The ‘fully protected backbone’ approach as a versatile tool for a new solid-phase PNA synthesis strategy

Cu2+-controlled hybridization of peptide nucleic acids

We have prepared cyclic peptide nucleic acids (PNAs). These compounds do not bind complementary nucleic acids. One carboxylic ester group was introduced in the backbone of the cyclic PNAs. This group is cleaved in the presence of Cu(2+) or coordinatively unsaturated Cu(2+) complexes. The cleavage products are linear PNAs. In contrast to the cyclic PNAs, they are efficient nucleic acid binders. The rate of formation of the linear PNAs is proportional to the concentration of the cleaving agents. Therefore, one may apply highly sensitive methods of detection of linear PNAs for determination of Cu(2+) concentration. In particular, we have demonstrated that both fluorescent spectroscopy in combination with molecular beacons and MALDI-TOF mass spectrometry are suitable for the detection of Cu(2+). A range of related divalent metal ions and Eu(3+), Ln(3+), Pr(3+), Ce(3+), and Zr(4+) do not interfere with Cu(2+) detection.

A convenient route to N-[2-(Fmoc)aminoethyl]glycine esters and PNA oligomerization using a Bis-N-Boc nucleobase protecting group strategy

A simple and practical synthesis of the benzyl, allyl, and 4-nitrobenzyl esters of N-[2-(Fmoc)aminoethyl]glycine is described starting from the known N-(2-aminoethyl)glycine. These esters are stored as stable hydrochloride salts and were used in the synthesis of peptide nucleic acid monomers possessing bis-N-Boc-protected nucleobase moieties on the exocyclic amino groups of ethyl cytosin-1-ylacetate, ethyl adenin-9-ylacetate and ethyl (O(6)-benzylguanin-9-yl)acetate. Upon ester hydrolysis, the corresponding nucleobase acetic acids were coupled to N-[2-(Fmoc)aminoethyl]glycine benzyl ester or to N-[2-(Fmoc)aminoethyl]glycine allyl ester in order to retain the O(6) benzyl ether protecting group of guanine. The Fmoc/bis-N-Boc-protected monomers were successfully used in the Fmoc-mediated solid-phase peptide synthesis of mixed sequence 10-mer PNA oligomers and are shown to be a viable alternative to the currently most widely used Fmoc/Bhoc-protected peptide nucleic acid monomers.