Engineering small interfering RNAs by strategic chemical modification.

Synthetic small interfering RNAs (siRNAs) have revolutionized functional genomics in mammalian cell cultures due to their reliability, efficiency, and ease of use. This success, however, has not fully translated into siRNA applications in vivo and in siRNA therapeutics where initial optimism has been dampened by a lack of efficient delivery strategies and reports of siRNA off-target effects and immunogenicity. Encouragingly, most aspects of siRNA behavior can be addressed by careful engineering of siRNAs incorporating beneficial chemical modifications into discrete nucleotide positions during siRNA synthesis. Here, we review the literature (Subheadings 1 -3) and provide a quick guide (Subheading 4) to how the performance of siRNA can be improved by chemical modification to suit specific applications in vitro and in vivo.

[1]  G. Rettig,et al.  Progress Toward In Vivo Use of siRNAs-II , 2006, Molecular Therapy.

[2]  M. Maeda,et al.  Synthesis, structure, and biological activity of dumbbell-shaped nanocircular RNAs for RNA interference. , 2011, Bioconjugate chemistry.

[3]  Z. Mourelatos,et al.  A human, ATP-independent, RISC assembly machine fueled by pre-miRNA. , 2005, Genes & development.

[4]  S. Bartz,et al.  The siRNA sequence and guide strand overhangs are determinants of in vivo duration of silencing , 2010, Nucleic acids research.

[5]  R. Griffey,et al.  Fully 2'-modified oligonucleotide duplexes with improved in vitro potency and stability compared to unmodified small interfering RNA. , 2005, Journal of medicinal chemistry.

[6]  D. Gorenstein,et al.  The effects of thiophosphate substitutions on native siRNA gene silencing. , 2005, Biochemical and biophysical research communications.

[7]  K. Ui-Tei,et al.  Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect , 2008, Nucleic acids research.

[8]  M. Amarzguioui,et al.  Similar behaviour of single-strand and double-strand siRNAs suggests they act through a common RNAi pathway. , 2003, Nucleic acids research.

[9]  S. Akira,et al.  Sequence-specific potent induction of IFN-α by short interfering RNA in plasmacytoid dendritic cells through TLR7 , 2005, Nature Medicine.

[10]  A. Lee,et al.  Design of noninflammatory synthetic siRNA mediating potent gene silencing in vivo. , 2006, Molecular therapy : the journal of the American Society of Gene Therapy.

[11]  Wei Ge,et al.  Synthetic shRNAs as potent RNAi triggers , 2005, Nature Biotechnology.

[12]  T. Tuschl,et al.  Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells , 2001, Nature.

[13]  A. Khvorova,et al.  Potent and systematic RNAi mediated silencing with single oligonucleotide compounds. , 2011, RNA.

[14]  S. Crooke,et al.  Binding and Cleavage Specificities of Human Argonaute2 , 2009, The Journal of Biological Chemistry.

[15]  Anastasia Khvorova,et al.  Off-target effects by siRNA can induce toxic phenotype. , 2006, RNA.

[16]  T. Aboul-Fadl Antisense oligonucleotides: the state of the art. , 2005, Current medicinal chemistry.

[17]  Sangdun Choi,et al.  Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy , 2005, Nature Biotechnology.

[18]  K. Alexander,et al.  High potency silencing by single-stranded boranophosphate siRNA , 2006, Nucleic acids research.

[19]  B. Williams,et al.  TLR7 Is Involved in Sequence-Specific Sensing of Single-Stranded RNAs in Human Macrophages1 , 2008, The Journal of Immunology.

[20]  A. Willingham,et al.  Analysis of acyclic nucleoside modifications in siRNAs finds sensitivity at position 1 that is restored by 5′-terminal phosphorylation both in vitro and in vivo , 2009, Nucleic acids research.

[21]  J. Kjems,et al.  Naked siLNA-mediated gene silencing of lung bronchoepithelium EGFP expression after intravenous administration. , 2009, Oligonucleotides.

[22]  K. Ui-Tei,et al.  Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. , 2004, Nucleic acids research.

[23]  P. Herdewijn,et al.  Biological effects of hexitol and altritol-modified siRNAs targeting B-Raf. , 2009, European journal of pharmacology.

[24]  M. Zavolan,et al.  Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. , 2007, RNA.

[25]  T. Tuschl,et al.  Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. , 2004, Molecular cell.

[26]  Mark E. Davis,et al.  Lack of interferon response in animals to naked siRNAs , 2004, Nature Biotechnology.

[27]  A. Krieg,et al.  Problems in interpretation of data derived from in vitro and in vivo use of antisense oligodeoxynucleotides. , 1994, Antisense research and development.

[28]  D. Weissman,et al.  Small Interfering RNAs Mediate Sequence-Independent Gene Suppression and Induce Immune Activation by Signaling through Toll-Like Receptor 31 , 2004, The Journal of Immunology.

[29]  J. Kjems,et al.  A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity , 2009, Nucleic acids research.

[30]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[31]  N. Sonenberg,et al.  Synergistic effects between analogs of DNA and RNA improve the potency of siRNA-mediated gene silencing , 2010, Nucleic acids research.

[32]  Keith Bowman,et al.  Potent and persistent in vivo anti-HBV activity of chemically modified siRNAs , 2005, Nature Biotechnology.

[33]  M. Miyagishi,et al.  Effect of asymmetric terminal structures of short RNA duplexes on the RNA interference activity and strand selection , 2008, Nucleic acids research.

[34]  N. Minakawa,et al.  Study of Modification Pattern–RNAi Activity Relationships by Using siRNAs Modified with 4′‐Thioribonucleosides , 2007, Chembiochem : a European journal of chemical biology.

[35]  Tariq M Rana,et al.  Target accessibility dictates the potency of human RISC , 2005, Nature Structural &Molecular Biology.

[36]  Maria Grahn,et al.  Analysis of siRNA specificity on targets with double-nucleotide mismatches , 2008, Nucleic acids research.

[37]  Houping Ni,et al.  Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA. , 2005, Immunity.

[38]  R. Griffey,et al.  Improving RNA interference in mammalian cells by 4'-thio-modified small interfering RNA (siRNA): effect on siRNA activity and nuclease stability when used in combination with 2'-O-alkyl modifications. , 2006, Journal of medicinal chemistry.

[39]  J. Kjems,et al.  The effect of chemical modification and nanoparticle formulation on stability and biodistribution of siRNA in mice. , 2009, Molecular therapy : the journal of the American Society of Gene Therapy.

[40]  David P. Bartel,et al.  Passenger-Strand Cleavage Facilitates Assembly of siRNA into Ago2-Containing RNAi Enzyme Complexes , 2005, Cell.

[41]  A. Klippel,et al.  Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells. , 2003, Nucleic acids research.

[42]  S. Jayasena,et al.  Functional siRNAs and miRNAs Exhibit Strand Bias , 2003, Cell.

[43]  B. Baker,et al.  Small interfering RNAs containing full 2'-O-methylribonucleotide-modified sense strands display Argonaute2/eIF2C2-dependent activity. , 2006, RNA.

[44]  M. Behlke,et al.  Increased potency and longevity of gene silencing using validated Dicer substrates. , 2008, Journal of biomolecular techniques : JBT.

[45]  A. Moreira,et al.  Degradation of hammerhead ribozymes by human ribonucleases , 1998, Molecular and General Genetics MGG.

[46]  D. Weissman,et al.  Exogenous siRNA Mediates Sequence-Independent Gene Suppression by Signaling through Toll-Like Receptor 3 , 2004, Cells Tissues Organs.

[47]  V. Vlassov,et al.  Selective protection of nuclease-sensitive sites in siRNA prolongs silencing effect. , 2009, Oligonucleotides.

[48]  P. Bevilacqua,et al.  Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure‐specific manner , 2008, RNA.

[49]  Shizuo Akira,et al.  Innate Antiviral Responses by Means of TLR7-Mediated Recognition of Single-Stranded RNA , 2004, Science.

[50]  Stefan L Ameres,et al.  The impact of target site accessibility on the design of effective siRNAs , 2008, Nature Biotechnology.

[51]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[52]  K. Alexander,et al.  RNA interference using boranophosphate siRNAs: structure-activity relationships. , 2004, Nucleic acids research.

[53]  J. Wengel,et al.  NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS, 20(4–7), 389–396 (2001) LNA (LOCKED NUCLEIC ACID) AND THE DIASTEREOISOMERIC α-L-LNA: CONFORMATIONAL TUNING AND HIGH-AFFINITY RECOGNITION OF DNA/RNA TARGETS , 2003 .

[54]  M. Caruthers,et al.  Synthesis and Biological Activity of Phosphonocarboxylate DNA , 2007, Nucleosides, nucleotides & nucleic acids.

[55]  Gunther Hartmann,et al.  5'-Triphosphate RNA Is the Ligand for RIG-I , 2006, Science.

[56]  D. Sørensen,et al.  Cationic liposome-mediated delivery of siRNAs in adult mice. , 2003, Biochemical and biophysical research communications.

[57]  M. Maszewska,et al.  Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA. , 2007, RNA.

[58]  Simon W. Jones,et al.  MALDI-TOF mass spectral analysis of siRNA degradation in serum confirms an RNAse A-like activity. , 2007, Molecular bioSystems.

[59]  Matthias John,et al.  Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs , 2004, Nature.

[60]  Henning Urlaub,et al.  Single-Stranded Antisense siRNAs Guide Target RNA Cleavage in RNAi , 2002, Cell.

[61]  Xiaoan Ruan,et al.  siRNA-mediated off-target gene silencing triggered by a 7 nt complementation , 2005, Nucleic acids research.

[62]  M. Poidinger,et al.  Sequence determinants of innate immune activation by short interfering RNAs , 2009, BMC Immunology.

[63]  A. Caudy,et al.  Argonaute2, a Link Between Genetic and Biochemical Analyses of RNAi , 2001, Science.

[64]  J. Wengel,et al.  UNA (unlocked nucleic acid): a flexible RNA mimic that allows engineering of nucleic acid duplex stability. , 2009, Bioorganic & medicinal chemistry.

[65]  Jirí Vanícek,et al.  Efficient use of accessibility in microRNA target prediction , 2010, Nucleic Acids Res..

[66]  S. Sorrentino Human extracellular ribonucleases: multiplicity, molecular diversity and catalytic properties of the major RNase types , 1998, Cellular and Molecular Life Sciences CMLS.

[67]  Thomas Tuschl,et al.  RISC is a 5' phosphomonoester-producing RNA endonuclease. , 2004, Genes & development.

[68]  Michael Petersen,et al.  LNA: a versatile tool for therapeutics and genomics. , 2003, Trends in biotechnology.

[69]  R. Griffey,et al.  Positional effect of chemical modifications on short interference RNA activity in mammalian cells. , 2005, Journal of medicinal chemistry.

[70]  Thomas Tuschl,et al.  Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. , 2003, Antisense & nucleic acid drug development.

[71]  Frank Baas,et al.  Evaluation of locked nucleic acid–modified small interfering RNA in vitro and in vivo , 2007, Molecular Cancer Therapeutics.

[72]  J. Kjems,et al.  A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects , 2010, Nucleic acids research.

[73]  David R Corey,et al.  RNA interference in mammalian cells by chemically-modified RNA. , 2003, Biochemistry.

[74]  J. Lieberman,et al.  Sustained Small Interfering RNA-Mediated HumanImmunodeficiency Virus Type 1 Inhibition in PrimaryMacrophages , 2003, Journal of Virology.

[75]  C. Burrows,et al.  Chemical modification of siRNA bases to probe and enhance RNA interference. , 2011, The Journal of organic chemistry.

[76]  Anastasia Khvorova,et al.  3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets , 2006, Nature Methods.

[77]  G. Sczakiel,et al.  Local RNA target structure influences siRNA efficacy: a systematic global analysis. , 2005, Journal of molecular biology.

[78]  T. Tuschl,et al.  Structure of the guide-strand-containing argonaute silencing complex , 2008, Nature.

[79]  Fran Lewitter,et al.  siRNA Selection Server: an automated siRNA oligonucleotide prediction server , 2004, Nucleic Acids Res..

[80]  M. Sioud Single‐stranded small interfering RNA are more immunostimulatory than their double‐stranded counterparts: A central role for 2′‐hydroxyl uridines in immune responses , 2006, European journal of immunology.

[81]  T. Du,et al.  Asymmetry in the Assembly of the RNAi Enzyme Complex , 2003, Cell.

[82]  Anton P. McCaffrey,et al.  In vivo activity of nuclease-resistant siRNAs. , 2004, RNA.

[83]  S. Kauppinen,et al.  LNA-mediated microRNA silencing in non-human primates , 2008, Nature.

[84]  Nicholas S M Putz,et al.  Increased siRNA duplex stability correlates with reduced off-target and elevated on-target effects. , 2011, RNA: A publication of the RNA Society.

[85]  I. Ladunga More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature , 2006, Nucleic acids research.

[86]  H. Hohjoh,et al.  Enhancement of RNAi activity by improved siRNA duplexes , 2004, FEBS letters.

[87]  P. D. Cook,et al.  Evaluation of 2'-modified oligonucleotides containing 2'-deoxy gaps as antisense inhibitors of gene expression. , 1993, The Journal of biological chemistry.

[88]  P. Zamore,et al.  ATP Requirements and Small Interfering RNA Structure in the RNA Interference Pathway , 2001, Cell.

[89]  K. Taira,et al.  Effects on RNA interference in gene expression (RNAi) in cultured mammalian cells of mismatches and the introduction of chemical modifications at the 3'-ends of siRNAs. , 2002, Antisense & nucleic acid drug development.

[90]  D. Patel,et al.  Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain , 2004, Nature.

[91]  T. Tuschl,et al.  RNA interference is mediated by 21- and 22-nucleotide RNAs. , 2001, Genes & development.

[92]  A. Judge,et al.  Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA , 2005, Nature Biotechnology.

[93]  P. Herdewijn,et al.  Structural characterization and biological evaluation of small interfering RNAs containing cyclohexenyl nucleosides. , 2007, Journal of the American Chemical Society.

[94]  Volker A Erdmann,et al.  Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions. , 2005, Journal of molecular biology.

[95]  D. Golenbock,et al.  Alternating 2'-O-ribose methylation is a universal approach for generating non-stimulatory siRNA by acting as TLR7 antagonist. , 2010, Immunobiology.

[96]  T. Hökfelt,et al.  Potent and nontoxic antisense oligonucleotides containing locked nucleic acids. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[97]  G. Hutvagner,et al.  A microRNA in a Multiple-Turnover RNAi Enzyme Complex , 2002, Science.

[98]  J. Castle,et al.  Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs , 2005, Nature.

[99]  M. Sioud,et al.  Modulation of dendritic cell maturation and function with mono‐ and bifunctional small interfering RNAs targeting indoleamine 2,3‐dioxygenase , 2009, Immunology.

[100]  A. Reynolds,et al.  Rational siRNA design for RNA interference , 2004, Nature Biotechnology.

[101]  A. Dallas,et al.  Minimal-length short hairpin RNAs: the relationship of structure and RNAi activity. , 2010, RNA.

[102]  Hideyoshi Harashima,et al.  RNA interference induced by siRNAs modified with 4′‐thioribonucleosides in cultured mammalian cells , 2005, FEBS letters.

[103]  Han-Oh Park,et al.  Chemical modification of siRNAs to improve serum stability without loss of efficacy. , 2006, Biochemical and biophysical research communications.

[104]  F. Baas,et al.  Utilization of unlocked nucleic acid (UNA) to enhance siRNA performance in vitro and in vivo. , 2010, Molecular bioSystems.

[105]  T. Tuschl,et al.  Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate , 2001, The EMBO journal.

[106]  H. Schluesener,et al.  siRNA binding proteins of microglial cells: PKR is an unanticipated ligand , 2006, Journal of cellular biochemistry.

[107]  S. D. De Smedt,et al.  In situ analysis of single-stranded and duplex siRNA integrity in living cells. , 2006, Biochemistry.

[108]  A. Judge,et al.  2'-O-methyl-modified RNAs act as TLR7 antagonists. , 2007, Molecular therapy : the journal of the American Society of Gene Therapy.

[109]  Justine R. Smith,et al.  Sequence- and target-independent angiogenesis suppression by siRNA via TLR3 , 2008, Nature.

[110]  Mark E. Davis,et al.  Effect of siRNA nuclease stability on the in vitro and in vivo kinetics of siRNA‐mediated gene silencing , 2007, Biotechnology and bioengineering.

[111]  J. Kjems,et al.  Synthesis of 2'-O-modified adenosine building blocks and application for RNA interference. , 2008, Bioorganic & medicinal chemistry.

[112]  S. Kawakami,et al.  Strategies for In Vivo Delivery of siRNAs , 2010, BioDrugs.

[113]  Mandi J. Lopez,et al.  Fully 2′‐Deoxy‐2′‐Fluoro Substituted Nucleic Acids Induce RNA Interference in Mammalian Cell Culture , 2007, Chemical biology & drug design.

[114]  T. Holen Mechanisms of RNAi: mRNA cleavage fragments may indicate stalled RISC , 2005, Journal of RNAi and gene silencing : an international journal of RNA and gene targeting research.

[115]  E. Hovig,et al.  Gene expression analysis in blood cells in response to unmodified and 2'-modified siRNAs reveals TLR-dependent and independent effects. , 2007, Journal of molecular biology.

[116]  T. Rana,et al.  Potent RNAi by short RNA triggers. , 2008, RNA.

[117]  W. Li,et al.  Genetic studies of diseases , 2007, Cellular and Molecular Life Sciences.

[118]  Anastasia Khvorova,et al.  Induction of the interferon response by siRNA is cell type- and duplex length-dependent. , 2006, RNA.

[119]  T. Rana,et al.  siRNA function in RNAi: a chemical modification analysis. , 2003, RNA.

[120]  M. Behlke,et al.  Effects of chemical modification on the potency, serum stability, and immunostimulatory properties of short shRNAs. , 2010, RNA.

[121]  R. Flavell,et al.  Recognition of double-stranded RNA and activation of NF-κB by Toll-like receptor 3 , 2001, Nature.

[122]  B. Polisky,et al.  Improved specificity of gene silencing by siRNAs containing unlocked nucleobase analogs , 2010, Nucleic acids research.

[123]  A. Caudy,et al.  Role for a bidentate ribonuclease in the initiation step of RNA interference , 2001 .

[124]  Yoshihiro Ito,et al.  Dumbbell-shaped nanocircular RNAs for RNA interference. , 2007, Journal of the American Chemical Society.

[125]  S. Dowdy,et al.  The road to therapeutic RNA interference (RNAi): Tackling the 800 pound siRNA delivery gorilla. , 2009, Discovery medicine.

[126]  M. Caruthers,et al.  Biochemical properties of phosphonoacetate and thiophosphonoacetate oligodeoxyribonucleotides. , 2003, Nucleic acids research.

[127]  M. Damha,et al.  Improvements in siRNA properties mediated by 2′-deoxy-2′-fluoro-β-d-arabinonucleic acid (FANA) , 2006, Nucleic acids research.

[128]  Chi Yu Chan,et al.  Effect of target secondary structure on RNAi efficiency. , 2007, RNA.

[129]  M. Amarzguioui,et al.  Tolerance for mutations and chemical modifications in a siRNA. , 2003, Nucleic acids research.

[130]  V. Vlassov,et al.  2'-O-methyl-modified anti-MDR1 fork-siRNA duplexes exhibiting high nuclease resistance and prolonged silencing activity. , 2010, Oligonucleotides.

[131]  J. Bourke,et al.  Exon skipping and dystrophin restoration in patients with Duchenne muscular dystrophy after systemic phosphorodiamidate morpholino oligomer treatment: an open-label, phase 2, dose-escalation study , 2011, The Lancet.

[132]  L. Lim,et al.  Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing. , 2006, RNA.

[133]  Dieter Huesken,et al.  Design of a genome-wide siRNA library using an artificial neural network , 2005, Nature Biotechnology.

[134]  J. Pelletier,et al.  2'-Fluoro-4'-thioarabino-modified oligonucleotides: conformational switches linked to siRNA activity. , 2007, Nucleic acids research.

[135]  N. Dean,et al.  Competition for RISC binding predicts in vitro potency of siRNA , 2006, Nucleic acids research.

[136]  S. Akira,et al.  Species-Specific Recognition of Single-Stranded RNA via Toll-like Receptor 7 and 8 , 2004, Science.

[137]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[138]  V. Erdmann,et al.  Comparison of different antisense strategies in mammalian cells using locked nucleic acids, 2'-O-methyl RNA, phosphorothioates and small interfering RNA. , 2003, Nucleic acids research.

[139]  J. Kjems,et al.  Improved silencing properties using small internally segmented interfering RNAs , 2007, Nucleic acids research.

[140]  C. Wahlestedt,et al.  Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality , 2005, Nucleic acids research.

[141]  Bernd Jagla,et al.  Sequence characteristics of functional siRNAs. , 2005, RNA.

[142]  Aleksey Y. Ogurtsov,et al.  Computational models with thermodynamic and composition features improve siRNA design , 2006, BMC Bioinformatics.

[143]  Stefan L Ameres,et al.  Cleavage of the siRNA passenger strand during RISC assembly in human cells , 2006, EMBO reports.

[144]  Robert H. Silverman,et al.  Activation of the interferon system by short-interfering RNAs , 2003, Nature Cell Biology.

[145]  P. Herdewijn,et al.  Inhibition of MDR1 expression with altritol-modified siRNAs , 2007, Nucleic acids research.

[146]  W. Pathmasiri,et al.  Five- and six-membered conformationally locked 2',4'-carbocyclic ribo-thymidines: synthesis, structure, and biochemical studies. , 2007, Journal of the American Chemical Society.

[147]  Claes Wahlestedt,et al.  A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites , 2005, Nucleic acids research.

[148]  N. Seidah,et al.  A Locked Nucleic Acid Antisense Oligonucleotide (LNA) Silences PCSK9 and Enhances LDLR Expression In Vitro and In Vivo , 2010, PloS one.

[149]  Georg Sczakiel,et al.  The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides. , 2003, Nucleic acids research.

[150]  Chaoyang Zhang,et al.  Comparing 2-nt 3' overhangs against blunt-ended siRNAs: a systems biology based study , 2009, BMC Genomics.

[151]  Paul A. Serbinowski,et al.  A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells , 2006, Nature Biotechnology.

[152]  B. Li,et al.  Expression profiling reveals off-target gene regulation by RNAi , 2003, Nature Biotechnology.

[153]  M. Mathews,et al.  Interactions between double-stranded RNA regulators and the protein kinase DAI , 1992, Molecular and cellular biology.

[154]  J. Pober,et al.  Knockdown of TNFR1 by the sense strand of an ICAM-1 siRNA: dissection of an off-target effect , 2007, Nucleic acids research.

[155]  N. Walter,et al.  siRNA-Like Double-Stranded RNAs Are Specifically Protected Against Degradation in Human Cell Extract , 2011, PloS one.

[156]  M. Stephenson,et al.  Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[157]  K. Tokunaga,et al.  Influence of assembly of siRNA elements into RNA-induced silencing complex by fork-siRNA duplex carrying nucleotide mismatches at the 3'- or 5'-end of the sense-stranded siRNA element. , 2005, Biochemical and biophysical research communications.

[158]  Landon R. Whitby,et al.  Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification , 2006, Nucleic acids research.

[159]  John J Rossi,et al.  RNAi and small interfering RNAs in human disease therapeutic applications. , 2010, Trends in biotechnology.

[160]  S. Akira,et al.  Nucleic acid agonists for Toll‐like receptor 7 are defined by the presence of uridine ribonucleotides , 2006, European journal of immunology.

[161]  T. P. Prakash An Overview of Sugar‐Modified Oligonucleotides for Antisense Therapeutics , 2011, Chemistry & biodiversity.

[162]  J. Chattopadhyaya,et al.  Antisense oligonuclotides with oxetane-constrained cytidine enhance heteroduplex stability, and elicit satisfactory RNase H response as well as showing improved resistance to both exo and endonucleases. , 2003, Organic & biomolecular chemistry.

[163]  H. A. Rogoff,et al.  Asymmetric RNA duplexes mediate RNA interference in mammalian cells , 2008, Nature Biotechnology.

[164]  M. Behlke Chemical modification of siRNAs for in vivo use. , 2008, Oligonucleotides.