The bases of the stable duplex target are rendered specifically reactive to the bases of the probe because of the activity of intercalated YOYO-1, which is known to decondense duplex locally 1.3 fold.
Some degree of detection power does remain because we accurately detect changes from the rs10965215 SNP, a SNP that is found in the middle of the first probe of exon 2. This SNP is linked with rs2891168 (D' = 0.603, R2 = 0.34) in the CEU population [15], and will affect the hybridization efficiency of the probe because of the sequence change.
For example, in a supervised analysis of all probes, an enrichment bias towards type I probes may be created when ranking probes because of the higher range of type I probes (Maksimovic et al, 2012).
However, as the microarray probes were designed based on the NCTC11168 genome sequence, several IA3902 genes were represented by mismatch probes because of the nucleotide differences between IA3902 and NCTC11168.
Typical methylene blue peak currents range from ∼50 pA to several hundred pA which is likely a result of both the increased surface area of the electrode as well as differences in the packing density and reduced steric hindrance between neighboring probes because of the nanostructured surface.
Importantly, differences between recent and novel probes at these time points are unlikely to reflect activation prior to the onset of the probe, because the identity of the probe as recent or novel is unknown until its presentation.
For further testing in humans, we favour the probe QE; because of the applied probe design strategies, the introduction of negatively charged d-glutamic acids favoured probe characteristics more than multimerization of the molecule.
In practice the LNA probes function as classical TaqMan probes, but because of the LNA properties they are much shorter, only 8 9 bases.
B1_Q and BC1 both have low scores because they only probe a subset of the proteins of the complete vesicle.
The RT App will help simplify probe selection because of the complexity of the ITS1 in C. difficile even in a single genome and because other allele-specific regions (16S and 23S genes) of variability can be relationally compared to design extra probes to increase sensitivity.
