Cyclopentane-modified FIT-PNAs as Highly Emissive and Selective RNA/DNA Sensors for Use in Clinical Diagnostics

This technology includes Cyclopentane-modified Peptide Nucleic Acids (cp-PNAs) which can be combined with (forced-intercalation) FIT-PNAs to create highly sensitive probes that detect the presence of complementary RNA sequences. We have studied the beneficial effects of incorporating cyclopentane groups into the backbone of PNAs, which leads to proper preorganization of the PNA backbone into the conformations needed to bind complementary RNA sequences. The cp-PNAs typically have improved thermodynamic stability for binding to complementary nucleic acids compared to unmodified PNAs. FIT-PNAs have a fluorescent group attached to one position in a PNA sequence so that the fluorescent group replaces one nucleobase in the sequence. When a FIT-PNA binds to complementary RNA, the fluorescence increases due to steric hindrance in the bound PNA. By combining cp-PNA and FIT-PNA strategies, more sensitive RNA detection is achieved. The PNAs that contain both cyclopentane groups and also a FIT group are called cpFIT-PNAs.