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.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6319925PMC
http://dx.doi.org/10.1016/j.ymeth.2016.04.016DOI Listing

Publication Analysis

Top Keywords

ring catalog
8
designing self-assembling
8
self-assembling rna
8
rna
6
ring
4
catalog resource
4
resource designing
4
rna nanostructures
4
nanostructures designing
4
rna ring
4

Similar Publications

Ion Spectroscopy in the Context of the Diffuse Interstellar Bands: A Case Study with the Phenylacetylene Cation.

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 PDF
Article Synopsis
  • Scorpion stings are a major public health issue, especially in tropical and subtropical areas, with varying venom profiles leading to different symptoms of envenomation.
  • Scorpion venoms contain unique peptides that could be valuable for drug development, prompting the need for a database cataloging scorpion species and their venom components.
  • ScorpDb is a new database focused on Iranian scorpions, providing research access to venom data and symptoms, with plans to expand to include more varieties of scorpions in the future.
View Article and Find Full Text PDF

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 PDF
Article Synopsis
  • * Researchers found 10 LAB strains that are approved for use in feed additives, demonstrating strong resilience to simulated digestive conditions.
  • * Specifically, the strain YH-15 showed promise for clinical use due to its ability to inhibit harmful bacteria and effectively adhere to human intestinal cells.
View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!