The most common modifications are at the end of the string – at the 3’ or 5’ end, or combined. The modifying molecule may be in the middle of the chain, the bases in the chain may be replaced by their analogs; spacers of different lengths and nature, functional groups or molecules may be inserted into the chain. Modified phosphate linkage may be in the chain in all or only in selected positions. Less frequent modifications or their combinations are recommended to be consulted first because there are many limitations for synthesis and for purification of the resulting product.
2’F-RNA 2'-F-RNA is even more stable than 2'-O-methyl-RNA. 2'-F-RNA & RNA duplexes do not activate RNase H and are more stable (with higher Tm) than RNA & 2'-O-methyl-RNA duplexes. It serves mainly for antisense applications. May be attached anywhere within the oligonucleotide sequence.
2’OMe-RNA Compared to RNA 2'-O-methyl-RNA is more chemically stable (being stable against nucleases for several days). 2'-O-methyl-RNA & RNA duplexes do not activate RNase H and are more stable (with higher Tm) than DNA & RNA duplexes. It is used mainly in antisense applications. May be attached anywhere within the oligonucleotide sequence.
2’3′-ddC It serves as a blocker of 3' polymerase extension. 2',3'-ddC may be attached to the 3' end of the oligonucleotide.
5-Br-dU May be attached anywhere within the oligonucleotide sequence except for the 3' end. It is used for crystallographic studies of oligonucleotide structures. 5-Br-dC is photolabile, the feature which is utilized in cross-linking studies investigating protein-DNA complex structures.
5-I-dU May be attached anywhere within the oligonucleotide sequence except for the 3' end. It is used for crystallographic studies of oligonucleotide structures. 5-I-dU is photolabile, the feature which is utilized in cross-linking studies investigating protein-DNA complex structures.
5-Me-dC Increases duplex stability and is suitable for antisense applications. May be attached anywhere within the oligonucleotide sequence.
6-FAM Denotes pure 6-carboxyfluorescein isomer. This is among the most used oligonucleotide fluorescent modifications and is compatible with the majority of fluorescent devices. 6-FAM may be attached either to the 5' end or the 3' end of the oligonucleotide.
7-Deaza-dA It is used to study oligonucleotide activity changes following alteration of the main structural component. 7-Deaza-dA may be attached anywhere within the oligonucleotide sequence except for the 3' end.
7-Deaza-8-aza-dG It is used to study oligonucleotide activity changes following alteration of the main structural component. 7-Deaza-8-aza-dG may be attached anywhere within the oligonucleotide sequence except for the 3' end.
8-Amino-dA May be attached anywhere within the oligonucleotide sequence except for the 3' end. 8-Amino-dA modified oligonucleotides are utilized for triplex formation, enabled by the presence of an additional amino group.
8-Amino-dG May be attached anywhere within the oligonucleotide sequence except for the 3' end. 8-Amino-dG modified oligonucleotides are utilized for triplex formation, enabled by the presence of an additional amino group.
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