Pentabase is the manufacturer of a proprietary technology that easily substitutes TaqMan® MGB, Molecular Beacon and other DNA Third generation real-time PCR primers and probes.

They also supply their own modified primers, SuPrimers™, that ensure less primer-dimer and higher working temperature. Standard probes and primers of high quality are also supplied.

NEW! PentAdapters – Indexed NGS adapters designed for Illumina NGS.

Pentabase supplies;

  • DNA primers
  • SuPrimers – Super primers with higher affinity, less primer dimer formation and higher multiplexing capacity
  • DNA probes
  • HydrolEasy™ probes – the perfect hydrolysis probe for SNPs and methylation
  • EasyBeacon™ – the easy to design and use alternative to molecular beacons, incl. increased affinity and more..
  • PentAdapters – Indexed NGS adapters
  • Custom oligos
  • Branched DNA
  • Random hexamer primers modified with pentabases
  • Oligo dT primers

PentaBase Technology

PentaBase’s products are composed of standard oligonucleotides with covalently attached insertions of Hydrophobic, intercalating moieties (pentabases) which introduces novel features to the oligonucleotides. The pentabases do not replace any nucleotides in your sequence, but add stability to the interactions between the sequence and it’s complementary target sequence.

Pentabases comprise a flat hetero aromatic and hydrophobic molecule, which, when they cannot intercalate between base pairs in a complementary duplex, tends to stack on top of each other having hydrophobic interactions. In this way the system is minimising the hydrophobic surface exposure to water and hence maximising the entropy of the system (this mechanism is known from protein folding, where proteins usually have a hydrophilic outer surface and a more hydrophobic inner core). When hybridised to a complementary target, the fluorophore and the quencher of the probes are separated in spatial distance allowing the fluorophore to shine.






Pentabases add well-known features like high-affinity binding and increased specificity as well as unique features like nuclease stability, second structure formation and QC ability of the real-time PCR assay. Therefore pentabase based research tools can be exploited to solve many of the challenges related to ordinary hybridisation based assays. Especially in assays where optimal performance is critical, as well as to contribute with new and innovative tools.

The invention of Real-Time PCR has revolutionized the way of determining the status of genes in a fast and precise manner. Despite many advances in the technology there has been a need to find molecular probes that are easy to design and manufacture, highly specific and easy to implement.

Currently there are two major probe based Real-Time PCR platforms: Molecular Beacons and TaqMan® (Hydrolysis probes).PentaBase™ is offering probes and primers based on our proprietary new pentabases. These special hydrofobic modifications and our experimence in Real-Time design make our products into some of the best performing Real-Time PCR probes and primers. PentaBase is offering two different probe technologies:

    • EasyBeacons™ – these can replace Molecular Beacons and be used for both Real-Time and end-point measurements
    • HydrolEasy™ probes – these can replace other hydrolysis probes like old fashioned TaqMan®, TaqMan®MGB and LNA modified TaqMan® probes

PentaBase’s Real-Time PCR technologies are easy to use, compatible with all Real-Time PCR platforms and there is no need for special reagents.

Features offered are:

    • High affinity
    • High sensitivity
    • High specificity
    • High signal-to-noise ratio
    • Low background fluorescence
    • Less primer-dimer formation
    • Less unspecific amplification
    • Improved temperature range

PentaBase’s Real-Time PCR technologies are excellent for detections of SNPs, mutants, methylation (MeCPG), alleles, consensus sequences, expression etc. EasyBeacons™ and HydrolEasy™ probes are composed of a fluorophore like FAM, HEX™, TET™, or others and a quencher such as Black Hole Quenchers™, Tamra™, Dabcyl, or others normally linked respectively to the 5’- and 3’-end of a short, modified oligonucleotide.