Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities.

Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Research Abstract Details 

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Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Abstract Text:

Masatoshi Ichihara,Yoshiki Murakumo,Akio Masuda,Toru Matsuura,Naoya Asai,Mayumi Jijiwa,Maki Ishida,Jun Shinmi,Hiroshi Yatsuya,Shanlou Qiao,Masahide Takahashi,Kinji Ohno,

We developed a simple algorithm, i-Score (inhibitory-Score), to predict active siRNAs by applying a linear regression model to 2431 siRNAs. Our algorithm is exclusively comprised of nucleotide (nt) preferences at each position, and no other parameters are taken into account. Using a validation dataset comprised of 419 siRNAs, we found that the prediction accuracy of i-Score is as good as those of s-Biopredsi, ThermoComposition21 and DSIR, which employ a neural network model or more parameters in a linear regression model. Reynolds and Katoh also predict active siRNAs efficiently, but the numbers of siRNAs predicted to be active are less than one-eighth of that of i-Score. We additionally found that exclusion of thermostable siRNAs, whose whole stacking energy (DeltaG) is less than -34.6 kcal/mol, improves the prediction accuracy in i-Score, s-Biopredsi, ThermoComposition21 and DSIR. We also developed a universal target vector, pSELL, with which we can assay an siRNA activity of any sequence in either the sense or antisense direction. We assayed 86 siRNAs in HEK293 cells using pSELL, and validated applicability of i-Score and the whole DeltaG value in designing siRNAs.

Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Publishing Authors By Initials

M Ichihara,Y Murakumo,A Masuda,T Matsuura,N Asai,M Jijiwa,M Ishida,J Shinmi,H Yatsuya,S Qiao,M Takahashi,K Ohno,

For similar natural sciences: physics: thermodynamics research abstracts see: natural sciences: physics: thermodynamics research

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Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Journal Published:

PUBLICATION TYPE: Validation Studies

Journal: Nucleic acids research

VOLUME: 35

Page Numbers: e123

Journal Abbreviation: Nucleic Acids Res.

ISSN: 1362-4962

DAY: 20

MONTH: 09

YEAR: 2007

Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Information

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LANGUAGE: eng

NlmUniqueID: 411011

Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Keywords Mesh Terms:

KEYWORDS: Thermodynamics

MESH TERMS: chemistry

Chemical & Substance for Abstract: Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Information

Substance Name: RNA, Small Interfering

Registry Number: 0

Grant and Affiliation Information for Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities.

AFFILIATION: Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, 1200 Matsumoto, Kasugai 487-8501, Japan.

Country: England

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MEDLINETA: Nucleic Acids Res

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