The effect of adding borax and boric acids on the nucleobase orientation and recognition behavior of novel mono-and oligomeric peptide ribonucleic acids (PRNAs) has been investigated. The base orientation of 5′-amino-5′-deoxyuridine and 5′-amino-5′-deoxycytidine was shown by CD and NOE difference spectral studies to switch from anti to syn in borate buffer or upon addition of borax. The origin of this phenomenon is elucidated to be the cooperative effect of the cyclic borate esterification of the sugar's cis-2′,3′-diol and the hydrogen-bonding interaction between the sugar's 5′-amino proton and the base's 2-carbonyl oxygen. Because this new strategy for switching the base orientation through the addition of borate is potentially applicable to the recognition control of nucleic acids if the sugar's 5′-proton and cis-2′,3′-diol remain unmodified, we synthesized a series of PRNAs, in which the 5′-amino-5′-deoxypyrimidine ribonucleoside moiety was appended to a mono-or oligo(γ-L-glutamic acid) backbone through the 5′-amino group. The orientation switching through the addition of borate was also confirmed with the monomeric model, and the switching efficiency was enhanced for oligomeric γ-PRNA. Finally, it was unambiguously demonstrated that the γ-PRNA 8-mer with an isopoly-(L-glutamic acid) backbone can form a tight complex with DNA, and further, the recognition of DNA with γ-PRNA 8-mer is controlled by the borate added as an external factor.

We have demonstrated for the first time that the syn-anti orientation of 5′-amino-5′-deoxyuridine (1b) can readily be switched by adding borate as an extermal controlling factor. In borate added phosphate buffer, the syn/anti ratio of 1b dramatically increased with increasing borate concentration. This unique syn preference is most probably driven by the cooperative action of cyclic esterification of the 1b’s 2′,3′-cis-diol with borate and of hydrogen-bonding formation between 2-carbonyl oxygen and 5′-amino proton.

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