A Eurogentec product line, distributed in Malaysia by Infenix Sdn Bhd.
What They Are
Eurogentec manufactures custom qPCR probes in three chemistries. All three are HPLC purified and quality controlled by MALDI-TOF MS + UHPLC; they differ in how they generate signal, how long they can be, and what they are best at.
Comparison
| Double Dye | MGB probes | Molecular Beacons | |
|---|---|---|---|
| Length | 8 to 45 bases | 8 to 30 bases | 25 to 50 bases |
| Purification | HPLC | HPLC | HPLC |
| Quality control | MALDI-TOF MS + UHPLC | MALDI-TOF MS + UHPLC | MALDI-TOF MS + UHPLC |
| Formats | Lyophilised in individual tubes, or in solution (H2O or TE) | In solution (H2O or TE); dried, or dried aliquoted in 10 nmol on request | In solution (H2O or TE); dried in individual tubes |
| Quantities | 10 • 40 • 200 • 1000 nmol (synthesis scale — larger on request) |
6 • 20 • 50 nmol (delivered quantity) |
40 • 200 • 1000 nmol • 2.5 µmol • 5 µmol • 10 µmol (synthesis scale) |
| Backbones | DNA, LNA® | DNA | DNA, LNA® |
Note when comparing quotes: MGB figures are a delivered quantity, whereas Double Dye and Molecular Beacon figures are a synthesis scale. These are not directly comparable.
Double Dye — the general-purpose workhorse
A linear probe carrying a fluorescent reporter at the 5′ end and a quencher at the 3′ end. While the probe is intact the two labels sit close enough for quenching, so the reporter is dark. During each annealing step the probe hybridises inside the amplicon; as the polymerase extends from the upstream primer it displaces the probe’s 5′ end, which is then degraded by the enzyme’s 5′→3′ exonuclease activity. This releases the fluorophore into solution, producing an irreversible rise in fluorescence proportional to the amplicon accumulated.
Eurogentec describes these as the most widely used type of qPCR probe and often the method of choice for scientists starting out in real-time PCR. Reporters include FAM, HEX, TET, Yakima Yellow, Cy3, Cy5, ATTO, ROX, Texas Red and Dragonfly Orange; quenchers include TAMRA, BHQ®, Eclipse Dark Quencher, Deep Dark Quencher and QXL.
Choose it when you want the easiest chemistry to design, the widest dye palette, an LNA® backbone option, or the largest synthesis scales.
MGB probes — short probes, sharp discrimination
A DNA hydrolysis probe with a 5′ reporter dye and, at the 3′ end, both an Eclipse dark quencher and a minor groove binder moiety. The crescent-shaped MGB ligand folds into the DNA minor groove, stabilising the probe–target duplex and raising its melting temperature. That lets a much shorter probe reach a usable Tm, and because a mismatch costs proportionally more in a short probe, single-base discrimination sharpens.
Eurogentec states that the MGB increases the Tm and offers very high specificity toward the complementary sequence, with a high signal-to-noise ratio supporting detection of low-copy targets. More than 15 dyes are available covering all qPCR channels.
Choose it when sequence real estate is tight — AT-rich regions, splice junctions, short conserved stretches — or for SNP genotyping and allelic discrimination. Note this chemistry is DNA-only.
Eurogentec states that MGB Eclipse probes made at Eurogentec are not limited by any licence. Commercial use of probes labelled with ATTO, Yakima Yellow or Texas Red may nevertheless be subject to third-party intellectual property.
Molecular Beacons — specificity by shape
A single-stranded probe with a target-complementary loop flanked by two short self-complementary arms. In free solution those arms anneal into a stem that holds the fluorophore and quencher in direct contact, so the unbound probe is essentially dark. When the loop meets its complementary sequence the probe–target duplex becomes more favourable than the stem, the hairpin springs open, and the fluorophore is physically separated from the quencher.
Because opening the stem carries an energetic penalty, hybridisation is sharply temperature-dependent and a mismatched target fails to open the hairpin at the chosen annealing temperature. The probe is not consumed, so the signal is a reversible hybridisation equilibrium rather than a cleavage event.
Available in standard, wavelength-shifting and 2′-O-Me RNA versions, with DABCYL, BHQ-1® or BHQ-2® quenchers.
Choose it when discrimination matters more than convenience, or for isothermal and non-PCR hybridisation formats that hydrolysis probes cannot serve. Eurogentec notes beacons may fold into alternate conformations that are not well quenched, so stem or loop sequences sometimes need reworking.
Applications
- Gene expression profiling, relative and absolute quantification
- Multiplex qPCR using spectrally separated dye and dark-quencher pairs
- Allelic discrimination and SNP genotyping
- Detection of single base mutations and small deletions
- Pathogen detection and identification
- Digital PCR (dPCR) probe assays
- IVD assays and laboratory-developed tests
Enquiries
Infenix Sdn Bhd distributes Eurogentec in Malaysia. Call +6012 882 6283 / +6012 882 6289 or email enquiry@infenix.com.my.