A novel program to design siRNAs simultaneously effective to highly variable virus genomes

Hui Sun Lee, Jeonghyun Ahn, Eun Jung Jun, Sanghwa Yang, Chul Hyun Joo, Yoo Kyum Kim, Heuiran Lee

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)431-435
Number of pages5
JournalBiochemical and Biophysical Research Communications
Volume384
Issue number4
DOIs
StatePublished - Jul 10 2009
Externally publishedYes

Fingerprint

Viruses
Small Interfering RNA
Genes
Genome
Antiviral Agents
Viral Genome
Application programs
Human Enterovirus B
Viral RNA
RNA
Mutation Rate
Bioinformatics
Computational Biology
HeLa Cells

Keywords

  • Antiviral activity
  • CAPSID
  • Enterovirus
  • Genetic instability
  • Sequence diversity
  • Small-interfering RNA

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Cell Biology
  • Molecular Biology

Cite this

A novel program to design siRNAs simultaneously effective to highly variable virus genomes. / Lee, Hui Sun; Ahn, Jeonghyun; Jun, Eun Jung; Yang, Sanghwa; Joo, Chul Hyun; Kim, Yoo Kyum; Lee, Heuiran.

In: Biochemical and Biophysical Research Communications, Vol. 384, No. 4, 10.07.2009, p. 431-435.

Research output: Contribution to journalArticle

Lee, Hui Sun ; Ahn, Jeonghyun ; Jun, Eun Jung ; Yang, Sanghwa ; Joo, Chul Hyun ; Kim, Yoo Kyum ; Lee, Heuiran. / A novel program to design siRNAs simultaneously effective to highly variable virus genomes. In: Biochemical and Biophysical Research Communications. 2009 ; Vol. 384, No. 4. pp. 431-435.
@article{eba6dfadbc764a18a8209cabf46a3902,
title = "A novel program to design siRNAs simultaneously effective to highly variable virus genomes",
abstract = "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.",
keywords = "Antiviral activity, CAPSID, Enterovirus, Genetic instability, Sequence diversity, Small-interfering RNA",
author = "Lee, {Hui Sun} and Jeonghyun Ahn and Jun, {Eun Jung} and Sanghwa Yang and Joo, {Chul Hyun} and Kim, {Yoo Kyum} and Heuiran Lee",
year = "2009",
month = "7",
day = "10",
doi = "10.1016/j.bbrc.2009.04.143",
language = "English (US)",
volume = "384",
pages = "431--435",
journal = "Biochemical and Biophysical Research Communications",
issn = "0006-291X",
publisher = "Academic Press Inc.",
number = "4",

}

TY - JOUR

T1 - A novel program to design siRNAs simultaneously effective to highly variable virus genomes

AU - Lee, Hui Sun

AU - Ahn, Jeonghyun

AU - Jun, Eun Jung

AU - Yang, Sanghwa

AU - Joo, Chul Hyun

AU - Kim, Yoo Kyum

AU - Lee, Heuiran

PY - 2009/7/10

Y1 - 2009/7/10

N2 - 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.

AB - 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.

KW - Antiviral activity

KW - CAPSID

KW - Enterovirus

KW - Genetic instability

KW - Sequence diversity

KW - Small-interfering RNA

UR - http://www.scopus.com/inward/record.url?scp=65649135488&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=65649135488&partnerID=8YFLogxK

U2 - 10.1016/j.bbrc.2009.04.143

DO - 10.1016/j.bbrc.2009.04.143

M3 - Article

VL - 384

SP - 431

EP - 435

JO - Biochemical and Biophysical Research Communications

JF - Biochemical and Biophysical Research Communications

SN - 0006-291X

IS - 4

ER -