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There was perfect complementarity between the seed region (the core sequence that encompasses the first 2 8 bases of the mature miRNA) and the putative target sequence.
The perfect complementarity between the mir122 binding sites we have inserted and microRNA mir122 should result in substantial E1A mRNA cleavage through a mechanism similar to RNAi.
We observed that there is perfect complementarity between miR-27a and the 3'UTR of FADD over the seed region (2 9 bases of the mature miRNA).
The most stable combinations of miRNA and the target gene or MIRNA genes were normalized to percent minimum free energy which works well for plant miRNAs because plants possess near perfect complementarity between miRNA and target genes [65], [115].
The miRNA-target recognition is mainly due to the perfect complementarity between a short 7 8 nt stretch at 5' end of the miRNA molecule (miRNA seed) and the corresponding stretch on the 3'UTR of the target gene (seed match).
These results are consistent with previous studies which demonstrated that the miRNA-target RNA interaction is restricted to the 5'-end of the miRNA sequence and that the perfect complementarity between the miRNA 2 8 bases and the targeted RNA is essential for target recognition [30] [33].
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Such studies indicate that the criteria of perfect/near perfect complementarities between miRNA/mRNAs need to be relaxed and additional features should be included for accurate target prediction.
Perfect or nearly perfect complementarities between miRNAs and their 3'UTRs induce mRNA cleavage by the RNA-induced silencing complex (RISC), whereas imperfect base matching induces translational silencing through various molecular mechanisms [ 7], namely inhibition of translation initiation and activation of mRNA storage in P-bodies and/or stress granules [ 1].
In the RISC complex, miRNAs bind to mRNA and inhibit gene expression through perfect or near-perfect complementarity between the miRNA and the mRNA [ 18].
Although, initial studies in Arabidopsis proposed near-perfect complementarity between the smRNAs and their targets as a general rule, deviations from this rule were soon evident, indicating that pairing at some sites may be less perfect than others [ 1, 24, 25].
These 13 ISs (IS Kra2, 4, 5 and 6; IS Casp2 and 3, IS Lfe1 and 2; IS Hhy1; IS Acce1; IS Tvi1; IS Uncu20; and IS Desp4) are characterized by an almost perfect complementarity (83 100%) between the right and left IRs.
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