Designing self-assembling RNA ring structures based on known 3D structural elements connected via linker helices is a challenging task due to the immense number of motif combinations, many of which do not lead to ring-closure. We describe an in silico solution to this design problem by combinatorial assembly of RNA 3-way junctions, bulges, and kissing loops, and tabulating the cases that lead to ring formation. The solutions found are made available in the form of a web-accessible Ring Catalog. As an example of a potential use of this resource, we chose a predicted RNA square structure consisting of five RNA strands and demonstrate experimentally that the self-assembly of those five strands leads to the formation of a square-like complex. This is a demonstration of a novel "design by catalog" approach to RNA nano-structure generation. The URL https://rnajunction.ncifcrf.gov/ringdb can be used to access the resource.
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http://dx.doi.org/10.1016/j.ymeth.2016.04.016 | DOI Listing |
ACS Earth Space Chem
December 2024
School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, King's Buildings, Edinburgh EH9 3FJ, Scotland, U.K.
Identification of the molecular carriers of diffuse interstellar bands (DIBs) requires gas phase electronic spectra of suitable candidate structures. Recording the spectra of these in the laboratory is challenging because they include large, carbon-rich molecules, many of which are likely to be ionic. The electronic spectra of ions are often obtained using action spectroscopy methods, which can induce small perturbations to the absorption characteristics and hinder comparison with astronomical observations.
View Article and Find Full Text PDFOne new extinct genus and six new extinct species of Zopheridae are described and illustrated from Eocene Baltic amber: Usechus andrushchenkoi Alekseev et Bukejs sp. nov., Coxelus carstengroehni Alekseev et Bukejs sp.
View Article and Find Full Text PDFToxins (Basel)
November 2024
LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.
RSC Adv
November 2024
Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University Riyadh 11451 Saudi Arabia
The development of novel and efficient tyrosinase inhibitors is a critical necessity of agricultural, cosmetic and medicinal chemistry. Bearing in mind the therapeutical potential of naphthofuran-containing organic compounds, we carried out the CTAB-catalyzed ultrasound-assisted synthesis of a library of novel naphthofuran-triazole joined -aryl/alkyl acetamides 20(a-j) in 74-92% yield, which were further assessed for their tyrosinase inhibitory potential by taking kojic acid and ascorbic acid as standard inhibitors. The tyrosinase inhibitory assay demonstrated the promising tyrosinase inhibiting tendency of all prepared derivatives 20(a-h) as they all were found to be more efficient in comparison to the standard kojic acid.
View Article and Find Full Text PDFHeliyon
October 2024
Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China.
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