A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity

Jesper B Bramsen; Maria Bach Laursen; Anne F Nielsen; Thomas B Hansen; Claus Bus; Niels Langkjær; Bolle Ravindra Babu; Torben Højland; Mikhail Abramov; Arthur Van Aerschot; Dalibor Odadzic; Romualdas Smicius; Jens Haas; Cordula Andree; Jharna Barman; Malgorzata Wenska; Puneet Srivastava; Chuanzheng Zhou; Dmytro Honcharenko; Simone Hess; Elke Müller; Georgii V Bobkov; Sergey N Mikhailov; Eugenio Fava; Thomas F Meyer; Jyoti Chattopadhyaya; Marino Zerial; Joachim W Engels; Piet Herdewijn; Jesper Wengel; Jørgen Kjems

doi:10.1093/nar/gkp106

A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity

Jesper B Bramsen, Maria Bach Laursen, Anne F Nielsen, Thomas B Hansen, Claus Bus, Niels Langkjær, Bolle Ravindra Babu, Torben Højland, Mikhail Abramov, Arthur Van Aerschot, Dalibor Odadzic, Romualdas Smicius, Jens Haas, Cordula Andree, Jharna Barman, Malgorzata Wenska, Puneet Srivastava, Chuanzheng Zhou, Dmytro Honcharenko, Simone HessElke Müller, Georgii V Bobkov, Sergey N Mikhailov, Eugenio Fava, Thomas F Meyer, Jyoti Chattopadhyaya, Marino Zerial, Joachim W Engels, Piet Herdewijn, Jesper Wengel, Jørgen Kjems

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

307 Citations (Scopus)

Abstract

The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3'-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.

Original language	English
Journal	Nucleic Acids Research
Volume	37
Issue	9
Pages (from-to)	2867-81
Number of pages	15
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gkp106
Publication status	Published - 2009

Keywords

Cell Line, Tumor
Cell Survival
Humans
RNA Interference
RNA Stability
RNA, Small Interfering
RNA-Induced Silencing Complex

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10.1093/nar/gkp106

Cite this

Bramsen, J. B., Laursen, M. B., Nielsen, A. F., Hansen, T. B., Bus, C., Langkjær, N., Babu, B. R., Højland, T., Abramov, M., Van Aerschot, A., Odadzic, D., Smicius, R., Haas, J., Andree, C., Barman, J., Wenska, M., Srivastava, P., Zhou, C., Honcharenko, D., ... Kjems, J. (2009). A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity. Nucleic Acids Research, 37(9), 2867-81. https://doi.org/10.1093/nar/gkp106

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title = "A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity",

abstract = "The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3'-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.",

keywords = "Cell Line, Tumor, Cell Survival, Humans, RNA Interference, RNA Stability, RNA, Small Interfering, RNA-Induced Silencing Complex",

author = "Bramsen, {Jesper B} and Laursen, {Maria Bach} and Nielsen, {Anne F} and Hansen, {Thomas B} and Claus Bus and Niels Langkj{\ae}r and Babu, {Bolle Ravindra} and Torben H{\o}jland and Mikhail Abramov and {Van Aerschot}, Arthur and Dalibor Odadzic and Romualdas Smicius and Jens Haas and Cordula Andree and Jharna Barman and Malgorzata Wenska and Puneet Srivastava and Chuanzheng Zhou and Dmytro Honcharenko and Simone Hess and Elke M{\"u}ller and Bobkov, {Georgii V} and Mikhailov, {Sergey N} and Eugenio Fava and Meyer, {Thomas F} and Jyoti Chattopadhyaya and Marino Zerial and Engels, {Joachim W} and Piet Herdewijn and Jesper Wengel and J{\o}rgen Kjems",

year = "2009",

doi = "10.1093/nar/gkp106",

language = "English",

volume = "37",

pages = "2867--81",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

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Bramsen, JB, Laursen, MB, Nielsen, AF, Hansen, TB, Bus, C, Langkjær, N, Babu, BR, Højland, T, Abramov, M, Van Aerschot, A, Odadzic, D, Smicius, R, Haas, J, Andree, C, Barman, J, Wenska, M, Srivastava, P, Zhou, C, Honcharenko, D, Hess, S, Müller, E, Bobkov, GV, Mikhailov, SN, Fava, E, Meyer, TF, Chattopadhyaya, J, Zerial, M, Engels, JW, Herdewijn, P, Wengel, J & Kjems, J 2009, 'A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity', Nucleic Acids Research, vol. 37, no. 9, pp. 2867-81. https://doi.org/10.1093/nar/gkp106

A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity. / Bramsen, Jesper B; Laursen, Maria Bach; Nielsen, Anne F et al.
In: Nucleic Acids Research, Vol. 37, No. 9, 2009, p. 2867-81.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

TY - JOUR

T1 - A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity

AU - Bramsen, Jesper B

AU - Laursen, Maria Bach

AU - Nielsen, Anne F

AU - Hansen, Thomas B

AU - Bus, Claus

AU - Langkjær, Niels

AU - Babu, Bolle Ravindra

AU - Højland, Torben

AU - Abramov, Mikhail

AU - Van Aerschot, Arthur

AU - Odadzic, Dalibor

AU - Smicius, Romualdas

AU - Haas, Jens

AU - Andree, Cordula

AU - Barman, Jharna

AU - Wenska, Malgorzata

AU - Srivastava, Puneet

AU - Zhou, Chuanzheng

AU - Honcharenko, Dmytro

AU - Hess, Simone

AU - Müller, Elke

AU - Bobkov, Georgii V

AU - Mikhailov, Sergey N

AU - Fava, Eugenio

AU - Meyer, Thomas F

AU - Chattopadhyaya, Jyoti

AU - Zerial, Marino

AU - Engels, Joachim W

AU - Herdewijn, Piet

AU - Wengel, Jesper

AU - Kjems, Jørgen

PY - 2009

Y1 - 2009

N2 - The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3'-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.

AB - The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3'-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.

KW - Cell Line, Tumor

KW - Cell Survival

KW - Humans

KW - RNA Interference

KW - RNA Stability

KW - RNA, Small Interfering

KW - RNA-Induced Silencing Complex

U2 - 10.1093/nar/gkp106

DO - 10.1093/nar/gkp106

M3 - Journal article

C2 - 19282453

SN - 0305-1048

VL - 37

SP - 2867

EP - 2881

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 9

ER -

A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity

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Keywords

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