Functional Groups (for RNA)

A primary amino group can be used to attach a variety of modifiers (such as fluorescent dyes) to an oligonucleotide or used to attach an oligonucleotide to a solid surface. Amino modifiers can be positioned at the 5’-end with either a standard (C6) or longer (C12) spacer arm. Amino modifications can be positioned at the 3’-end. Internal amino modifications can be introduced using an amino-dT base.

Phosphate

5’ Phosphorylation is needed if an oligo is used as a substrate for DNA ligase. 3’ Phosphorylation will inhibit degradation by some 3’-exonucleases and can be used to block extension by DNA polymerases.

Phosphorothiate (PTO)

The phosphorothioate (PTO) bond substitutes a sulfur atom for a non-bridging oxygen in the phosphate backbone of an oligo. This modification renders the internucleotide linkage resistant to nuclease degradation. Phosphorothioate bonds can be introduced between the last 3-5 nucleotides at the 5'- or 3'-end of the oligo to inhibit exonuclease degradation. Including phosphorothioate bonds throughout the entire oligo will help reduce attack by endonucleases as well.