Duplex Stability Applications

Duplex Stability Applications

For antisense and siRNA work, incorporation of modifications that enhance duplex stability may be needed to counteract the destabilizing effect of phosphorothiolation (which confers nuclease resistance on an oligo). In addition, increasing the duplex stability can augment the ability of an oligo to suppress gene expression, as a highly stable DNA-RNA duplex can effectively block translation via steric hindrance (2). Both C5-propyne base analogs and 2’-O-substituted bases (for example, 2’-OMethyl RNA bases) have been used for these purposes. For SNP detection assays, incorporation of duplex-stability-enhancing modifications into SNP detection probes lead to improvements in mis-match discrimination. 2’-fluoro RNA bases, for example, increase duplex Tm by 1.8C per modified residue (3), and thus can provide an excellent low-cost substitute for LNA bases in SNP detection assays. 5-Me-dC-modified PCR primers have been shown to prime far better than their unmodified counterparts in PCR reactions, consistently yielding more product per cycle, permitting amplification at very high annealing temperatures (as high as 72degC), and interestingly, allowing excellent priming from within palindromic sequences (4).

References

(1) Swayze, E.E., Balkrishen, B. The Medical Chemistry of Oligonucleotides. In: Antisense drug technology: principles, strategies, and applications, 2nd Ed., Crooke, S.T. (Ed), CRC Press, Boca Raton (FL), 2008, 143-182.
(2) Kurreck, J. Antisense technologies. Improvement through novel chemical modifications. Eur. J. Biochem. (2003), 270: 1628-1644.
(3) Schulz, R.G., Gryaznov, S.M. Oligo-2’-fluoro-2’-deoxynucleotide N3’P5’phosphoramidites: synthesis and properties. Nucleic Acids Res. (1996), 24: 2966-2973.
(4) Lebedev, Y.; Akopyants, N.; Azhikina, T.; Shevchenko, Y.; Potapov, V.; Stecenko, D.; Berg, D.; Sverdlov, E.. Oligonucleotides containing 2-aminoadenine and 5-methylcytosine are more effective as primers for PCR amplification than their nonmodified counterparts. Genet Anal. (1996), 13: 15-21.
(5) Saenger, W. in Principles of Nucleic Acid Structure, C.R. Cantor, Ed., Springer Advanced Texts in Chemistry, Springer-Verlag, New York, 1984.
(6) Tidd, David M. Specificity of antisense oligonucleotides. in Perspectives in Drug Discovery and Design, Vol. 4, ESCOM Science Publishers, B.V., 1996, pp. 51-60.
(7) Takagi-Sato, M., Tokuhiro, S., Kawaida, R., Koizumi, M. Fine-Tuning of ENA Gapmers as Antisense Oligonucleotides for Sequence-Specific Inhibition. Oligonucleotides (2007), 17: 291-301.