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modified oligonucleotides

Modified oligonucleotides – options & examples

Our modified oligonucleotides cover end modifications at the 3′ and 5′ ends as well as internal positions.
We offer base analogs, spacers, fluorophores, quenchers, backbone changes and functional groups for applications such as antisense, sequencing, duplex stabilization, structural studies or click-chemistry conjugations.
All modifications are delivered with high purity and can be combined on request (where chemistry allows).

Popular modifications & use cases

Universal/modified bases:
2′-DeoxyNebularine,
3-Deaza-dA
RNA analogs for antisense:
2′F-RNA,
2′OMe-RNA
3′ end extension blockers:
2′3′-ddC
Halogenated bases for structural/X-ray work:
5-Br-dC,
5-I-dU
Duplex T_m enhancers:
5-(1-Propynyl)-dC,
5-(1-Propynyl)-dU

Looking for labeled probes? See
RT-PCR dual-labeled probes
or browse all oligonucleotides.

Position of modification

Tiles List

CFR 610

CFR 610 is an orange-red fluorophore. It is also used as a good alternative to fluorophore Texas Red. CFR 610 may be attached only to 5´end of an oligonucleotide.

CFR 635

CFR 635 is an orange-red fluorophore. It is used as a good alternative to LC red 640. CFR 635 may be attached only to 5´end of an oligonucleotide.

Cy3

May be attached within the oligonucleotide sequence at the 5' end.

Cy3.5

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

Cy5.5

It is a deep red fluorophore. May be attached to the 5‘ end of the oligonucleotide. Oligonucleotide purification is a necessity.

Cy5

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

D-spacer

May be attached anywhere within the oligonucleotide sequence except for the 3' end. It is used to introduce a stable abasic position to the oligonucleotide chain.

dU

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

Fluorescein

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

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.

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.

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.

Position of modification