A Novel Strategy for Active Control of DNA Recognition by External Stimulates -Peptide Ribonucleic Acids (PRNA)-

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In the development of nucleic acid models for the next generation of functional materials, if the recognition control and/or reversible recognition control of nucleic acids by a novel nucleic acid model could be achieved, the dynamic expression/suppression of functions as to external stimulates and/or factor could be materialized. Thus, the subject of this work was dynamic and reversible control of nucleic acid recognition by an external factor and/or stimulate, which cannot be realized by the conventional nucleic acid model compounds based on a structure of nucleic acids. In this work, focusing on the importance of reversible DNA recognition dependent, the author found the novel strategy for reversible DNA recognition control by change of pH system with peptide ribonucleic acids (PRNAs). The author established the synthetic routes to a series of PRNA monomers, carrying adenine, cytosine, hypoxanthine, and uracil nucleobases as recognition sites. This enabled us to fully expand the ran … More ge of available PRNA monomers. The author further demonstrated that the newly synthesized Fmoc-protected PRNA monomers are compatible with the standard solid-phase peptide synthesis protocol, and oligomeric PRNAs with purine-pyrimidine mixed sequences can be prepared. It was demonstrated that the orientation switching of pyrimidine-purine mixed sequence PRNAs. In this and preceding studies, we have proposed a new methodology and effective tools for controlling DNA/RNA recognition through the use of an external agent. This-strategy employs novel nucleic acid analogues, i.e. □-peptide ribonucleic acids (^-PRNAs), as the recognition moiety which has a built-in switch triggered by an external factor. In the cases of not only homo-pyrimidine PRNAs but also pyrimidine-purine mixed sequenced PRNAs, the formation of a borate ester of the ribose's cis-2',3'-diol and the simultaneous hydrogen-bonding interaction between the 5'-amide proton and the 2-carbonyl oxygen act as the external and internal switching devices. The results obtained in these studies are encouraging, demonstrating that ^-PRNA form stable hybrid complexes with the complementary oligonucleotides, which are readily dissociated upon addition of borax or boric acid. Moreover, it was investigated that the chirality effect of peptide backbone upon the structure and DNA recognition behavior of PRNA. The orientation of PRNA monomers and oligomers tethered to L-and D-0-glutamic acid backbone could readily be switched from anti to syn by adding borax as an external controlling factor. The cooperative orientation switching and borate formation were enhanced by oligomerization. Furthermore, D-, L-PRNA oligomers were induced different higher-order structure each other. Certainly, D-, L-PRNA were determined right-handed and left-handed coiled structure respectively. The complex of right-handed coiled D-PRNA with complementary DNA was more stable than that of L-PRNA with DNA to indicate that the complexation, which was formed between same right-handed coiled structures of D-PRNA and DNA, was preferable. Then, the on-off switching of DNA recognition with pyrimidine-purine mixed sequence PRNA was demonstrated. PRNA with mixed sequence formed more stable complex with complementary DNA than natural DNA. Moreover, it was revealed that the on-off switching of the DNA recognition of PRNA could be materialized by the synergistic puckering change through borate formation of 2',3'-diol and base orientation switching from anti to syn through the hydrogen bonding formation between 5'-amide proton and carbonyl oxygen at 2 position of pyrimidine nucleoside. Furthermore, nucleic acid models were improved the recognition selectivity as well as its recognition ability. PRNA formed a more stable complex with complementary DNA and binding of PRNA with complementary DNA was sequence specific.This study was the first work for reversible nucleic acid recognition in the rage of physiological condition. These results will demonstrate a strategy for designing the antisense molecule for the next generation, which reacts by environmental stimulation in cell and/or nucleus. Less