The MethyLight assay involves treatment of genomic DNA with sodium bisulphite followed by an alkaline treatment.The homologous regions to be avoided can be filtered on the basis of either the identity or the e value or both, the defaults for e value being 0 and that of identity being 100%. Primers and TaqMan® probes designed by Beacon Designer™ are highly specific as they are designed by avoiding regions of significant cross homology identified by automatically interpreting BLAST search results. You can also design suitable control primers and probes for MethyLight assays by designing them for unmethylated and untreated DNA sequences. The CpG islands are displayed in green in the Sequence view tab and the regions that are rich in GC are displayed in red.īeacon Designer™ designs TaqMan® probes and methyl sensitive PCR primers for the specified CpG islands. You can also specify the CpG regions manually in a sequence. Only the primers satisfying all the parameters of High Resolution Melting Analysis are reported.īeacon Designer™ displays the sequence properties of both the wild and mutant amplicons along with their melting temperatures.įacilitates verifying the specificity of the primers designed by primer BLAST.Įvaluates pre-designed proven primers and designs a compatible primer for a given sense or anti-sense HRMA primer.īeacon Designer™ predicts CpG islands in accordance with Gardiner-Garden and Frommer guidelines. The program identifies template structures and then automatically avoids them while designing HRMA primers, improving the PCR efficiency.īeacon Designer™ checks the Tm, GC % and other parameters of the primers designed.
Reference gene or housekeeping genes supported for normalization.ĭesigns mutation flanking HRMA primers such that they generate the shortest possible amplicon, for mutation detection. Multiplex assays are supported in the TaqMan® design mode. Read about how TaqMan® probes work! Multiplex Real Time PCR Assay Designīeacon Designer™ uses innovative proprietary algorithms to design optimal primer-probe sets for single tube multiplex assays.
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You can also specify their placement and the LNA free region on each end of the probe to design LNA™ spiked TaqMan® probes. You can specify the number of LNA™ bases that you wish to have in the probe. LNA™ substituted TaqMan® probes are shorter probes and have LNA™ bases that impart higher stability. Beacon Designer™ can design LNA™ probes.You can even import the primers designed in the SYBR® Green primer design mode and design a compatible probe.ĭisplays a graphical view of TaqMan® probe secondary structures. Similarly, a pre-designed TaqMan® probe can be evaluated and compatible primers be designed. Pre-designed primer sets can be evaluated and a compatible TaqMan® probe be designed. Screens SYBR® Green primers for thermodynamic properties and secondary structures.Īvoids homologies with all other primers to reduce primer dimers in a multiplex reaction.ĭesigns optimal TaqMan® probes free of dimers, repeats and runs to ensure signal fidelity.ĭesigns wild and mutant TaqMan® probes for SNP identification for SNP genotyping assays Presents the design results in a ranked order. It then proceeds to design optimal dual labeled probes for use with well proven SYBR® Green primers.įor SNP genotyping studies, designs SYBR® Green primers such that the SNP site at or towards t he 3' end position.Ĭalculates SYBR® Green primer Tm using nearest neighbor thermodynamic algorithm. This functionality helps visualize where the designed oligos are located with respect to both the regions.Įvaluates pre-designed primers and designs a compatible primer a given sense or anti-sense primer. This helps verify the SYBR® Green primer design and visualize primer and amplicon specificity.īeacon Designer™ identifies template structures and then automatically avoids them while designing SYBR® Green primers.ĭisplays the regions of homology and secondary structures for the sequence graphically in the Sequence View pane. The SYBR® Green primers designed can be BLAST searched against genomic databases available at NCBI. Beacon Designer™ Features SYBR® Green Primer Designĭesigns primers optimized for SYBR® Green PCR assays.īeacon Designer™ designs highly specific SYBR® Green primers by BLAST searching sequences, automatically interpreting the results and then designing SYBR® Green primers by avoiding regions of significant homology.
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