Compounds and methods for rna sensing

Abstract

The sequence-specific fluorescent detection of RNA using a tricyclic cytidine analogue such as DEAtC included as a surrogate for natural cytidine in DNA probe strands and that reports directly on Watson-Crick base pairing. The DEAtC-containing DNA oligonucleotide probes exhibit an average 8-fold increase in fluorescent intensity when hybridized to matched-RNA with DEAtC base paired with G, and no fluorescence turn-on when DEAtC is base paired with A. Time resolved fluorescence measurements in buffered H2O vs D2O show that DEAtC's fluorescence turn-on is primarily the result of protection against excited-state proton transfer in the matched hybrid duplex. Stern-Volmer quenching experiments and computational studies indicate that the combination of greater π stacking and narrower grooves in the A-form DNA-RNA heteroduplex provides additional shielding and favorable electronic interactions between bases, explaining why DEAtC's fluorescence turn-on response to an RNA target is about 3-fold greater than for DNA targets.

Dependencies are inferred from the claim text.