HEX
Hexachlorofluorescein is commonly used in multiplex reactions together with FAM and TET. Hexachlorofluorescein may be attached to the 5' end of the oligonucleotide.
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.
Hexachlorofluorescein is commonly used in multiplex reactions together with FAM and TET. Hexachlorofluorescein may be attached to the 5' end of the oligonucleotide.
It is used for conjugations based on the click chemistry principle. Hexynyl may be attached to the 5' end of the oligonucleotide.
Adding cholesterol increases oligonucleotide lipophility. Furthermore, cholesterol improves the permeability of oligonucleotide chains through cellular membranes in antisense oligonucleotides (phosphorothioates or other derivatives). Cholesterol may be attached either to the 5' end or the 3' end of the oligonucleotide.
6-karboxy-4', 5'-dichlor-2', 7'-dimethoxyfluorescein is commonly used in multiplex reactions together with FAM. JOE may be attached to the 5' end of the oligonucleotide.
2'deoxyinosin is a "universal" base (it has the ability to bind to each of the 4 standard bases). It can be located anywhere in the oligonucleotide chain.
ROX (6-Carboxy-X-Rhodamine) is a red fluorophore. It can be linked to the 3 'end of the chain, or by using the NHS ester at 5'. In case of binding at the 5 'end, the amino linker is first attached to the oligonucleotide through which the post-synthetic binding of ROX then proceeds.
May be attached anywhere within the oligonucleotide sequence except for the 3' end. It is the longest spacer available within a single modification.
May be attached anywhere within the oligonucleotide sequence. Repeated spacer attachment is possible, forming a long hydrophobic arm. When bound to the 3' end it serves as a blocker of 3' polymerase extension.
May be attached anywhere within the oligonucleotide sequence except for the 3' end. Repeated spacer attachment is possible.
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