Synthesis and Nucleic Acids Binding Properties of Diastereomeric Aminoethylprolyl Peptide Nucleic Acids (aepPNA)

Abstract

A general synthetic method for Fmoc-protected monomers of all four diastereomeric aminoethyl peptide nucleic acid (aepPNA) has been developed. The key reaction is the coupling of nucleobase-modified proline derivatives and Fmoc-protected aminoacetaldehyde by reductive alkylation. Oligomerization of the aepPNAs up to 10mer was achieved by Fmoc-solid phase peptide synthesis methodology. Preliminary binding studies of these aepPNA oligomers with nucleic acids suggested that the “cis-” homothymine aepPNA decamers with (2′R,4′R) and (2′S,4′S) configurations can bind, albeit with slow kinetics, to their complementary RNA [poly(adenylic acid)] but not to the complementary DNA [poly(deoxyadenylic acid)]. On the other hand, the trans homothymine aepPNA decamers with (2′R,4′S) and (2′S,4′R) configurations failed to form stable hybrid with poly(adenylic acid) and poly(deoxyadenylic acid). No hybrid formation could be observed between a mixed-base (2′R,4′R)-aepPNA decamer with DNA and RNA in both antiparallel and parallel orientations.

Keywords:

• PNA
• RNA
• hybridization
• triplex forming oligonucleotides

Acknowledgments

Financial support for this work comes from the Thailand Research Fund (RTA5280002) and Chulalongkorn University (Rachadapisek Sompoj Endowment to OSRU).

Notes

^a N-Ac, C-LysNH₂ capped.

^bMALDI-TOF, α-cyano-4-hydroxy cinnamic acid (CCA) matrix.

^a T _m were measured at [PNA] = [DNA] = 1 μM, 10 mM sodium phosphate pH 7.0, heating rate 1°C/min.