pH-Dependent Switching of Base Pairs Using Artificial Nucleobases with Carboxyl Groups

Abstract

In this study, we report the synthesis of modified oligonucleotides consisting of benzoic acid or isophthalic acid residues as new nucleobases. As evaluated by UV thermal denaturation analysis at different pH conditions (5.0, 6.0, 7.0, and 8.0), these modified oligonucleotides exhibited pH-dependent recognition of natural nucleobases and one is first found to be capable of base pair switching in response to a pH change. The isophthalic acid residue incorporated into the oligonucleotide on a d-threoninol backbone could preferentially bind with adenine but with guanine in response to a change in the pH conditions from pH 5 to pH 7 (or 8) without significant difference in duplex stability. These findings would be valuable for further developing pH-responsive DNA-based molecular devices.

8-Pyrenylvinyl Adenine Controls Reversible Duplex Formation between Serinol Nucleic Acid and RNA by [2 + 2] Photocycloaddition

“…A useful function is stimulus-responsivity in which a function is activated in response to an external stimulus such as pH, heat, or metal ion binding. − Among potential external stimuli, light is an ideal trigger because spatiotemporal control is possible without contaminating the solution. − For reversible photoregulation, photochromic molecules that isomerize upon irradiation have been developed. − Wagenknecht and Jaschke designed photoresponsive nucleobases involving diarylethene. , Guanine analogues carrying arylvinyl moieties synthesized by Ogasawara and coworkers have also been used to reversibly photoregulate DNA duplex or G-quadruplex formation. , Our group has developed photoresponsive DNA and RNA by introducing azobenzene via d -threoninol or other acyclic diols into oligonucleotides . Despite the great applicability of XNAs, photoregulation of the XNA duplex has not yet been achieved.…”