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It is worth noting that the clone library of cel5 revealed that this primer set picked up a large proportion of a non-specific sequence of 483 bp (29 out of 91 clones sequenced).
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In order to measure the binding behavior of PhaR to 5′-biotinylated dsDNAs (50 bp), the DNA fragments with phaR-binding sequences (the promoter regions of phaR and phaP) and a non-specific sequence (negative control) were immobilized on the electrode of a QCM by biotin-avidin linkage, according to methods outlined in previous papers (Matsuno et al. 2001; Okahata et al. 1998).
The target mRNA sequence was as follows: CCAAACUGCCAGACUAUAA. LVs that expressed shRNAs that targeted a non-specific sequence (TTCTCCGAACGTGTCACGT) were used as the controls.
Surprisingly, insertion of a non-specific spacer sequence of comparable size (1 kb) reduced the Wnt3a-induced activation, implying that the DE functions in a distance-sensitive manner.
This was compared to an empty U6 vector to ensure that the non-specific sequence had no effect on levels of target expression (data not shown).
In order to ascertain that the observed signals were not originating from the annealing of random non-specific sequences, specificity validation was conducted through a simple detection test using species- and gene-specific primers and by gene-specific microarray hybridization.
Fusion curves were performed to eliminate the possibility of quantifying non-specific sequences.
Powerful techniques have been developed to process the sequencing data and to isolate the binding sites from the background noise generated by non-specific sequences, such as statistical tests, use of controls, techniques for signal de-convolution or lag-analysis among others [ 23].
These RT reactions were carried out in presence of a non-specific primer of a sequence that is unrelated to the target RNA.
A non-specific random oligonucleotide sequence did not affect the binding of the SHOX2 GST to the BMP4 oligonucleotide.
A non-specific competitor ssDNA derived from the 15 nt of spacer DNA of the telomerase extension assay substrates with sequence 5′-CTAGACCTGTCATCA-3′ was added where indicated.
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