federico Gonzalez / Douglas Fox / Eddie Wehri / Arjun Rustagi / Benjamin A. Pinsky / Julia Schaletzky / Catherine A. Blish / Charles Chiu / Eva Harris / Ruslan I. Sadreyev /
    Sarah Stanley / Sakari Kauppinen / Silvi Rouskin / Anders M. Näär

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 13

    Abstract: Despite approved vaccines and anti-virals to prevent and treat SARS-CoV-2 infection, there is a need for further development of efficient antiviral therapeutic strategy. Here, Zhu et al. develop locked nucleic acid antisense oligonucleotides (LNA ASOs) ... ...

    Abstract Despite approved vaccines and anti-virals to prevent and treat SARS-CoV-2 infection, there is a need for further development of efficient antiviral therapeutic strategy. Here, Zhu et al. develop locked nucleic acid antisense oligonucleotides (LNA ASOs) targeting the 5’ leader sequence of SARS-CoV-2 RNA to interfere with replication of wildtype virus and variants of concern. Daily intranasal administration in K18-hACE2 humanized mice suppresses viral infection in lung.
    Keywords Science ; Q
    Language English
    Publishing date 2022-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Operon mRNAs are organized into ORF-centric structures that predict translation efficiency

    David H Burkhardt / Silvi Rouskin / Yan Zhang / Gene-Wei Li / Jonathan S Weissman / Carol A Gross

    eLife, Vol

    2017  Volume 6

    Abstract: Bacterial mRNAs are organized into operons consisting of discrete open reading frames (ORFs) in a single polycistronic mRNA. Individual ORFs on the mRNA are differentially translated, with rates varying as much as 100-fold. The signals controlling ... ...

    Abstract Bacterial mRNAs are organized into operons consisting of discrete open reading frames (ORFs) in a single polycistronic mRNA. Individual ORFs on the mRNA are differentially translated, with rates varying as much as 100-fold. The signals controlling differential translation are poorly understood. Our genome-wide mRNA secondary structure analysis indicated that operonic mRNAs are comprised of ORF-wide units of secondary structure that vary across ORF boundaries such that adjacent ORFs on the same mRNA molecule are structurally distinct. ORF translation rate is strongly correlated with its mRNA structure in vivo, and correlation persists, albeit in a reduced form, with its structure when translation is inhibited and with that of in vitro refolded mRNA. These data suggest that intrinsic ORF mRNA structure encodes a rough blueprint for translation efficiency. This structure is then amplified by translation, in a self-reinforcing loop, to provide the structure that ultimately specifies the translation of each ORF.
    Keywords mRNA secondary structure ; DMS-seq ; translation efficiency ; ribosome profiling ; codon usage ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 410
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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