Computational prediction of potential siRNA and human miRNA sequences to silence orf1ab associated genes for future therapeutics against SARS-CoV-2.

Informatics in Medicine Unlocked
Mahedi HasanShamim Ahmed

Abstract

The coronavirus disease 2019 (COVID-19) is an ongoing pandemic caused by an RNA virus termed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 possesses an almost 30kbp long genome. The genome contains open-reading frame 1ab (ORF1ab) gene, the largest one of SARS-CoV-2, encoding polyprotein PP1ab and PP1a responsible for viral transcription and replication. Several vaccines have already been approved by the respective authorities over the world to develop herd immunity among the population. In consonance with this effort, RNA interference (RNAi) technology holds the possibility to strengthen the fight against this virus. Here, we have implemented a computational approach to predict potential short interfering RNAs including small interfering RNAs (siRNAs) and microRNAs (miRNAs), which are presumed to be intrinsically active against SARS-CoV-2. In doing so, we have screened miRNA library and siRNA library targeting the ORF1ab gene. We predicted the potential miRNA and siRNA candidate molecules utilizing an array of bioinformatic tools. By extending the analysis, out of 24 potential pre-miRNA hairpins and 131 siRNAs, 12 human miRNA and 10 siRNA molecules were sorted as potential therapeutic agents agains...Continue Reading

References

Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Aug 2, 2001·Proceedings of the National Academy of Sciences of the United States of America·N J CaplenR A Morgan
Jul 12, 2002·Nature·Gregory J Hannon
Sep 17, 2002·Cell·Javier MartinezThomas Tuschl
Oct 3, 2002·Nature Reviews. Genetics·Michael T McManus, Phillip A Sharp
Oct 9, 2002·Genes & Development·Akira IshizukaHaruhiko Siomi
Feb 21, 2003·Proceedings of the National Academy of Sciences of the United States of America·Qing GeJianzhu Chen
Feb 6, 2004·Nature Biotechnology·Angela ReynoldsAnastasia Khvorova
Mar 27, 2004·Biochemical and Biophysical Research Communications·Mohammed Amarzguioui, Hans Prydz
Jul 3, 2004·Veterinary Pathology·M L CasalP S Henthorn
Sep 24, 2004·RNA·Marc RehmsmeierRobert Giegerich
Jun 28, 2005·Nucleic Acids Research·Nicholas R Markham, Michael Zuker
Jul 6, 2005·European Journal of Echocardiography : the Journal of the Working Group on Echocardiography of the European Society of Cardiology·Marinela SerbanCarmen Ginghina
Nov 1, 2005·Nature Biotechnology·Volker PatzelStefan H E Kaufmann
Dec 31, 2005·Nucleic Acids Research·Sam Griffiths-JonesAnton J Enright
Feb 1, 2006·Bioinformatics·Ulrike MücksteinIvo L Hofacker
Mar 1, 2006·Virus Research·Alexander E GorbalenyaEric J Snijder
Mar 25, 2006·Nature Reviews. Cancer·Aurora Esquela-Kerscher, Frank J Slack
May 26, 2006·Algorithms for Molecular Biology : AMB·Stephan H BernhartIvo L Hofacker
Jul 18, 2006·Nucleic Acids Research·Jan Krüger, Marc Rehmsmeier
Nov 17, 2006·Nature Chemical Biology·David BumcrotDinah W Y Sah
Jul 12, 2007·PloS One·Enikö SonkolyAndor Pivarcsi
Sep 13, 2007·PloS One·Thomas HansenThomas Werge
Oct 19, 2007·Nature·Irene M PedersenMichael David
Dec 8, 2007·Circulation Research·Michael V G LatronicoGianluigi Condorelli
Dec 13, 2007·Pharmaceutical Research·Yong ChenRam I Mahato
Feb 26, 2009·Cell·Richard W Carthew, Erik J Sontheimer
Dec 8, 2009·Nature Structural & Molecular Biology·Mayuko YodaYukihide Tomari
Jan 1, 2010·Nature Reviews. Drug Discovery·Aimee L Jackson, Peter S Linsley
Oct 12, 2010·Methods in Molecular Biology·Zhiguo Wang
Mar 25, 2011·Methods in Molecular Biology·Adam Grundhoff

❮ Previous
Next ❯

Software Mentioned

VMir Analyzer
VMir
RNAfold
siDirect
BLASTn
BLAST ( Basic Local Alignment Search Tool )
VMIir analyzer
DNAmelt Server
VMir Viewer
DNAMelt

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.