We offer a comprehensive range of high-quality probes for qPCR and RT-qPCR applications, including hydrolysis probes like TaqMan™ and hybridization probes such as HybProbe and LightCycler® probes. We also provide Molecular Beacon and Scorpion probes, designed for precise target detection. With a choice of single or double quenched options, as well as Minor Groove Binder (MGB) modifications, you can choose the best fit for your specific applications. Each probe is synthesized to strict quality standards to ensure reliable performance in real-time PCR assays.

In addition, we manufacture our diagnostic oligos in a separate, dedicated laboratory to minimize the risk of contamination. This assures that they meet the highest standards of purity and reliability, giving you confidence in their accuracy for diagnostic applications.

Length

We offer custom probes ranging from 8 to 40 nucleotides, with high fidelity synthesis and reliable performance. For different lengths or special requests, please inquire for tailored solutions.

Scales and Yields

We begin probe synthesis at either 40 nmol or 200 nmol scale. The final yield depends on several factors, including the synthesis scale, the purification method chosen, and the complexity of the modifications.

High-purity options such as HPLC or PAGE purification ensure the highest quality oligos, but may result in lower yields. Additionally, the incorporation of complex dye or quencher labels can further impact yield, as it requires additional purification steps.

Modifications

Fluorophores and Quenchers

Fluorophore and quencher modifications are key to sensitive detection in real-time PCR and SNP assays. At Ella Biotech, we provide a selection of fluorophores that ranges from the visible to the near-infrared spectrum. These fluorophores are often paired with customizable quencher options, allowing for precise, low-background signal detection in various probe configurations.

For a comprehensive list of available fluorophores and quenchers, please refer to the Fluorophores and Quenchers page.

Double and Internal Quencher

We offer the synthesis of probes with internal quencher or double quencher. These probes are suitable for even lower fluorescence background detection.

Duplex Stabilization

Duplex stabilization for probe oligonucleotides has been shown to improve selectivity and mismatch sensitivity, leading to more accurate target detection. It also makes it possible to use shorter probes, which helps reduce background fluorescence and improve overall signal clarity. The end result is more efficient and reliable assays.

* Please note that MGBs intercalate 100x stronger in A/T (Ka ~ 10^7 M^-1) rich regions than in G/C rich regions
(Ka ~ 10^5 M^-1) of ~ 5 nt.

* * Values may vary depending on your oligo design.

For more detailed information, please refer to the Duplex Stablization page.

DNA/RNA Chimeras

Single or multiple RNA bases and/or RNA analogue bases such as 2’O-Methyl, 2’Fluoro, and 2’O-Methoxyethyl (MOE) can improve the stability and binding affinity of DNA and RNA targets. These modifications can reduce mismatch tolerance, making them ideal for many high specificity applications.

We offer the synthesis of full RNA or chimeric DNA/RNA probes for specific qPCR applications.

RNA and DNA/RNA Chimeras: 2’O-Methyl, 2′-Fluoro, 2′-O-Methoxyethyl (MOE), RNA and LNA.

Degenerate Bases

In oligonucleotide synthesis, the deliberate incorporation of degenerate bases (or „wobbles“) at specific positions within an oligonucleotide sequence is referred to as „degeneration“. The use of such degenerate bases allows the synthesis of oligonucleotides with mixed or variable sequence at specific positions, e.g. to convey tolerance to SNPs, providing a versatile approach to oligonucleotide synthesis.

At Ella Biotech, we offer a range of standard wobbles for different combinations: for example, „K“ represents a mixture of Guanine (G) and Thymine (T), „M“ combines Adenine (A) and Cytosine (C), and „R“ includes Adenine (A) and Guanine (G). For more complex applications, wider degeneracy options such as „N“ (A/G/C/T) can be used.

The universal codes for wobbles:
K (G/T), M (A/C), R (A/G), S (G/C), W (A/T), Y (C/T), B (G/C/T), D (A/G/T), H (A/C/T), V (A/G/C), N (A/G/C/T)

In addition, custom wobble compositions, such as 80% Adenine (A) and 20% Guanine (G), allow for customized nucleotide ratios to meet specific experimental needs.

These wobbles are also compatible with alternative backbones such as Locked Nucleic Acids (LNA) and 2′-O-Methyl RNA, providing researchers with the flexibility to incorporate degeneration modifications into a variety of oligonucleotide chemistries.

In addition to standard wobbles, we also offer degenerate bases designed to increase oligonucleotide flexibility by pairing with multiple bases. For example, the degenerate base dK can pair with cytosine (C) and thymine (T), while dP complements adenine (A) and guanine (G). Another versatile option is Inosine (dI), which pairs with all four bases (A, G, C, and T), making it ideal for applications requiring base pairing versatility.

We also provide abasic positions such as dSpacer, which leaves a gap in the sequence and can be used to mimic natural DNA damage or to study structural changes in oligos. These specialized options, along with our selection of wobbles, provide scientists with greater control over sequence flexibility and target binding in complex experimental designs.

Purification

 All our qPCR probes are purified by RP-HPLC as a minimum requirement. Please inquire if additional purification is required. 

Delivery Form and Packaging

We offer oligonucleotides in a variety of packaging formats, including single tubes, multi-well plates, and bulk options, in a range of concentrations, solutions, and aliquot options. Custom vial labeling is also available upon request.

* Possible concentration may depend on scale/yield since low yields at high concentrations will lead to extremely low volumes
   which are very hard to handle e.g., 5 nmol at 5 mM would lead to a volume of 1 µL.

Quality and Quality Control (QC)

We are dedicated to maintaining the highest standards for the quality of our synthesised oligonucleotides. We conduct strict quality control tests on each oligonucleotide to ensure that our products meet the highest possible standards. All oligonucleotides are manufactured in accordance with ISO 13485 standards, ensuring exceptional purity and reliability.

For detailed information please read Quality Control in our Resource section.

Additional Services

Prepaid Oligo Service: You can set up a credit account to make your purchases easier by paying by direct debit from your prepaid credit account.

For quality assurance purposes, we can provide comprehensive Certificate of Analysis (CoA) documentation upon request.

Production Time and Shipment

Oligo production time varies with modification complexity, yield requirements, and order volume. Probes with complex modifications take longer than standard primers, and higher yields or larger orders may also extend production time.

The production time for probes averages 5 working days, typically ranging from 3 to 7 working days depending on the yield/order volume and additional services like CoAs or custom purification.

We use FedEx for shipment, offering both national and international delivery options. For temperature-sensitive shipments, we provide the option of dry ice or blue ice (gel packs).