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:
Cradic KW., Wells JE., Allen L., Kruckeberg KE., Singh RJ., Grebe SK. Substitution of 3'-phosphate cap with a carbon-based blocker reduces the possibility of fluorescence resonance energy transfer probe failure in real-time PCR assays. Clin Chem. 2004 Jun;50(6):1080-2.