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. 2014 Jul 23;42(15):10050–10060. doi: 10.1093/nar/gku662

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© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 7. — Possible thermodynamic control of miRNA-mediated gene-silencing activity and correlations between Tm values of 7-bp seed-target duplexes and differential fold-changes of expression levels of target transcripts determined by microarray experiments or relative luciferase activities determined by reporter assays. (A) The miRNA with low miTm_1–5 value promotes miRNA unwinding into a single-stranded RNA in the RISC, and that with high Tm_2–8 value promotes stable base-pairing between miRNA seed region and target mRNA. Thus, the efficacies of miRNA-mediated silencing are determined by the combined thermodynamic parameters that might reflect their unwinding properties (miTm_1–5) in addition to their base-pairing stabilities in the seed-target duplex (Tm_2–8) shown as a formula, miScore = Tm_2–8 − 0.5 x miTm_1–5. (B) The duplex structures formed between 7-mer seed sequence of miR-376a-3p containing adenosine, inosine, or guanosine in the possible editing site and target mRNA sequence with uridine or cytidine at the opposite site of editing position, and the measured Tm values of these 7-bp duplexes. The Tm value of the duplex formed between AGAUACU and UCCAUGA could not be measured, probably due to fairly unstable base-pairing and was shown as not determined (N.D). (C) The correlations between the 7-bp Tm values and fold-changes in the expression levels of target mRNAs containing seed complementary sequences in their 3′-UTRs (red), or relative luciferase activities at 50 nM of miRNA duplex (blue). The correlation coefficient (R) between Tm values and differential fold-changes was 0.82, and R between Tm values and relative luciferase activities was -0.91.