Incorporation of a thiol reactive functional group at specific sites within an oligonucleotide allows for subsequent post-synthesis conjugation of the oligo with a number of different moieties such as fluorescent markers and biotin, depending on the application. Such labels need to be reactive towards the incorporated functional group: for example, thiols will react with iodoacetate and maleimide derivatives to form thioether linkages.

In general, thiol modification at the 5'-end of the oligonucleotide is achieved with C6 5'-thiol-modifier phosphoramidite (LK2125/BNS-5019) or, more commonly, the thiol-modifiers C6 S-S phosphoramidite (LK2126/BNS-5042) or the C8 version (LK2820). As with the MMT protected amino-modifiers, the trityl group on LK2125/BNS-5019 is usually retained after cleavage of the oligonucleotide to assist purification. However, because the S-trityl group is not acid labile, it must be removed by treatment with silver nitrate.

Although this procedure is commonly used, it must be very carefully carried out. Use of LK2126/BNS-5042/LK2820 offers an alternative and more robust protocol, whereby the thiol is liberated by use of tris(2-carboxyethyl)phosphine (TCEP). This disulphide product can also be used to modify the 3'-position by using the phosphoramidite as the first adduct in the oligo sequence. Incorporation of LK2126/BNS-5042/LK2820 at the 5'-end allows the possibility of DMT-ON purification prior to reduction of the disulphide bridge.