Spectroscopic Investigation of Na+-Dependent Conformational Changes of a Cyclobutane Pyrimidine Dimer-Repairing Deoxyribozyme

Tatsuya Iwata; Yuhi Kurahashi; I Made Mahaputra Wijaya; Hideki Kandori

doi:10.1021/acsomega.3c05083

Spectroscopic Investigation of Na⁺-Dependent Conformational Changes of a Cyclobutane Pyrimidine Dimer-Repairing Deoxyribozyme

ACS Omega. 2023 Sep 29;8(40):37274-37281. doi: 10.1021/acsomega.3c05083. eCollection 2023 Oct 10.

Authors

Tatsuya Iwata¹, Yuhi Kurahashi², I Made Mahaputra Wijaya², Hideki Kandori^{2

3}

Affiliations

¹ Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan.
² Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
³ OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.

Abstract

UV1C is an enzymatically active DNA sequence (deoxyribozyme, DNAzyme) that functions as a cyclobutane pyrimidine dimer (CPD) photolyase. UV1C forms parallel guanine quadruplexes (G-quadruplexes) with a DNA substrate in the presence of 240 mM Na⁺, the structure of which is important for the enzymatic activity. To investigate the repair mechanism of CPD by UV1C, we designed light-induced Fourier transform infrared (FTIR) spectroscopy. Prior to FTIR measurements, circular dichroism (CD) spectroscopy was conducted to determine the Na⁺ concentration at which the most G-quadruplexes were formed. We found that UV1C also forms a hybrid G-quadruplex structure at over 500 mM Na⁺. By assuming a concentration equilibrium between G-quadruplexes and Na⁺, 1.3 and 1.8 Na⁺ were found to bind to parallel and hybrid G-quadruplexes, respectively. The hybrid G-quadruplex form of UV1C was also suggested to exhibit photolyase activity. Light-induced FTIR spectra recorded upon the photorepair of CPD by UV1C were compared for parallel G-quadruplex-rich and hybrid G-quadruplex-rich samples. Spectral variations were indicative of structural differences in parallel and hybrid G-quadruplexes before and after CPD cleavage. Differences were also observed when compared to the CPD repair spectrum by CPD photolyase. The spectral differences during CPD repair by either protein or DNAzyme suggest the local environment of the substrates, the surrounding protein, or the aqueous solution.