Moment analysis for kinetics of gene silencing by RNA interference

Takahashi, Yuki; Yamaoka, Kiyoshi; Nishikawa, Makiya; Takakura, Yoshinobu

doi:10.1002/bit.20718

Cited by 9 publications

(8 citation statements)

References 15 publications

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“…We used the pharmacokinetic parameters, that is, the area under the curve of the inhibitory effect (AUC IE ) as an index of the total intensity of RNAi activity and the mean response time of the inhibitory effect (MRT IE ) as an index of its duration, which were proposed by Takahashi et al . (20). These parameters can be calculated by simple numerical integration using time-course experimental data.…”

Section: Resultsmentioning

confidence: 99%

“…According to the report of Takahashi et al (20), the area under the curve of the inhibitory effect (AUC IE ) and the mean response time of the inhibitory effect (MRT IE ) values were calculated using following equations: AUC IE = ∫ R GEI dt ; MRT IE = ∫ t·R GEI dt / ∫ R GEI dt , where R GEI represents the ratio of inhibition of gene expression.…”

Section: Methodsmentioning

confidence: 99%

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Intracellular stability of 2′-OMe-4′-thioribonucleoside modified siRNA leads to long-term RNAi effect

Takáhashi

Nagai

Hatakeyama

et al. 2012

Nucleic Acids Research

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Chemically modified siRNAs are expected to have resistance toward nuclease degradation and good thermal stability in duplex formation for in vivo applications. We have recently found that 2′-OMe-4′-thioRNA, a hybrid chemical modification based on 2′-OMeRNA and 4′-thioRNA, has high hybridization affinity for complementary RNA and significant resistance toward degradation in human plasma. These results prompted us to develop chemically modified siRNAs using 2′-OMe-4′-thioribonucleosides for therapeutic application. Effective modification patterns were screened with a luciferase reporter assay. The best modification pattern of siRNA, which conferred duration of the gene-silencing effect without loss of RNAi activity, was identified. Quantification of the remaining siRNA in HeLa-luc cells using a Heat-in-Triton (HIT) qRT–PCR revealed that the intracellular stability of the siRNA modified with 2′-OMe-4′-thioribonucleosides contributed significantly to the duration of its RNAi activity.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Intracellular stability of 2′-OMe-4′-thioribonucleoside modified siRNA leads to long-term RNAi effect

Takáhashi

Nagai

Hatakeyama

et al. 2012

Nucleic Acids Research

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“…Early studies evaluating the rate of RNAi activity defined the optimal window for target knockdown and functional gene analysis [11,12]. Medicinal chemistry also enabled usage and identification of modifications to siRNAs that improved mechanistic analysis and pharmacological properties [13-15].…”

Section: Introductionmentioning

confidence: 99%

Defining Features and Exploring Chemical Modifications to Manipulate RNAa Activity

Place¹,

Noonan²,

Földes-Papp³

et al. 2010

CPB

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RNA interference (RNAi) is an evolutionary conserved mechanism by which small double-stranded RNA (dsRNA) – termed small interfering RNA (siRNA) – inhibits translation or degrades complementary mRNA sequences. Identifying features and enzymatic components of the RNAi pathway have led to the design of highly-effective siRNA molecules for laboratory and therapeutic application. RNA activation (RNAa) is a newly discovered mechanism of gene induction also triggered by dsRNAs termed small activating RNA (saRNA). It offers similar benefits as RNA interference (RNAi), while representing a new method of gene overexpression. In the present study, we identify features of RNAa and explore chemical modifications to saRNAs that improve the applicability of RNAa. We evaluate the rate of RNAa activity in order to define an optimal window of gene induction, while comparing the kinetic differences between RNAa and RNAi. We identify Ago2 as a conserved enzymatic component of both RNAa and RNAi implicating that saRNA may tolerate modification based on Ago2 function. As such, we define chemical modifications to saRNAs that manipulate RNAa activity, as well as exploit their effects to design saRNAs with enhanced medicinal properties. These findings reveal functional features of RNAa that may be utilized to augment saRNA function for mechanistic studies or the development of RNAa-based drugs.

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“…Their model could be used to select the appropriate time of siRNA transfection in function of gene induction. Moment analysis was used by Takahashi et al to evaluate the time course of endogenous protein expression in function of siRNA concentration [144]. Likewise, an interesting report by Arciero et al describes mathematical modelling as a tool to predict tumour-immune evasion and to study the impact of siRNA administration directed against the immune suppressive cytokine TGF-b on tumour growth [145].…”

Section: Reviewsmentioning

confidence: 99%

Maintaining the silence: reflections on long-term RNAi

Raemdonck

Vandenbroucke

Demeester

et al. 2008

Drug Discovery Today

104

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Since the demonstration of RNA interference (RNAi) in mammalian cells, considerable research and financial effort has gone towards implementing RNAi as a viable therapeutic platform. RNAi is, without doubt, the most promising strategy for the treatment of human genetic disorders. Because many of the targets proposed for RNAi therapy require chronic treatment, researchers agree that the emphasis must now be placed on the safe and long-term application of RNAi drugs to reap the benefits at last.

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Moment analysis for kinetics of gene silencing by RNA interference

Cited by 9 publications

References 15 publications

Intracellular stability of 2′-OMe-4′-thioribonucleoside modified siRNA leads to long-term RNAi effect

Intracellular stability of 2′-OMe-4′-thioribonucleoside modified siRNA leads to long-term RNAi effect

Defining Features and Exploring Chemical Modifications to Manipulate RNAa Activity

Maintaining the silence: reflections on long-term RNAi

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