Spacer, Linker, Base & Sugar Modifications

2'-Deoxyinosine (INO) is a universal base that is less destabilising than mismatches found within a wobble or degenerated base.

2'-Deoxyinosine structure

2'-Deoxyuridine (URI) are often used as a substitute for dT.

2'-Deoxyuridine structure

5-Methyl-dC stabilises the DNA duplex due to an increase in the melting temperature during the replacement of the dC.

5-Methyl-dC structure

Amino C6-dT allows internal modifications within the oligonucleotides sequence.

Amino C6-dt structure

Biotin-dT can be used for an internal biotin modification (e.g. for hybridisation studies).

Biotin-dt structure

3'-ddC prevents extension by DNA polymerases and prevents degradation by 3'-exonucleases.

3'-ddC structure

The dSpacer is used to create a stable abasic site within an oligonucleotide.

dSpacer structure

Spacer C3 can be coupled to the 3'-end and internally of an oligonucleotide sequence. This can prevent e.g. the elongation of the oligo during a PCR without a major influence to its annealing properties. Oligos with C3 spacers are therefore ideal hybridisation probes in PCR reactions.

C3 spacers structures

The following IUB code is used to describe degenerated bases (wobbles). Wobbles are available with a defined and non defined ratio.