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SmartBaseTM siRNA Modifications

SmartBaseTM siRNA Pathway Interactions

SmartBaseTMmodifications go beyond the traditional use of RNA bases for constructing synthetic siRNAs to specifically increase duplex stability, nuclease resistance and cell permeation. SmartBaseTM modifications can be incorporated based on the following observations

1. 2'- OH is not required for siRNA to enter the RNAi pathway.
2. The major groove of the A-form helix is required for RNAi.
3. Guide strand 5' end (Antisense) has a seed region of 2-8 bases that should be A-U rich. Modified siRNAs that stabilize A-U base-pair interactions can induce RNAi.
4. Modified siRNAs enter into the RNAi pathway in vitro.
5. Phosphorothioate increases stability but with slight decreased or no effect on silencing.
6. Add 3'-thiol for conjugation to cell penetrating peptides (CPPs).

SmartBaseTMsiRNA Recommended Modifications

1. Alternating 2'-F bases and 2'OMe bases in siRNA enhances duplex stability and are more resistant to RNase degradation.
2. Use a few 2'OMe bases in the seed region of the guide strand to decrease the Tm below 21.5 of this region. 2'O methyl base hybridization with RNA has a lower TM. (5' end of guide or antisense strand has a seed region of 2-8 bases that should be A-U rich). Modified siRNAs that stabilize A-U base-pair interactions can induce RNAi.
3. Phosphorothioate linkages confer oligonucleotides resistance to nuclease degradation.
4. Incorporate 2'-F bases, 5-me dC or 2-amino dA preferentially at the 5' end of the sense strand to block incorporation of the sense strand in to the RISC.
5. 2'F U and C substituted siRNA are more resistant to RNase degradation.
6. 3' Cholesterol modification helps in cellular uptake. Alternates are PEG and long chain spacers.

effective sirna design
Effective siRNA design features based on sequence requirements and suggested modified bases to impart specific desired characteristics.

Increased Duplex Stability and Manipulation of Duplex Stability

Specific and stable hybridization of the oligo to its cognate sequence is the desired outcome of a successful experimental protocol. The melting temperature of the oligo dictates the strength of the affinity and thus the stability of the hybridization. Manipulation of the oligo sequence to increase the duplex stability or in some cases to decrease the duplex stability in certain loop structure will lead to oligos with increased affinity for the target molecule. There are many nucleic acid modifiers that increase duplex stability, examples are 5-methyl dC, 2-amino dA, locked nucleic acids etc.

A summary is presented in the table below. Gene Link does not presently offer LNA substituted oligo synthesis due to licensing issues and as such LNA base modifications are not included in this guide.

Increased Nuclease Resistance

As with most natural molecules synthetic DNA and RNA oligos are prone to degradation under normal conditions, specifically once introduced in body fluids. Ubiquitous nucleases as well as chemical instability lead to fast degradation with a finite half life. Nucleic acids are degraded rapidly once introduced in bodily fluids, RNA are more susceptible to degradation under normal laboratory conditions particularly due to RNase contamination. Special precautions must be taken to prevent RNA degradation. Nuclease resistant modifications can be introduced chemically in oligonucleotides that still retain its molecular structure and its shape based molecular interaction. These modifications are almost indispensable and have been used intensely in antisense applications. Also nucleic acids with mirror image chemistry have been developed that evade natural nucleases completely. Examples are converting the normal phosphodiester linkages to phosphorothioate or phosphorodithioate linkages, 2'O methyl, propyne bases etc.

Antisense oligonucleotides refer to short, synthetic oligonucleotide that are complementary in sequence and upon specific hybridization to its cognate gene product induces inhibition of gene expression. Oligonucleotides, as short as 15 mer have the required specificity to inhibit gene expression of a particular gene by annealing to the cellular mRNA (1,2). The mechanism of gene expression inhibition is based on two properties; the first is the physical blocking of the translation process by the presence of the short double stranded region, secondly the presence of the RNA-DNA duplex is susceptible to cellular RNase H activity. RNase H cleaves the RNA-DNA duplex region of the mRNA thus preventing the faithful translation of the mRNA (3).

The stability of the RNA-DNA duplex in terms of hybridization and half-life is crucial to successful gene inhibition. Vigorous research activity in the area of nucleic acid chemistry has been devoted in developing novel base analogs that are resistant to degradation and that possess strong hybridization properties. This product profile aims at listing some analogs that meet the above criteria and are amenable to be synthesized by currently available standard DNA synthesis chemistry. This includes the classical phosphorothioate linkages (4), propyne analogs (5) and 2'Fluoro bases.

RNA interference studies have shown the effectiveness of short interfering RNA (siRNA) in gene silencing. siRNA technology is now extensively recognized as a powerful tool for the specific suppression of gene expression and is presently being used by researchers in a wide range of disciplines for the assessment of gene function. These are generally 21mer double stranded RNA. Active research to render the siRNA more stable to degradation and to increase the duplex stability has led to the use of modified bases. 2'O methyl and/or 2'Fluoro bases are an attractive substitute together with phosphorothioate linkages to impart greater duplex stability and resistance to nuclease degradation

Gene Link offers an extensive array of modifications to accomplish duplex stability and nuclease resistance to synthetic oligos. We have the ability to synthesize complex combinations of modifications, chimeric oligos and fluorescent probes. In addition to the synthesis of these modified oligos, we routinely assist customers in the design of the oligos that are particularly suited to their application.

Duplex Stabilization

Using these base substitutions, duplex stability and therefore melting temperatures are raised by the approximate amounts shown below.

Modifications Increasing Duplex Stability and Nuclease Resistance
Modification Duplex Stability [Tm Increase] Nuclease Resistance
Phosphorothioate Slightly decreased Increased
2'-O Methyl Increased Increased
2'-Fluoro Increased [1-2o per substitution] Increased
2-Amino-dA Increased [3.0o per substitution] No effect
5-Methyl-dC Increased [1.3o per substitution] No effect
C-5 propynyl-C Increased [2.8o per substitution] Increased
C-5 propynyl-U Increased [1.7o per substitution] Increased

Careful selection of modifications and verifying the performance of modified siRNA is required; the guidelines presented are based on documented physical and chemical properties of the modifications. Design rules may have to be established empirically for very specific or novel assay settings, but following these recommendations will provide a good start.

smart sirna modifications design

References
1. Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., and Mello, C.C. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806-811. 2. Elbashir, S.M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. 2001. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494-498. 3. Reynolds, A., Leake, D., Boese, Q., Scaringe, S., Marshall, W. & Khvorova, A. 2004. Rational siRNA design for RNA interference. Nat. Biotechnol. 22:326330. 4. Amarzguioui, M., Lundberg, P., Cantin, E., Hagstrom, J., Behlke, M. & Rossi, J. 2006. Rational design and in vitro and in vivo delivery of Dicer substrate siRNA. Nature Protocols. 1:508-517. 5. Naito. Y., Yoshimura, J., Morishita, S. and Ui-Tei, K. 2009. siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioinformatics 10:392. 6. Wang, H., Ghosh, A., Baigude, H., Yang, C-S., Qiu, L., Xia, X., Zhou, H., Rana, T.M. and Xu, Z. 2008. Therapeutic Gene Silencing Delivered by a Chemically Modified Small Interfering RNA against Mutant SOD1 Slows Amyotrophic Lateral Sclerosis Progression. J. Biol. Chem. 283: 15845-5852. 7. Jackson, A. L., Burchard, J., Schelter, J., Chau, B.N., Cleary, M., Lim, L. and Linsey, P.S. (2006) Widespread siRNA off-target transcript silencing mediated by seed region sequence complementarity.RNA 12:11791187. 8. Bramsen, J.B., Laursen, M.B., Nielsen, A.F., et al. 2009. A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity. Nucleic Acids Res. 37:28672881. 9. Vaish, N., Chen, F., Seth, S. et al. 2011. Improved specificity of gene silencing by siRNAs containing unlocked nucleobase analogs. Nucleic Acids Res. 39:18231832.

Appendix References:
1. B.S. Sproat, A.I. Lamond, B. Beijer, P. Neuner, and U. Ryder, Nucleic Acids Res., 1989, 17, 3373. 2. T. Imanishi, and S. Obika, Chem Commun (Camb), 2002, 1653-1659. 3. S. Obika, Y. Hari, M. Sekiguchi, and T. Imanishi, Angew Chem Int Ed, 2001, 40, 2079-2081. 4. A.A. Koshkin, et al., Tetrahedron, 1998, 54, 3607-3630. 5. M. Petersen, and J. Wengel, Trends Biotechnol, 2003, 21, 74-81. 6. A. Sabahi, J. Guidry, G.B. Inamati, M. Manoharan, and P. Wittung-Stafshede, Nucleic Acids Res., 2001, 29, 2163-2170. 7. T. Ono, M. Scalf, and L.M. Smith, Nucleic Acids Res., 1997, 25, 4581-4588. *RNAi and siRNA
RNA interference (RNAi) is a specific and sequence dependent targeted gene silencing activity. RNAi acts by post transcriptional degradation of mRNA by small interfering RNAs (siRNA's) of the same sequence. The silencing approaches 100% and has to be empirically determined and optimized. Not every siRNA can effectively down regulate a gene. The process of RNA interference varies by individual siRNA while some do not exhibit any interference at all.

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