5'-Phosphate

Oligos are synthesized with a 5'-hydroxyl group, not the phosphate. As an option, we can synthesize a 5'-phosphate group on your oligo. Oligonucleotides with an added 5’ phosphate can still be purified using the Trityl-On purification columns. Oligonucleotides require a 5'-phosphate in order to be ligated by a ligase. This phosphate can be added enzymatically using polynucleotide kinase, or it can be added chemically during oligonucleotide synthesis.

Biotin

Biotin (also known as vitamin H) is a non-aromatic heterocyclic compound with a 4-carboxybutyl tail. A variety of derivatives of biotin are available in which the biotin moiety is connected (through the 4-carboxybutyl group) to some linker molecule that can be attached directly to an oligonucleotide. The biotin moiety has a remarkable affinity towards streptavidin and related proteins. A biotin-labeled oligo can be used to link the oligo to streptavidin-protein conjugates, streptavidin affinity columns, or labeled streptavidin.

Fluorescent Labeling

The most common fluorescent compounds used to label oligonucleotides are fluorescein, and various fluorescein analogs. Fluorescein is a multi-ring aromatic compound that is strongly fluorescent. Fluorescent dye-labeled oligos are now used routinely in automated DNA sequencing with fluorescent detection. Fluorescent-labeled oligos are also useful in PCR quantification and as probes for in situ hybridization.

DeoxyInosine

This is a deoxynucleoside with the base hypoxanthine (6-hydroxypurine). DeoxyInosine can be placed at any position in an oligonucleotide, and can be used multiple times within a sequence. When used within a hybridization probe, deoxyinosine residues can form base-pairs with dA, dC, dG, or T residues on the target strand. DeoxyInosine can be used instead of mixed bases and has the advantage that the hybridization probe is not "diluted" by the non-pairing components of the mixture. Do not use deoxyinosine in applications in which this base must serve as part of a template strand (e.g., PCR primers), since DNA polymerases may fall off when encountering this residue in a template.

DeoxyUridine

This is a deoxynucleoside with the base uracil (2,4-dihydroxypyrimidine). Deoxyuridine can be incorporated at any position in an oligonucleotide, and can be used multiple times within a sequence. The uracil base within a DNA sequence behaves much like a thymine base. However, the enzyme Uracil-N-glycosylase can specifically remove uracil to create baseless sites at the deoxyuridine positions. This property can be used to generate specific strand breaks in a DNA structure.