A novel program to design siRNAs simultaneously effective to highly variable virus genomes.
A major concern of antiviral therapy using small interfering RNAs (siRNAs) targeting RNA viral genome is high sequence diversity and mutation rate due to genetic instability. To overcome this problem, it is indispensable to design siRNAs targeting highly conserved regions. We thus designed CAPSID (Convenient Application Program for siRNA Design), a novel bioinformatics program to identify siRNAs targeting highly conserved regions within RNA viral genomes. From a set of input RNAs of diverse sequences, CAPSID rapidly searches conserved patterns and suggests highly potent siRNA candidates in a hierarchical manner. To validate the usefulness of this novel program, we investigated the antiviral potency of universal siRNA for various Human enterovirus B (HEB) serotypes. Assessment of antiviral efficacy using Hela cells, clearly demonstrates that HEB-specific siRNAs exhibit protective effects against all HEBs examined. These findings strongly indicate that CAPSID can be applied to select universal antiviral siRNAs against highly divergent viral genomes.
Lee
Hui Sun
HS
Department of Physiology, University of Ulsan College of Medicine, Seoul, Republic of Korea.
Ahn
Jeonghyun
J
Jun
Eun Jung
EJ
Yang
Sanghwa
S
Joo
Chul Hyun
CH
Kim
Yoo Kyum
YK
Lee
Heuiran
H
D000818:Animals; D002522:Chlorocebus aethiops; D019295:Computational Biology / Q000379:methods*; D029822:Enterovirus B, Human / Q000145:classification / Q000235:genetics; D004769:Enterovirus Infections / Q000628:therapy; D016679:Genome, Viral; D006367:HeLa Cells; D006801:Humans; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014709:Vero Cells
D034741:RNA, Small Interfering