A small interfering RNA (siRNA) database for SARS-CoV-2

  1. Inácio Gomes Medeiros
  2. André Salim Khayat
  3. Beatriz Stransky
  4. Sidney Santos
  5. Paulo Assumpção
  6. Jorge Estefano Santana de Souza

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Abstract

Coronavirus disease 2019 (COVID-19) rapidly transformed into a global pandemic, for which a demand for developing antivirals capable of targeting the SARS-CoV-2 RNA genome and blocking the activity of its genes has emerged. In this work, we presented a database of SARS-CoV-2 targets for small interference RNA (siRNA) based approaches, aiming to speed the design process by providing a broad set of possible targets and siRNA sequences. The siRNAs sequences are characterized and evaluated by more than 170 features, including thermodynamic information, base context, target genes and alignment information of sequences against the human genome, and diverse SARS-CoV-2 strains, to assess possible bindings to off-target sequences. This dataset is available as a set of four tables, available in a spreadsheet and CSV (Comma-Separated Values) formats, each one corresponding to sequences of 18, 19, 20, and 21 nucleotides length, aiming to meet the diversity of technology and expertise among laboratories around the world. A metadata table (Supplementary Table S1), which describes each feature, is also provided in the aforementioned formats. We hope that this database helps to speed up the development of new target antivirals for SARS-CoV-2, contributing to a possible strategy for a faster and effective response to the COVID-19 pandemic.

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  1. Version published to 10.1038/s41598-021-88310-8
  2. Version published to 10.1101/2020.09.30.321596v2 on bioRxiv
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  4. Version published to 10.1101/2020.09.30.321596v1 on bioRxiv