EasyBeacon™ Probe

The EasyBeacon™ probe is an improved alternative to molecular beacon probes and the perfect probe for end-point melt analysis.

The INA® technology used in EasyBeacon™ probes creates a secondary structure in the unbound state that efficiently quenches the signal resulting in a very low background fluorescence without adding a stem sequence. The added IPNs to the probe sequence furthermore render the probes nuclease resistant and therefore intact after PCR amplification.

The high target affinity and specificity provided by the added IPN molecules additionally makes it possible to easily differentiate between single nucleotide polymorphisms (SNPs) as well as multiplexing in end-point melting curve analyses.

  • Nuclease resistant – improved signal after PCR
  • Quenched at all temperatures without adding a stem
  • Improved target affinity and specificity for easy single nucleotide variant detection
  • Ideal for multiplexed genotyping – evaluate up to 27 or 81 genotypes using 3 or 4 fluorophores
Product Details

Reference Numbers                                                439-458

Product Name                                                          EasyBeacon™ probe 14-35 mer

Flourophores                                                            More than 35 fluorophores including PentGreen/Yellow/Orange/Red, CAL Flour, Quasar, ATTO and CYanine – see catalogue for details

Purification                                                                HPLC

Yield                                                                           10/50 nmol or higher delivered

Format                                                                        Lyophilized or dissolved in water/TE buffer                                                               

Verification                                                                Melt analysis using complementary target


EasyBeacons for the detection of methylation status of single CpG duplets

Christensen – Methods Mol Biol – 2008

Read chapter

10-Plex Digital Polymerase Chain Reaction with Four-Color Melting Curve Analysis for Simultaneous KRAS and BRAF Genotyping

Nakagawa et al. – Anal Chem. – 2020

Read article

Related Files
File name
Customised Oligos and PCR Assays Catalogue V.2.5

Nuclease Resistant and Naturally Quenched

By adding hydrophobic IPN molecules at the outmost ends of the dual-labeled EasyBeacon™ probe, hydrolysis is prevented and therefore the probe is intact after PCR amplification. This leads to higher signal strength in the following end-point melt procedure.

The fluorophore and quencher are furthermore brought into close proximity due to interactions between IPN molecules. This leads to quenching of the unbound probe at all temperatures.

The addition of IPN molecules to EasyBeacon™ probes is automatically done by PentaBase when receiving an order and is included in the price. The number of added IPN molecules depends on the desired melting temperature of the probe. The addition of IPN molecules typically adds 4-8°C to the melting temperature.

Ideal for Multiplexed Genotyping and HRM

The nuclease resistance, high target affinity and specificity combined with low background fluorescence of EasyBeacon™ probes make them ideal for end-point PCR multiplexed genotyping and high resolution melt (HRM) applications.

With EasyBeacon™ probes, single nucleotide variation in the target sequence leads to large differences in the melting temperature. This makes it easy to distinguish between a homozygous wild type (blue line), homozygous mutant (green line) and heterozygous target (red line) using a single EasyBeacon™ probe. Hence, with different fluorophores it is easy and straight forward to multiplex genotyping reactions in a closed tube format.

Improved Performance

EasyBeacons™ have superior performances compared to molecular beacon probes.

The graphs show a comparison of the target binding properties of an EasyBeacon™ (bold line) with those of a molecular beacon with identical sequence. The used target has 100% sequence similarity to the probes including the stem sequence of the molecular beacon.

The melting temperature (+ target) of the EasyBeacon™ probe is significantly higher than the corresponding molecular beacon probe.

In addition, the background fluorescence of the EasyBeacon™ probe is lower than the molecular beacon when no target is included – and when adding a target – the EasyBeacon™ fluorescence level is higher. The resulting melt peak height is consequently higher for the EasyBeacon™ probe compared to the corresponding molecular beacon.

The improved performance of EasyBeacons™ can be used to design PCR assays with higher sensitivities and lower requirements to the amount of sample input.

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