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. BaseBlocker™ features and advantages include:
- Reduced false positive PCR assay results
- Extremely high target affinity and specifity
- Sequence specific blocking of PCR amplification
- Particularly useful as part of low frequency SNV detection assays
Binary Binding Dynamics
BaseBlockers™are otherwise unmodified INA® oligos containing particularly many IPN molecules that provides BaseBlockers™ with an extremely 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.
Customized BaseBlockers™ can be designed by PentaBase for your specific targets and applications.
Reduced Off-target Amplification
The 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 therefore 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.
The graph shows amplification curves of an assay with and without the inclusion of a BaseBlocker™ when using a wild type and a single nucleotide mutated template.
Quality Controlled
Evaluation of BaseBlocker™ performance in melt studies are part of our quality control during production.
