cpFIT-PNAs as molecular probes for RNA diagnostics

PNAs (peptide nucleic acid) are synthetic DNA analogs that have been used for therapeutic (antisense) and diagnostic purposes. One diagnostic approach relies on the introduction of a cyanine dye replacing a natural base in the PNA sequence (FIT-PNA: forced intercalation-PNA). Such a surrogate base, when introduced into FIT-PNA, fluoresces only upon FIT-PNA hybridization to the complementary target DNA/RNA.

We have previously designed FIT-PNAs to detect several RNA cancer biomarkers. For example, a lncRNA (long noncoding RNA) termed CCAT1, has been shown as an oncogenic lncRNA over-expressed in a variety of cancers. To these FIT-PNAs we have introduced the bis-quinoline (BisQ) cyanine dye that emits light in the red region (605-610 nm) of the visible spectrum. Most strikingly, spraying fresh human tissue taken from patients during cytoreductive surgery for either peritoneal metastasis of colon cancer or ovarian tumor tissue from OC patients with an aqueous solution of CCAT1 FIT-PNA results in bright fluorescence in a matter of minutes. In fresh healthy tissue (from bariatric surgeries), no appreciable fluorescence is detected. We have now introduced cyclopentane (cp) modified PNA monomers adjacent to BisQ and shown a dramatic increase in brightness of the newly designed cpFIT-PNA. Our current efforts are in the design of cpFIT-PNAs for improved diagnostic of RNA in cancer.