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Among them, miRU [ 17] is a web server for plant miRNA target prediction utilizing the concepts of nearly perfect binding between a miRNA and its targets.
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These events are possible because the sequences that mediate binding between an miRNA and mRNA are short and thus recognizable by many miRNAs [ 39].
Computational algorithms for target identification (Table 2), mainly based on the free binding energy between a miRNA and a putative target mRNA sequence, are by definition prediction tools, which need an experimental validation.
In that regard, chemically modified oligonucleotides that would specifically disrupt the binding between the miRNA and a single mRNA might be good therapeutic candidates.
It is likely that some special characteristics exist for binding between human miRNA and viral RNA.
This indicates that the binding between human miRNA and viral RNAs may be much tighter than that between human miRNA and human mRNA.
If there is perfect binding between the miRNA and target, the mRNA target is cleaved by the endonuclease Ago2, possibly in RNA processing bodies (P-bodies) [ 28, 29].
Indeed, miRNA target prediction databases employing algorithms based upon complementary binding between the miRNA seed region and the miRNA recognition elements within target mRNA 3' UTR identify multiple targets for the miRNAs potentially involved in inflammatory responses.
At present, miRNAs are believed to either repress mRNA translation or reduce mRNA stability following imperfect binding between the miRNA and the miRNA-recognition elements (MRE) within the 3′ untranslated region (UTR) of target genes.
Three of these classes (I III) featured binding between the miRNA seed and the target but differed in the presence and positioning of additional base-paired nucleotides within the miRNA.
Our study provided an interesting hypothesis concerning the miRNA-based antiviral defense mechanism against influenza virus in human, i.e., the binding between human miRNA and viral RNAs may not result in gene silencing but rather may block the viral RNA replication.
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