2'-O methyl cytosine C

Antisense Oligos (ODN) & siRNA Oligo Modifications

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

2'-O-Methyl bases are classified as a 2'-O-Methyl RNA monomer. 2'-O-Methyl nucleotides are most commonly used to confer nuclease resistance to an oligo designed for anti-sense, siRNA or aptamer-based research, diagnostic or therapeutic purposes, when specific 2'-OH is not required. Nuclease resistance can be further enhanced by phosphorothiolation of appropriate internucleotide linkages within the oligo.

The hydrogen bonding behavior of a 2'-O-Methyl RNA/RNA base pair is closer to that of an RNA/RNA base pair than a DNA/RNA base pair. Consequently, the presence of 2'-O-Methyl nucleotides improves duplex stability. Indeed, incorporation of a 2'-O-Methyl nucleotide into an anti-sense oligo (resulting in a 2'-O-Methyl RNA/DNA chimeric), lead to a increase in the Tm of its duplex with RNA, relative to that formed by an unmodified anti-sense DNA oligo, of 1.3^oC per 2'-O-Methyl RNA residue added (2). Moreover, from a synthesis standpoint, the coupling efficiency of 2'-O-Methyl phosphoramidites are higher than those of RNA monomers, resulting in higher yield of full-length oligos.

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

ASO's and siRNA Modifications.

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ASO's and siRNA Delivery.

The development of effective delivery systems for antisense oligonucleotides is essential for their clinical therapeutic application. The most common delivery system involves a relatively hydrophobic molecule that can cross the lipid membrane. Cholesterol TEG, alpha-Tocopherol TEG ( a natural isomer of vitamin E), stearyl and GalNAc modifications have been shown to effective for delivery of ASO's and siRNA in addition to cell penetrating peptides.

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References
1. Cotton, M.; Oberhauser, B.; Burnar, H. et al. 2'O methyl and 2'O ethyl oligoribonucleotides as inhibitors of the in vitro U7 snRNP-dependent messenger-RNA processing event. Nucleic Acids Res. (1991) , 19:2629-2635.
2. Kawasaki, A.M. et al., Uniformly modified 2'-deoxy-2'-fluoro phosphorothioate oligonucleotides as nuclease resistant antisense compounds with high affinity and specificity for RNA targets, Journal of Medicinal Chemistry (1993), 36: 831-841.
- 2'-O methyl cytosine C