Description:
SynaProbe™ (v1.2.2) is an application for designing oligonucleotide probes for genes of interest. The application utilizes the exhaustive SynaBASE™ pattern network to rapidly design highly specific and sensitive probes. Although most applications are able to report a unique probe for a gene, they do not verify the impact of mismatches on probe specificity. By using the complete genome as a reference, the probability of false positives is reduced. Studies have indicated that mismatches occurring at the ends can also result in probe-target hybridisation. SynaProbe has been designed to take account of mismatches, to ensure that probes remain specific to the target gene even if there are closely related sequences in other genes.

Application Example:
It has been reported that at least 29 inherited variants of the SORL1 neuronal sorting receptor gene contribute to the late onset of Alzheimer's disease¹. When under-expressed, this gene directs trafficking of the amyloid precursor protein (APP) into amyloid beta peptide (Abeta)-generating compartments which play a role in the development of Alzheimer's. As more research is needed to determine how different versions of the SORL1 gene influence the development of Alzheimer's, probes designed for this gene using SynaProbe have wide applicability toward deciphering the impact of differential expression in disease progression.

To run the example above, please:

Go to www.mgrc.com.my.
Click on SynaProbe.
Click on Test Sequence.
Select the Application Note test sequence - May 2007 by clicking on Copy next to the sequence.
Select a Probe Length of 70 and leave all other parameters at default.
Click on PROBE to run analysis.
Click on which directly links to SynaHybridise for probe specificity confirmation.
Click on HYBRIDISE to view results.

Figure 1: The input page of SynaProbe (v1.2.2)

Figure 2: SynaProbe candidate 70mer probes designed based on conserved regions of the Human Genome SynaBASE in 198 milliseconds.

Figure 3: Confirmation of probe specificity using SynaHybridise.

References:
1. Rogaeva E et al. The neuronal sortilin receptor SORL1 is genetically associated with Alzheimer's disease. Nat Genet 2007;39(2):168-177.

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