Skip to content
LoginCreate Account
MENUMENU
  • Contact
  • Technical Support
  • Ordering
  • Find your local distributor
  • Become a distributor
  • Resources
  • Policies
  • đź›’ CART
WOOCS 2.2.4
PentaBase
MENUMENU
  • BOOK TEST
  • COVID-19
    • BOOK COVID-19
    • COVID-19 for Companies
    • Antibody ELISA test
    • CoviDetect™ Assay
    • CoviDetect™ FAST Assay
    • SARS-CoV-2 Oligos
    • SARS-CoV-2 Mutations
  • Products
    • Diagnostics
    • Equipment
    • Custom Oligos
    • Consumables
    • Reagents
    • Sequencing
  • Ordering
    • How to order
    • General Terms & Conditions
  • Services
    • SNP Genotyping Services
    • Real-Time PCR Assay Development
  • Technology
    • NGS Adapters
    • BaseBlockers™
    • (Su)Primers™
    • Fluorescent Probes
  • About Us
    • News
    • Mission and Visions
    • Meet the team
    • Advisory Board
    • Quality Management System
    • PentaBase in the Press

Frontpage - Our proprietary technology - Fluorescent Probes

Our Products

  • Cancer Mutations
    • SensiScreen® Cancer IVD Assays
    • PlentiPlex™ MYD88
  • Microsatellite Instability
    • MicroSight® MSI Assays
    • PlentiPlex™ MSI
  • Mastocytosis
    • PlentiPlex™ Mastocytosis
  • Sequencing
    • NGS Adapters
  • Reagents
    • cDNA Supreme
  • Consumables
    • Vials and tubes
    • Pipette tips
  • Equipment
    • Real-time PCR Instruments
    • DNA Purification Instrument
  • COVID-19 BOOKING
    • Antibody test (IgM) in Herlev
    • Antibody test (IgM) in Odense
    • COVID-19 RT-PCR test in Herlev
    • COVID-19 RT-PCR test in Odense
    • COVID-19 RT-PCR test in Esbjerg
    • COVID-19 RT-PCR test in Aarhus

Our Technologies

  • NGS Adapters
  • BaseBlockers™
  • (Su)Primers™
  • Fluorescent Probes

Fluorescent Probes

Custom Oligos Ordering Page >

Fluorescent probes for real-time PCR, in situ hybridisations and more 

PentaBase is offering high quality of dual-labeled DNA probes and improved DNA probes with a broad range of different quenchers and fluorophores. Dual-labeled probes normally contain a quencher at the 3′-end and a fluorophore at the 5′-end, but can also contain the fluorophore and/or quencher internally in the sequence. For example we offer two types of dual-labeled probes for Real-Time PCR: Molecular Beacons/EasyBeacons™ and TaqMan®/HydrolEasy™ probes. Available quenchers and fluorophores can be seen in the shop. Some of the modifications are listed below. Please inquire for further informations.

HydrolEasy™ probes – PentaBase’s great alternative to TaqMan® MGB probes

HydrolEasy™ probes are hydrolysis probes with significantly better signal-to-noise ratio, a higher specificity and a higher sensitivity than conventional probes. When the HydrolEasy probe is intact the fluorophore and the quencher are, in contrast to “standard” TaqMan® probes, kept in close proximity by hydrophobic interactions between pentabases. During the amplification reaction the probe hybridizes to the target and exonuclease activity of the polymerase cleaves of the fluorophore from the probe whereby a strong fluorescence signal is generated. The figure below shows how a HydrolEasy™ probe degrades in the same way as normal TaqMan® probes do.
HydrolEasy™ Probes are developed to provide TaqMan® users, TaqMan®MGB users and users of other hydrolysis probes with an improved alternative for better signal-to-noise ratio, a higher specificity and sensitivity. A HydrolEasy™ Probe is a dual-labelled probe, with a standard fluorophore in the 5’ end and a quencher in the 3’ end, and added our proprietary pentabases to improve sensitivity, specificity, affinity and signal-to-noise ratio.

HydrolEasy™ mechanism

We convert your TaqMan®MGB designs and standard hydrolysis probe designs into HydrolEasy™ probes for free! Just send us an email with your sequences. It is no problem if you do not have a design already, just send an email with the details that you have. Please note that TaqMan®MGB is a registered trademark of Life Technologies. Our probes do not comprise a minor groove binder, but instead they comprise several pentabases. The pentabases not only increase signal-to-noise ratios, but also increase affinity, specificity and sensitivity.

EasyBeacons™ – The easy to use and design alternative to Molecular Beacons

EasyBeacons™ are nuclease resistant probes developed by PentaBase™ to be used in 3-step Real-Time PCR and in situ hybridisations. Like Molecular Beacons, EasyBeacons™ are quenched when the probes are unbound, but fluoresce at hybridization to a target sequence. However, unlike Molecular Beacons, EasyBeacons™ do not require an internal stem to be quenched efficiently. The pentabases in EasyBeacons™ will, by having hydrofobic interactions with each other in the unbound probe, ensure that the quencher and fluorophore are kept in close proximity and hence resulting in an efficiently quenched probe with low background fluorescence. This mechanism of action is temperature independent and thereby increases the working temperature window of the probes and the ease of use significantly.

EasyBeacon™ differentiator

EasyBeacons™ are nuclease resistant, and can be used for real-time as well as end-point detection. This is a valuable feature, especially for genotyping almost similar genetic sequences like SNPs and CpG methylation status.

EasyBeacons™ mechanism

Due to EasyBeacons™ nuclease resistance, they can also be used for end-point detection or verification of your Real-Time signal. This is a valuable feature, especially if you want to discriminate between almost similar genetic sequences like SNPs or if you want a quality control on your quantification data.

EasyBeacon™ vs HydrolEasy™

When the EasyBeacon™ binds to a complementary target, the fluorophore and quencher are separated allowing the probe to fluoresce. The EasyBeacon™ is displaced by the polymerase during the PCR. Hence, EasyBeacons™ can be used for both real-time and endpoint measurements. When the TAQ polymerase meets a HydrolEasy™ probe, the probe is hydrolysed, releasing the fluorophore from the remaining probe and allowing it to fluoresce to its maximum potential. HydrolEasy™ Probes are used in real-time PCR and qPCR reactions.

Do you want to test EasyBeacons™, we design them for you for free! Just send us an email with your target sequences. It is no problem if you do not have a design already, just send an email with the details that you have.

Synthesis scale

PentaBase is providing probes and primers worldwide every day. All our oligo syntheses are performed using phosphoramidite chemistry. We use solid fase CPGs of the highest quality to insure a high yield. After end of synthesis the oligos are cleaved from the support and purified. Each oligo is followed using trityl monitoring during synthesis.

Synthesis scale Purificaiton Average yield Guaranteed yield
10 nmol HPLC 5-8 nmol 1 nmol
50 nmol HPLC 10-40 nmol* 10 nmol
200 nmol HPLC 20-130 nmol* 15 nmol

*Depends on fluorophore choice

Modifications

Available modifications can be seen in the tabel below and also in the shop. Please inquire for further informations or other modifications.

Fluorophore Exitation nm Emission nm Quencher Visible colour
FAM 495 516 BHQ-1, TAMRA, DABCYL Green
Fluorescein 495 518 BHQ-1, TAMRA, DABCYL Green
PantaGreen 495 516 GreenQuencher Green
HEX 535 556 BHQ-1, TAMRA, DABCYL Yellow
TET 522 539 BHQ-1, TAMRA, DABCYL Yellow
PentaYellow 533 557 YellowQuencher Yellow
Cal Fluor Red 610 BHQ-2 Orange
TAMRA 542 568 BHQ-2 Orange
CY3 550 570 BHQ-2 Orange
ROX 574 602 BHQ-2 Orange
PentaOrange 583 603 OrangeQuencher Orange
CY5 650 670 BHQ-2, BBQ650 Red
Quasar 670 amidite 647 670 BHQ-2, BBQ650 Red
PentaRed 650 670 RedQuencher Red
CY5,5 675 694 BBQ650 Red

Black Hole Quenchers (BHQ-1 and BHQ-2), Cal Fluor Red 610 and Quasar 670 amidite is registrated trademarks of Biosearch Technologies. CY3 and CY5 are registrated trademarks of Biological Detection System, now Amersham Pharmacia Biotech. 6-FAM and HEX are trademarks of Applied Biosystems.

Purification

All PentaBase probes are purified by reverse-phase HPLC in order to give the purest products. Primers are also purified by reverse-phase HPLC followed by desalting and removal of the final DMT group. Desalting removes residual by-products from the different processes.

Quality control

Every probe from PentaBase are strictly controlled for quality and fluorescens potential in an affinity test. To do this test we synthesize a complementary oligo target and run a melting curve from 95°C to 35°C. The figure below shows the result of such a test. The red curve shows the probe in presence of it’s complementary target and the yellow line shows the probe without a target. Half way down the dip in fluorescence of the red line corresponds to the melting temperature of the duplex. The exact melting temperature of the probe-target duplex is found by calculating the inverted derivative of the curve.

 

Publications

Prevalence and genotypes of Borrelia burgdorferi sensu lato infection in Ixodes ricinus ticks in southern Norway
  • Contact PentaBase
    • General Inquiries
    • How to Order
    • Technical Support
    • Request Demo Kit
Superior Oncology assays
Explore our sensitive oncology assays available for liquid and FFPE biopsies.
Learn more about our oncology products

Custom oligonucleotides


Our custom DNA oligos are produced, with thorough and careful quality control and quick turnaround

Order your oligos here

CONTACT US

  • Email: moc.esabatnep@ofni
  • Phone: +45 36 96 94 96
  • CVR: 30 19 78 52

VISIT US

PentaBase ApS
Petersmindevej 1A
DK-5000 Odense C
Denmark

KEEP IN TOUCH

FOLLOW US

This website uses cookies to improve your experience. We'll assume you're ok with this, but you can opt-out if you wish. Cookie settingsACCEPT
Privacy & Cookies Policy

Privacy Overview

This website uses cookies to improve your experience while you navigate through the website. Out of these cookies, the cookies that are categorized as necessary are stored on your browser as they are essential for the working of basic functionalities of the website. We also use third-party cookies that help us analyze and understand how you use this website. These cookies will be stored in your browser only with your consent. You also have the option to opt-out of these cookies. But opting out of some of these cookies may have an effect on your browsing experience.
Necessary
Always Enabled

Necessary cookies are absolutely essential for the website to function properly. This category only includes cookies that ensures basic functionalities and security features of the website. These cookies do not store any personal information.

Non-necessary

Any cookies that may not be particularly necessary for the website to function and is used specifically to collect user personal data via analytics, ads, other embedded contents are termed as non-necessary cookies. It is mandatory to procure user consent prior to running these cookies on your website.

×
Item Added to your Cart!
There are no products
Continue Shopping