Open AccessChanges of C≡C Triple Bond Vibration that Disclosed Non-Canonical Cytosine Protonation in i-Motif-Forming Oligodeoxynucleotides
Author(s) -
Ryota Itaya,
Wakana Idei,
Takashi Nakamura,
Tatsuya Nishihara,
Ryohsuke Kurihara,
Akimitsu Okamoto,
Kazuhito Tanabe
Publication year - 2021
Publication title -
acs omega
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.779
H-Index - 40
ISSN - 2470-1343
DOI - 10.1021/acsomega.1c04074
Subject(s) - protonation , cytosine , chemistry , dna , acetylene , raman spectroscopy , stereochemistry , nucleobase , photochemistry , crystallography , biophysics , biochemistry , biology , organic chemistry , physics , ion , optics
Non-canonical protonation at cytosine (C) in DNA is related to a formation of second order DNA structures such as i-motif, which has a role in gene regulation. Although the detailed structural information is indispensable for comprehension of their functions in cells, the protonation status of C in complicated environments is still elusive. To provide a reporter system of non-canonical protonation, we focused on the molecular vibration that could be monitored using the Raman spectroscopy. We prepared a cytosine derivative ( P C) with an acetylene unit as a Raman tag, and found that the Raman signal of acetylene in P C in oligodeoxynucleotides (ODNs) changed due to protonation at the cytosine ring which shortened an acetylene bond. The signal change in i-motif-forming ODNs was also observed in crowded environments with polyethylene glycol, evidencing protonation in i-motif DNA in complicated environments. This system would be one of tracking tools for protonation in DNA structures.