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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.

DNP

DNP DNP

DNP is a labelling molecule detectable by an anti-DNP antibody. DNP may be attached to the 5' end of the oligonucleotide. The dinitrophenyl molecule is separated from the 5' end of the oligonucleotide by a fifteen carbon spacer.

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dU

dU dU

Deoxyuridine is usually introduced to the oligonucleotide DNA instead of deoxythimine. May be attached anywhere within the oligonucleotide sequence.

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Dy547

Dy547 Dy547

May be attached to the 5' end of the oligonucleotide.

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Dy647

Dy647 Dy647

May be attached to the 5' end of the oligonucleotide. Oligonucleotide purification is a necessity.

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Eclipse

Eclipse Eclipse

Quencher suitable for fluorophores having an emission wavelength range from 480 to 580 nm. Eclipse may be attached to the 5'end or the 3'end of the oligonucleotide.

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Fluorescein

Fluorescein Fluorescein

It is a mixture of 5- and 6-carboxyfluorescein isomers. Fluorescein may be attached anywhere within the oligonucleotide sequence.

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Fluorescein-dT

Fluorescein-dT Fluorescein-dT

Fluorescein dT is attached by a six carbon spacer at position 5 of the thymine circle. Fluorescein dT may be attached anywhere within the oligonucleotide sequence.

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Phosphate

Phosphate Phosphate

It can be linked to an oligonucleotide at the 5 'end and the 3' end. The 5 'end is used for ligation. The 3 'end serves as a 3' polymerase extension blocker.

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Phosphorothioates

Phosphorothioates Phosphorothioates

Phosphorothioates contain the exchange of one oxygen in the phosphate bond with sulfur. By exchanging oxygen for sulfur, the resistance of the oligonucleotide to nucleases increases.

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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.

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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.

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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.

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