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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.

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.

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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.

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N4-Et-dC

N4-Et-dC N4-Et-dC

It serves as a substitute for dC in GC-rich sequences in order to prevent the formation of oligonucleotide secondary structures because N4-Et-dC specifically hybridizes with natural dG. N4-Et-dC may be attached anywhere within the oligonucleotide sequence except for the 3' end.

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N6-Me-dA

N6-Me-dA N6-Me-dA

It is used to increase duplex stability. N6-Me-dA may be attached anywhere within the oligonucleotide sequence except for the 3' end.

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PC-spacer

PC-spacer PC-spacer

A PC (Photo-cleavable) Spacer may be attached either between the oligonucleotide bases or between the oligonucleotide chain and its 5' end modifying group. UV iradiation at 300 - 350 nm cleaves the oligonucleotide to the portion carrying a spacer and the oligonucleotide with a 5' end phosphate modification.

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Pyrene

Pyrene Pyrene

It serves to increase duplex stability. Pyrene raises the melting temperature by up to 10°C. Furthermore, it enables manufacturing of hybridization probes with greater affinity to complementary sequences. Pyrene may be attached to the 5' end of the oligonucleotide.

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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.

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Spacer 9

Spacer 9 Spacer 9

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

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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.

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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.

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Spacer C12

Spacer C12 Spacer C12

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

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Spermine

Spermine Spermine

It is used for manufacturing of oligospermine-oligonucleotide conjugates (Zip Nucleic Acid - ZNA Oligos). ZNA oligos are employed e.g. in multiplex PCR, PCR of AT-rich sequences, RT qPCR, miRNA detection and improving SNP discrimination. Spermine may be attached anywhere within the oligonucleotide sequence except for the 3' end.

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