Creating mass signatures for the detection of microRNA

Abstract

MicroRNAs (miRNAs) play a crucial role in the post-transcriptional regulation of gene expression, and have already been associated with 160+ diseases. With the small sizes of miRNAs (19–25 nt) and the increasing number of human miRNAs (>2000) being reported, the accurate detection of a specific miRNA has continued to be a challenging issue. In this report, a new concept for improving the accuracy of direct mass spectrometric (MS) measurements of miRNAs is introduced. The concept aims at creating a unique signature in the mass spectrum of miRNA. To achieve this goal, one way is to capture a specific miRNA by using a complementary DNA probe. The miRNA is then eluted and digested with a specific endonuclease. The digested miRNA fragments are directly measured by using MS. The multiple peaks that correspond to the digested miRNA fragments are collectively defined as a mass signature of the miRNA being analyzed. Since the peak pattern is dependent on the intrinsic property, i.e. RNA sequence, of a specific miRNA, it is referred to as an intrinsic mass signature. Alternatively, a unique mass signature can be created by incorporating one or more extra nucleotides into the 3′ end of miRNA and the extended miRNA is measured by using MS. The molecular mass of the extended miRNA, which is defined as an extended mass signature, is expected to be different from the other miRNAs within the same sample. In comparison to matching the measured molecular mass of an undigested or unextended miRNA molecule to the expected molecular mass, the two different approaches to create a unique mass signature can improve the accuracy on qualitative MS detection of a specific miRNA.