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C3 spacer

3'- spacers are often used as an alternative to 3'-phosphate as blockers; the most common is the C3 spacer. In general, a spacer is incorporated to add a distance between the oligo and a modifier. Spacers can be hydrophilic (e.g., the HEG spacer) or hydrophobic (C3 or C6 spacers).

The C3 spacer represents an effective way to block polymerase extension, when positioned at the 3’-end of an oligonucleotide (Figure 1). Additionally, it can prevent exonuclease-dependent oligo cleavage.

Figure 1. Structure of the C3 spacer at the 3'-end (R = sequence, B = base).

metabion offers the C3 spacer as modification in its DNA and RNA portfolio: