BaseBlockers™

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.

Product Details

Reference Numbers                                                 436, 437, 438

Product Name                                                           BaseBlocker™ 14-35 mer

Product Description                                                 BaseBlocker™ design (436), 10 nmol delivered (437), 50 nmol or higher delivered (438)

Yield                                                                            10/50 nmol or higher delivered

Format                                                                        Lyophilized                                                               

Pricing                                                                        €500/€140/€280 (436/437/438)

Publications

SensiScreen® KRAS exon 2-sensitive simplex and multiplex real-time PCR-based assays for detection of KRAS exon 2 mutations

Riva et al. – PLoS One – 2017

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Occurence of RAS reversion in metastatic colorectal cancer patients treated with bevacizumab

Epistolio et al. – Oncotarget – 2021

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A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

Jensen et al. – PLoS One – 2021

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Detection of BRAF mutations in malignant melanoma and colorectal cancer by SensiScreen® FFPE BRAF qPCR assay

Sørensen et al. – PLoS One – 2023

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PlentiPlex™ MYD88 Waldenström lymphoma qPCR assay: A highly sensitive method for detection of MYD88 L265P mutation

Viscovo et al. – Int J Lab Hematol. – 2024

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Customised-Oligos-and-PCR-Assays-Catalogue-April-2024-V.2.5.pdf

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INA®-based IVD PCR assays with superior performances

Our IVD PCR assays are based on a unique INA® oligonucleotide chemistry with superior target affinity and specificity. The INA®-based IVD PCR assay portfolio including SensiScreen®, PlentiPlex™ and EpiDirect® product families offer excellent performances, are easy to implement in standard laboratory workflows and provide results in a couple of hours.

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