Cyclopentane-modified peptide nucleic acids (PNA): Synthesis and properties

ORGN 735

Mark A. Witschi, witschim@niddk.nih.gov and Daniel H. Appella. Laboratory of Bioorganic Chemistry, NIDDK, DHHS, National Institutes of Health, 9000 Rockville Pike, Bldg. 8 Rm. 1A 23, Bethesda, MD 20892
Peptide nucleic acids are nucleic acid analogues in which the sugar-phosphate backbone is replaced with an uncharged, achiral backbone. PNAs hybridizes to complementary DNA and RNA with high affinity and sequence specificity. These properties make PNA a promising molecule for DNA diagnostic applications. In unmodified PNAs, the aminoethylglycine backbone is flexible and, as a result, there is entropic loss associated with duplex formation. Restricting rotation about the C2-C3 bond could decrease entropic loss and favor hybridization. It has been shown that incorporation of trans-1,2-cyclopentane diamine into the PNA backbone increases the binding affinity and mismatch discrimination compared to unmodified PNAs. We report the preparation of modified PNA monomers containing the four natural nucleobases, as well as an pseudoisocytosine mimic, and their applications in PNA:DNA duplexes and triplexes.