While most probe types will deliver some degree of results, optimisation requires selecting the ideal probe technology based on your experimental goals and commercial vision. Try multiple probe types early in assay development to determine which option aligns with your requirements.

illustration of BHQ probe

BHQ Probes are traditional dual-labelled hydrolysis probes with a 5′ fluorophore dye and a 3′ Black Hole Quencher (BHQ). We offer a complete suite of fluorescent dyes spanning the entire visible spectrum. Take advantage of simple probe design with consistent and reliable performance. These probes excel at detecting the presence and quantifying the amount of a specific target sequence.

illustration of BHQnova probe

When designing long probes, double-quenched BHQnova Probes can significantly increase quenching efficiency and reduce background. These dual-labelled hydrolysis probes have a 5′ fluorophore dye, a 3′ BHQ and an internal nova quencher. With enhanced sensitivity, BHQnova Probes are well suited for gene expression analysis, copy number variation, presence/absence and infectious disease detection.

illustration of BHQplus probe

Dual-labelled BHQplus hydrolysis Probes consist of a 5' fluorescent reporter dye, a 3' BHQ and modified C and T nucleotides throughout the probe sequence that are responsible for enhanced probe-target binding stability. This proprietary duplex-stabilising chemistry permits the design of shorter probes, making BHQplus Probes ideal for detecting difficult target sequences such as SNPs and AT-rich sequences.

illustration of MGB probe

These dual-labelled hydrolysis probes consist of a 5′ fluorescent reporter dye and 3′ Eclipse Dark Quencher (EDQ) conjugated to a MGB moiety that stabilises the probe-target duplex, which effectively increases the Tm of the duplex and enables a shorter probe design, improved sequence specificity and assay sensitivity. This probe type is ideal for supporting detection of SNPs and difficult targets such as AT-rich sequences.

illustration of LNA probe

These dual-labelled hydrolysis probes include up to seven LNA bases (RNA bases “locked” in the C3′-endo conformation) in the probe. Each LNA insertion increases the Tm of the probe-target duplex by 2-8 °C, stabilising the duplex, which enables a shorter probe design, improved sequence specificity and assay sensitivity. LNA probes offer precise Tm control in SNP genotyping and gene expression assays.

illustration of molecular beacon probe

Dual-labelled Molecular Beacon probes form a stem-loop (hairpin) structure, bringing the reporter dye and quencher into proximity. The loop region contains a sequence that hybridises to the target, while the complementary sequences at both ends form the stem. These probes generate fluorescence under non-hydrolytic conditions, increase specificity and sensitivity and enable a post-PCR melt curve.

illustration of scorpions primers

Scorpions Primers combine primer and probe in one molecule with the primer at the 3' and a stem-loop structure at the 5'. The loop region hybridises to the target, while the complementary sequences at both ends form the stem bringing the dye and quencher into proximity. These probes fluoresce under non-hydrolytic conditions, increase specificity and sensitivity, and enable a post-PCR melt curve.

We provide industry-leading oligo synthesis expertise for every custom probe synthesis. Please contact us for more information about dye offerings outside of our standard probe portfolio, custom formulation, large scale synthesis and other probe chemistries such as FPG/RPA probes, LightCycler (FRET) probes, Amplifluor oligos, HyBeacon probes or probes for commercial use made under ISO 13485.

Which probe is best for your assay?

Selecting the best probe for your assay can provide increased data accuracy and reproducibility as well as streamlined logistics and troubleshooting options.

Answer a few simple questions to see which probe types we recommend for your experimental conditions. The tool below will introduce you to our different probe technologies with general guidance on assay suitability and performance. Our assay design and development team is available to support you if you have additional questions pertaining to your assay or are interested in more technical support for assay design and development.

How to order oligos

Option 1: online order tool

Convenient for small numbers of oligos and standard amounts synthesized up to 1 μmol scale. Use option 2 for LNA oligos. 

  1. Navigate to the appropriate product page.
  2. Access the online ordering tool for the probe type via the "Order now" tab on the product page.
  3. Enter your oligos in the ordering tool.
  4. Click "Add to cart."
  5. Check out to complete the purchase or request a quote.

Option 2: excel order form

Best for ordering many oligos and/or large amounts ( >1 μmol scale) and LNA oligos.

For LNA oligos

  1. Visit the LNA probes product page to download one of four excel order forms for LNA oligos in a single tube or as a ValuMix assay.
  2. Follow the directions on the order form to complete your order.

For all other probe types, including custom oligos and ValuMix assays

  1. Download the Excel spreadsheet that best matches your requirements from the order template library.
  2. Follow the directions on the template page to complete your order.
Need support?
Please reach out if you would like help placing your order.