Synthesis and DNA-recognition behavior of a novel peptide ribonucleic acid with a serine backbone (oxa-PRNA)

(2S)-2-Fmoc-amino-3-(5′-deoxyuridinylamino)-3-oxopropyloxyacetic acid was synthesized from l-serine as a monomer for preparing the second-generation peptide ribonucleic acid with an oxa-peptide backbone (oxa-PRNA). The ether linkage was incorporated to improve the modest solubility in aqueous solution of the original PRNA with an iso-glutamine backbone, without harming the ability of the amino-uridine side chain to switch the anti/syn nucleobase orientation by adding borax. Indeed, CD spectral examinations revealed that the Fmoc-protected oxa-PRNA uridine monomer (Fmoc-oxa-PRNA(U)), synthesized in three steps, switched the nucleobase orientation from anti to syn in phosphate buffer upon addition of borax. Homo-12mers of oxa-PRNA(U) with and without Arg end caps were prepared in moderate yields by the Fmoc solid-phase synthesis. Both of the N- and C-terminus-capped oxa-PRNA(U) 12mers thus synthesized were shown to hybridize with the complementary DNA 12mer (d(A12)) with stabilities comparable to that observed for the natural pair.