Home OLIGO & PROBES modified oligonucleotides

modified oligonucleotides

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.

Position of modification

Tiles List

2′-DeoxyNebularine

A universal base substituting position N in the oligonucleotide chain. 2'-DeoxyNebularine may be attached anywhere within the oligonucleotide sequence except for the 3' end.

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.

3-Deaza-dA

It is used to study oligonucleotide activity changes following alteration of the main structural component. 3-Deaza-dA may be attached anywhere within the oligonucleotide sequence except for the 3' end.

5-(1-Propynyl)-dC (pdC)

It is used to increase duplex stability and melting temperature while preserving specificity of hybridization. 5-(1-Propynyl)-dC may be attached anywhere within the oligonucleotide sequence except for the 3' end.

5-(1-Propynyl)-dU (pdU)

It is used to increase duplex stability and melting temperature while preserving specificity of hybridization. 5-(1-Propynyl)-dU may be attached anywhere within the oligonucleotide sequence except for the 3' end.

5-Br-dC

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-Br-dU

5-F-dU

May be attached anywhere within the oligonucleotide sequence except for the 3' end. It is used for crystallographic studies of oligonucleotide structures. 5-F-dU is photolabile, the feature which is utilized in cross-linking studies investigating protein-DNA complex structures.

5-I-dC

May be attached anywhere within the oligonucleotide sequence except for the 3' end. It is used for crystallographic studies of oligonucleotide structures. 5-I-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.

Position of modification