BaseBlockers™ are short INA® oligonucleotides that are highly modified with Intercalating pseudo-nucleotides (IPNs). BaseBlockers™ have extremely high target affinity and specificity which makes them useful for target-specific blocking of PCR amplification.

Binary binding dynamics

BaseBlockers™are otherwise unmodified INA® oligos containing particularly many IPN molecules that provides BaseBlockers™ with an etremely high target affinity and specificity. BaseBlockers™ are furthermore modified to ensure that they do not work as potential primers.

The resulting target vs. off-target binding dynamics og BaseBlockers™ resemble a binary response even with single nucleotide variation between target and off-target sequences. This extreme sensitivity of BaseBlocksers™ to target sequence variation can be utilised to prevent binding of e.g. allel-specific primers to wild type sequences.

BaseBlockers™ are particularly useful in PCR assays for detection of low frequency mutations where selective amplification can be highly improved by including a BaseBlocker™ that specifically binds and blocks amplification of the wild type sequence. The addition of a BaseBlocker™ thereby lowers the risk of false positive results without influencing the rate of false negatives.

  • Extremely high target affinity and specifity
  • Sequence specific blocking of PCR amplification
  • Reduced false positive PCR assay results
  • Partucularily useful in low frequency SNV detection assays


Nucleotides (without IPNs)

Available Yields (nmol delivered)


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