Peptide ribonucleic acids (PRNA). 2. A novel strategy for active control of DNA recognition through berate ester formation

The effect of adding borax and boric acids on the nucleobase orientation an d recognition behavior of novel mono- and oligomeric peptide ribonucleic ac ids (PRNAs) has been investigated. The base orientation of 5'-amino-5'-deox yuridine and 5'-amino-5'-deoxycytidine was shown by CD and NOE difference s pectral studies to switch from anti to syn in berate buffer or upon additio n of borax. The origin of this phenomenon is elucidated to be the cooperati ve effect of the cyclic berate esterification of the sugar's cis-2',3'-diol and the hydrogen-bonding interaction between the sugar's 5'-amino proton a nd the base's 2-carbonyl oxygen. Because this new strategy for switching th e base orientation through the addition of berate is potentially applicable to the recognition control of nucleic acids if the sugar's 5'-proton and c is-2',3'-diol remain unmodified, we synthesized a series of PRNAs, in which the 5'-amino-5'-deoxypyrimidine ribonucleoside moiety was appended to a mo no- or oligo(gamma-L-glutamic acid) backbone through the 5'-amino group. Th e orientation switching through the addition of berate was also confirmed w ith the monomeric model, and the switching efficiency was enhanced for olig omeric gamma-PRNA. Finally, it was unambiguously demonstrated that the gamm a-PRNA 8-mer with an isopoly-(L-glutamic acid) backbone can form a tight co mplex with DNA, and further, the recognition of DNA with gamma-PRNA 8-mer i s controlled by the berate added as an external factor.