Categories

modified oligonucleotides

modified oligonucleotides

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.

HEX

HEX HEX

Hexachlorofluorescein is commonly used in multiplex reactions together with FAM and TET. Hexachlorofluorescein may be attached to the 5' end of the oligonucleotide.

More
Hexynyl

Hexynyl Hexynyl

It is used for conjugations based on the click chemistry principle. Hexynyl may be attached to the 5' end of the oligonucleotide.

More
Cholesterol

Cholesterol Cholesterol

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.

More
JOE

JOE JOE

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.

More
Inosin

Inosin Inosin

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.

More
ROX

ROX ROX

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.

More
Spacer 9

Spacer 9 Spacer 9

May be attached anywhere within the oligonucleotide sequence except for the 3' end.

More
Spacer 18

Spacer 18 Spacer 18

May be attached anywhere within the oligonucleotide sequence except for the 3' end. It is the longest spacer available within a single modification.

More
Spacer C3

Spacer C3 Spacer C3

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.

More
Spacer C12

Spacer C12 Spacer C12

May be attached anywhere within the oligonucleotide sequence except for the 3' end. Repeated spacer attachment is possible.

More
TET

TET TET

Tetrachlorofluorescein is commonly used for multiplex reactions with FAM and HEX. It can be linked to an oligonucleotide at the 5 'end.

More
Thiol SH

Thiol SH 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.

More