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To further confirm that the observed apoptosis in our experiments was caused by specific downregulation of MMP-2 and not due to any off-target consequences, we supplemented cells with recombinant human MMP-2 (rhMMP-2).
A vital assumption in siRNA-mediated gene silencing is that knockdown of the target gene is exclusive, and without off-target consequences.
It can be envisaged how Hfq acts as a catalyst for such recognition in vivo, but the question naturally arises how sRNAs generally achieve precision, accuracy, and speed in producing their effects and avoid undesired off-target consequences.
More complete studies are needed to determine the role of MRJ-L in macrophages, as well as more directed therapeutic targeting to specific cells to avoid potentially devastating off-target consequences.
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This "rescue" experiment suggests that the enlargement of spine heads is a specific consequence of TRIM3 knockdown, and not an off-target effect of the shRNA.
Two different PINK1 siRNA pairs (PINK1 #1 and PINK1 #2) were used in all experiments in order to confirm that results are a direct consequence of PINK1 silencing, rather than an off-target effect.
No off-target effect including (major) metabolites.
The introduction of viral particles induces oxidative stress and can alter cellular antioxidant levels; this alteration of cellular protein levels [ 23, 24] may have unexpected redox-related consequences beyond potential off-target silencing, consequences that may substantially alter the redox capacity of the knockdown cells.
This type of systems level computational modeling has the potential to assess potential off-target effects, the consequences of pharmacologically active human metabolites, the effect of comedications, and the impact of well described genotypes.
This quantitative systems pharmacology approach is shown to be complementary to traditional animal models, with the potential to assess potential off-target effects, the consequences of pharmacologically active human metabolites, the effect of comedications, and the impact of a small number of well described genotypes.
However, these nucleases have also been shown to cut at off-target sites with mutagenic consequences.
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