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miRNA-mRNA seed interaction positions (2 12 position) can be represented either as (i) less than two G U wobbles, (ii) two mismatches and one G U wobble, (iii) only three mismatches and no G U wobble, with or without mismatch/gap/G U wobble at the 3' end of the miRNA target interaction.
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It has been determined that the study of nonlinear visco-elastic and plastic strain seed interactions and the damage and crack growth in such seeds can be significantly improved through computer simulations using an explicit FEM algorithm.
Interestingly, earthworm plant seed interactions vary with plant species and are driven by seed size, shape and surface structure [42].
Notably, noncanonical seed interactions were ∼1.7-fold more common than perfect base pairing.
Moreover, seed interactions are generally accompanied by specific, nonseed base pairing.
The results further suggested that the 3′ motif might act cooperatively with seed interactions.
Although seed-mediated interactions constitute the largest class in our data, only around 37% of seed interactions involve uninterrupted Watson-Crick base pairing.
Interestingly, a recent paper mapping the human miRNA-mRNA interactome suggests that 60% of seed interactions are non-canonical.
The recently published human AGO2 crystal structure (Elkayam et al., 2012) does not exclude the possibility of noncanonical seed interactions.
This discrepancy may be due to differences in the reliance on miRNA seed interactions to identify targets.
However, seed interactions alone are found in only a relatively small fraction of identified targets (class I, 19%).
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