Non Fluorescent Modifications & Their Structures

5' Amino groups are often used for coupling the oligonucleotides to solid supports. Amino groups can also be used to attach secondary modifications such as fluorescent dyes or large molecules like digoxigenin.

Structure of 5' Amino C6

Structure of 5' Amino C12

3' Amino C7 and C3 can be used to block polymerase and exonuclease activity.

3' Amino C3 structure

3' Amino C6 structure

3' Amino C7 structure

Biotinylated oligonucleotides are known for their ability to bind to streptavidin. Biotin added at the 3' end can be used to block exonuclease digestion.

5' Biotin structure

Biotin-TEG allows for an increase in binding to the streptavidin deep-binding pocket due to the fact that it has the longest linker arm from the Biotin group (e.g. used for hybridisation studies).

Biotin-TEG structure

Cholesterol is a hydrophobic molecule. Coupled at the 3’ end of an oligonucleotide cholesterol has been established as a reliable courier through membranes and facilitates uptake into cells.

3' Cholesterol structure

Digoxigenin is used primarily as a non isotopic label for oligonucleotides. Common applications include diagnostics, sequencing, and in-situ hybridisations.

Digoxigenin structure

Phosphorylation allows the oligonucleotides to be used as a substrate for DNA ligase. 3' modifications can be used to block further extension by DNA. Terminal phosphates are also useful for enabling the ligation of two individual oligonucleotides together.

Phosphate structure

It is used for the coupling of oligonucleotides to solid supports. Thiol can also be used for the attachment of fluorescent and non-fluorescent modifications.

3' Thiol C3 structure

5' Thiol C6 structure