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Blocker-oligos: PCR-Blocker and modifications for blocking the 3'-terminus of an oligonucleotide

Specific blocking of individual components in a reaction mixture can be a valuable tool for complex reaction processes.
These targeted blockages are used in PCR reactions or to prevent concatemer formation . As so-called PCR blocker oligonucleotides with a defined sequence they can inhibit the polymerase during elongation without participating as a primer itself.
More common is the use of blocking modifications in qPCR probes. As result of the modification the oligonucleotide probes lack the hydroxyl group at the 3'-end required for the extension in PCR.
Depending on different applications there are several possibilities for functionalized oligonucleotides . Below you will find a short overview with available modifications. 

3'-Spacer C3

Due to its small size a simple carbon chain does not influence other processes like hybridisation.
A good example of the preferred use of a C3 carbon spacer to block the 
3'-end of an oligonucleotide can be seen here.

3´-Spacer C3


Oligonucleotides do not bear terminal phosphate groups per se. But certainly terminal phosphate groups can be attached on request. Due to the requirement of a 3'-terminal hydroxyl group, many reactions can be blocked  by the addition of a phosphate group at the 3'-terminus of an oligonucleotide. 



Since the establishment of Sanger sequencing, dideoxy nucleotides are widely used to stop polymerisation reactions. Currently only dideoxy cytidine (ddC) can be offered for oligonucleotide synthesis; for the other nucleotides are not available yet.

dideoxy nucleotide 3´-ddC

3'-Inverted End

This modification consists of an inversely coupled nucleotide, generating an oligo with 5´-termini at both ends. 
Compared to the previous modifications, the addition of an entire nucleotide as blocking unit is more bulky. But like the phosphate group, it is a natural structure element, so that side-reactions during in vivo applications are not to be expected.

inverted end

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