Although this speculation is also supported by the observation that the PM/MM ratios of the mismatched positions 6 8 from the end showed the best specificity with most probe lengths, further studies are necessary to understand the effects of the mismatched position on hybridization behavior on microarrays.
However, because our results indicated high specificity with the chosen probe, we did not develop this approach further.
They reported that mismatches affected probe specificity, with mismatches at the ends of the probe having the least effect.
Along with probe specificity, the relationship between the 3' and 5' location of the mismatches was also assayed.
To verify probe specificity, a probe with two mismatched nucleotides (underlined, bold) was also used: 5′-AGGGATTCCTGGGAAAA G T C G T C′.
Our assay therefore combines the convenience of SYBR Green based analysis with the specificity of probe based analysis and is applicable to all models of Cre-lox mediated conditional gene deletion.
These include the use of different arrays and CNV detection algorithms, with varying sensitivity, specificity and probe density [5], [10], as well as technical problems with aCGH arising from, for example, the interference of SNPs with hybridization [15].
Fluorescein AM ethers are chemically stable esterase substrates that can be used to probe esterase specificity with low background.
To ensure sensitive detection of BWAs with high accuracy, the performance of this multiplexed, high-density array was assessed by examining the detection limits and specificity of probes with Cy3-labeled synthetic targets (the synthetic target is a 50-mer oligonucleotide complementary to the probe).
The requirements for designing the probes included high specificity, with no organism outside the intended target group having 100% similarity within the target sequence, and the target sequence being located within the high accessibility region of 16S rRNA molecule as suggested previously (Behrens et al. 2003).
