Synthesis of nonpolar peptide nucleic acid monomers containing fluoroaromatics

A general strategy for the synthesis of nonpolar peptide nucleic acid monomers containing fluoroaromatics (F-PNA) is described. These compounds have been designed as hybrid analogues of the difluorotoluene nucleoside, F (1) with PNA. Fluorophenylacetic acid derivatives 9 were coupled to the Boc-protected pseudopeptide backbone 8 by a standard peptide coupling reaction using DhbtOH and DCC in the presence of triethylamine to afford the doubly protected F-PNA monomers 14 in moderate to good yields. The ethyl esters 14a, 14c and 14e underwent hydrolytic cleavage under basic conditions to generate N-protected F-PNA monomers 15 in good yields. The tert-butyl esters 14b, 14d were treated with TFA in dichloromethane to produce the free F-PNA monomers 16 in good to excellent yields. The β-F-PNA monomers designed based on the structure of 2′,5′-linked isoDNA were also synthesized in a similar fashion to the preparation of F-PNA monomers in moderate to good yields as both N-protected and free monomers.