2'-O Me-5-Me-C

Antisense Oligos (ODN) & siRNA Oligo Modifications

Click here for more information on antisense modifications, design & applications.

2'-OMethyl-5-methyl cytosine (2'-OMe-5-Me-C) is an RNA monomer that pairs with G, and when substituted for C in an oligonucleotide, both increases the stability of the resulting duplex relative to the comparable unmodified form, and confers nuclease resistance at that position(1). This "double-methylated"-modified cytosine thus is an excellent choice for incorporation into anti-sense oligos, where both properties are particularly desirable. Furthermore, because anti-sense oligonucleotides containing a CpG motif are known to induce pro-inflammatory responses after in vivo administration to animals, including human, via activation of Toll-like receptor 9 (TLR9), substitution of 2'-OMe-5-Me-dC for C in these motifs can prevent or sharply reduce these undesirable immune responses (2,3).

Modifications Increasing Duplex Stability and Nuclease Resistance

Modification	Duplex Stability [Tm Increase]	Nuclease Resistance
Locked Analog Bases	Increased [2- 4C per substitution]	Increased
2-Amino-dA	Increased [3.0C per substitution]	Similar to DNA
C-5 propynyl-C	Increased [2.8C per substitution]	Increased
C-5 propynyl-U	Increased [1.7C per substitution]	Increased
2'-Fluoro	Increased [1.8C per substitution]	Increased
5-Methyl-dC	Increased [1.3C per substitution]	Similar to DNA
2'-O Methyl	Increased	Increased
Phosphorothioate	Slightly decreased	Increased
Click here for complete list of duplex stability modifications

References
1. Bundock, P.; de Both, M.T.J.; Hogers, R.C.J. 2006. Alternative nucleotides for improved targeted nucleotide exchange. Patent No. 2007073149, filed Dec 22. 2005, issued June 28, 2007. 2. Henry, S.P.; Stecker, K.; Brooks, D.; Monteith, D.; Conklin, B.; Bennett, C.F. Chemically modified oligonucleotides exhibit decreased immune stimulation in mice. J. Pharmacol. Exp. Ther. (2000), 292: 468-479.
3. Yu, D.; Wang, D.; Zhu, F.-G.; Bhagat, L.; Dai, M.; Kandimalia, E.R.; Agrawal, S. Modifications Incorporated in CpG Motifs of Oligodeoxynucleotides Lead to Antagonist Activity of Toll-like Receptors 7 and 9. J. Med. Chem. (2009), 52: 5108-5114.
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