Universal linkers for signal amplification in auto-ligating probes

We reported recently oligonucleotide ligation methods for detection of DNAs and RNAs in solution and in cellular imaging. In previous systems, ligated full-length oligonucleotide products have almost native DNA structure and bind tightly with target strand, which limits the resulting signals to one per target. When small amounts of RNAs are targeted, signal amplification becomes very important issue. Here, we report on a new universal linker to destabilize ligated products in template-dependent auto-ligation, which accelerates the dissociation of ligated product from target and allows as much as 92-fold amplification of signals in DNA and RNA detection without enzymes, reagents, or thermal cycling. This signal amplification is shown in solution experiments and in solid supported assays.