Labeling Small RNAs through Chemical Ligation at the 5′ Terminus: Enzyme-Free or Combined with Enzymatic 3′-Labeling

The discovery of small RNAs such as microRNAs (miRNAs), small interfering RNAs (siRNAs), or Piwi-associated RNAs (piRNAs) has led to new challenges in the selective detection of RNAs. Many noncoding RNAs act as post-translational regulators of gene expression and are involved in the regulation of cell proliferation or apoptosis, but are difficult to amplify, label, and detect. Standard microarray detection procedures involve pre-hybridization labeling or enzymatic 3'-labeling by polymerase-catalyzed extension. Dual labeling would improve the fidelity of detection, but no polymerases for 5'-extension are known. Here we report a novel labeling method for RNAs bearing natural 5'-phosphate groups, such as miRNAs, based on enzyme-free ligation of a biotin- or fluorophore-labeled oligonucleotide to the 5' termini. The method uses in situ activation of the natural 5'-phosphate groups in these RNAs and was optimized to give near-quantitative conversion in solution. With use of biotin- or fluorophore-bearing labeling strands, different miRNA sequences were detected on microarrays with little background fluorescence. In combination with an established method of enzymatic on-chip labeling at the 3' termini, highly selective detection of related miRNAs was achieved by dual recognition at both termini, even in the case of miRNAs differing in only one nucleotide.