The most common modifications are at the end of the string – at the 3’ or 5’ end, or combined. The modifying molecule may be in the middle of the chain, the bases in the chain may be replaced by their analogs; spacers of different lengths and nature, functional groups or molecules may be inserted into the chain. Modified phosphate linkage may be in the chain in all or only in selected positions. Less frequent modifications or their combinations are recommended to be consulted first because there are many limitations for synthesis and for purification of the resulting product.
Symetric doubler It is used to introduce symmetric branching of the oligonucleotide. Symmetric doubler may be attached anywhere within the oligonucleotide sequence except for the 3' end.
TET Tetrachlorofluorescein is commonly used for multiplex reactions with FAM and HEX. It can be linked to an oligonucleotide at the 5 'end.
Thiol SH It is used as an intermediate for further oligo modifications (attachment to special surfaces, conjugation) and as a blocker of 3' polymerase extension. Thiol SH may be attached either to the 5' end or the 3' end of the oligonucleotide.
Thiol S-S It is used as an intermediate for further oligo modifications (attachment to special surfaces, conjugation). Thiol S-S may be attached to the 5' end of the oligonucleotide.
Trimethoxystilben It serves to increase duplex stability. Trimetoxystilbene raises the melting temperature by up to 10°C. Furthermore, it enables manufacturing of hybridization probes with greater affinity to complementary sequences. Trimethoxystilbene may be attached to the 5' end of the oligonucleotide.
Uaq It serves to increase duplex stability. UAG raises the melting temperature and specificity of hybridization probes. UAG may be attached to the 3' end of the oligonucleotide.
Yakima Yellow Yakima Yellow may be attached either to the 5' end or the 3' end of the oligonucleotide.
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