Probe Design Services

Real-time QPCR Probe Design Services Design Assistance for Real-time qPCR Probes Dual-labeled DNA Probes Molecular Beacons LightCycler® Probes Scorpions™ Probes LNA® Base incorporation into all probe types

Highly Efficient Probes for QPCR
Using sophisticated algorithms, we can design dual-labeled probes and molecular beacons that will dramatically improve the success of your assays. Primers and probes on multiple sequences are designed in a single search run and are screened for all possible secondary structures to ensure optimal signal strength. Tm is calculated using nearest neighbor thermodynamic theory and highly accurate Santa Lucia values. We can also analyze properties of current assays you may already have pre-designed and evaluate the efficiency of those combinations.

Optimal Primer Design
Complimentary primer sets may also be designed for your real-time QPCR applications. Our software will BLAST your sequences, automatically interpret the results, and then design highly specific primers that avoid regions of cross-homology, using statistical optimization techniques.

Multiplex assays
Ensure the efficiency of your multiplex assays by letting us provide effective primer and probe designs that avoid homologies and provide robust signals. Pre-designed probes and design-compatible primers/probes for other targets may also be included for multiplex reactions.

Allele Discrimination Probes
Probes for detecting both wild and mutant alleles of your target of interest can be designed, with the sense of the output beacon for allelic discrimination clearly defined. For SNP genotyping assays with defined design parameters, we can propose optimal primer-probe sets, along with a list of alternative probes, to meet your specific experimental needs. Effective designs are achieved through access to thousands of SNPs using standard GenBank variation files or by cross-referencing against your own SNP information. Sequence batches are retrieved from Entrez and dbSNP with BLAST search as standard.

Template Secondary Structures
The highly accurate MFold program of the software enables effective folding of molecular beacon templates, calculates hairpin Tm, and automatically avoids secondary structures in the template when designing primer and probe sets.

Graphical Representation
Graphical representations of designed primers and probe sequences, showing all possible dimers, cross dimers, repeats and runs, may be obtained on request.

Contact your local Sigma Life Science Representative for more information.