3′ RNA ligase mediated rapid amplification of cDNA ends for validating viroid induced cleavage at the 3′ extremity of the host mRNA

5′ RNA ligase-mediated rapid amplification of cDNA ends (5′ RLM-RACE) is a widely-accepted method for the validation of direct cleavage of a target gene by a microRNA (miRNA) and viroid-derived small RNA (vd-sRNA). However, this method cannot be used if cleavage takes place in the 3′ extremity of the target RNA, as this gives insufficient sequence length to design nested PCR primers for 5′ RLM RACE. To overcome this hurdle, we have developed 3′ RNA ligase-mediated rapid amplification of cDNA ends (3′ RLM RACE). In this method, an oligonucleotide adapter having 5′ adenylated and 3′ blocked is ligated to the 3′ end of the cleaved RNA followed by PCR amplification using gene specific primers. In other words, in 3′ RLM RACE, 3′ end is mapped using 5′ fragment instead of small 3′ fragment. The method developed here was verified by examining the bioinformatics predicted and parallel analysis of RNA ends (PARE) proved cleavage sites of chloride channel protein CLC-b-like mRNA in Potato spindle tuber viroid infected tomato plants. The 3′ RLM RACE developed in this study has the potential to validate the miRNA and vd-sRNA mediated cleavage of mRNAs at its 3′ untranslated region (3′ UTR).