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Highly Specific Gene Silencing by Artificial miRNAs in Rice

Figure 4

Predicted amiRNA-mRNA interactions.

The program ‘RNAup’ [33] was used to assess the thermodynamics of RNA-RNA binding considering 80 bp surrounding the target site at 23°C. The predicted cleavage sites (between positions 10 and 11 of the miRNA) are highlighted in grey. ‘RNAup’ calculates the effective free hybridization energy (ΔG) as sum of the energies necessary to open the target site in the target mRNA (ΔGu_l), the internal folding of the amiRNA (ΔGu_s), and the energy gained from hybridization of amiRNA and target mRNA (ΔGint).

Figure 4