Computer Analysis of miRNA-mRNA Duplexes and Its Application to Predicting Possible Target mRNAS of Arabidopsis

Abstract

Prediction of possible targets for microRNAs (miRNAs) in complete genomic sequences is a difficult task due to potential bulges and loops occurring in miRNA-mRNA duplexes. Thermodynamic calculations of the free energy may assist in solving the problem of searching for such potential duplexes. The program GArna-duplex allows the duplexes of various degrees of complementarity to be detected and the free energy of stable duplexes to be assessed quantitatively. Analysis of several cases of formation of miRNAmRNA duplexes experimentally detected so far demonstrated that (1) GArnaduplex was capable of detecting both the duplexes able to guide mRNA cleavage and those inhibiting translation and (2) the free energy of duplex formation correlated with their function. Search for potential targets for 24 Arabidopsis miRNAs demonstrated that the miRNAs differed in both the number of potential duplexes they can form and the least free energy of binding with transcripts. Target mRNAs forming most stable duplexes with the miRNAs in question were predicted.