FTIR study of CPD photolyase with substrate in single strand DNA

• Wijaya I M. Mahaputra

  Department of Frontier Materials, Nagoya Institute of Technology

• Iwata Tatsuya

  Department of Frontier Materials, Nagoya Institute of Technology OptoBioTechnology Research Center, Nagoya Institute of Technology

• Yamamoto Junpei

  Graduate School of Engineering Science, Osaka University

• Hitomi Kenichi

  Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute

• Iwai Shigenori

  Graduate School of Engineering Science, Osaka University

• Getzoff Elizabeth D.

  Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute

• Kandori Hideki

  Department of Frontier Materials, Nagoya Institute of Technology OptoBioTechnology Research Center, Nagoya Institute of Technology

Abstract

Photolyases (PHRs) utilize near UV/blue light to specifically repair the major photoproducts (PPs) of UV-induced damaged DNA. The cyclobutane pyrimidine dimer (CPD)-PHR binds flavin adenine dinucleotide (FAD) as a cofactor and repairs CPD lesions in double-stranded DNA. To understand the activation and repair mechanism of CPD-PHR, we applied light-induced difference Fourier transform infrared (FTIR) spectroscopy to CPD-PHR, whose signals were identified by use of isotope-labeling. To further investigate the enzymatic function, here we study the activation and repair mechanism of CPD-PHR with the substrate in single strand DNA, and the obtained FTIR spectra are compared with those in double-stranded DNA, the natural substrate. The difference spectra of photoactivation, the fully-reduced (FADH^–) minus semiquinone (FADH^•) spectra, are almost identical in the presence of single strand and double-stranded DNA, except for slight spectral modification in the amide-I region. On the other hand, the difference spectra of photorepair were highly substrate dependent. Strong bands of the C=O stretch (1,720–1,690 cm^–1) and phosphate vibrations (1,090–1,060 cm^–1) of double-stranded DNA may have disappeared in the case of single strand DNA. However, an isotope-labeled enzyme study revealed that spectral features upon DNA repair are similar between both substrates, and the main reason for the apparent spectral difference originates from structural flexibility of DNA after repair.

Journal

• BIOPHYSICS

  BIOPHYSICS 11 (0), 39-45, 2015

  The Biophysical Society of Japan

Keywords

• DNA repair
• light-induced difference FTIR spectra
• FAD
• hydrogen bond

Details

• CRID: 1390282680198730240
• NII Article ID: 130004940808
• DOI: 10.2142/biophysics.11.39
• ISSN: 13492942
• Web Site: https://www.jstage.jst.go.jp/article/biophysics/11/0/11_39/_pdf
• Text Lang: en
• Data Source:
  • JaLC
  • Crossref
  • CiNii Articles
  • KAKEN
• Abstract License Flag: Disallowed