Collateral Damage Occurs When Using Photosensitizer Probes to Detect or Modulate Nucleic Acid Modifications

• Published in: Angewandte Chemie International Edition Vol. 61; no. 7; pp. e202110649 - n/a
• Main Authors: Fleming, Aaron M., Chabot, Michael B., Nguyen, Ngoc L. B., Burrows, Cynthia J.
• Format: Journal Article
• Language: English
• Published: Germany Wiley Subscription Services, Inc 07.02.2022
• Edition: International ed. in English
• Subjects: 5-Methylcytidine; Anthraquinone; Anthraquinones; Biological properties; DNA - analysis; DNA Damage; DNA probes; Dogs; Guanosine; N6-Methyladenosine; Nucleic Acid Conformation; Nucleic acids; Nucleosides; Nucleotides; Oxidants; Oxidation; Oxidizing agents; Photooxidation; Photosensitizing Agents - chemistry; Riboflavin; Riboflavin; 5-Methylcytidine; N6-Methyladenosine; Photooxidation; Guanosine
• ISSN: 1433-7851; 1521-3773
• DOI: 10.1002/anie.202110649

Nucleic acids are chemically modified to fine‐tune their properties for biological function. Chemical tools for selective tagging of base modifications enables new approaches; the photosensitizers riboflavin and anthraquinone were previously proposed to oxidize N6‐methyladenine (m6A) or 5‐methylcytosine (5mdC) selectively. Herein, riboflavin, anthraquinone, or Rose Bengal were allowed to react with the canonical nucleosides dA, dC, dG, and dT, and the modified bases 5mdC, m6A, 8‐oxoguanine (dOG), and 8‐oxoadenine (dOA) to rank their reactivities. The nucleoside studies reveal that dOG is the most reactive and that the native nucleoside dG is higher or similar in reactivity to 5mdC or m6A; competition in both single‐ and double‐stranded DNA of dG vs. 5mdC or 6mdA for oxidant confirmed that dG is favorably oxidized. Thus, photosensitizers are promiscuous nucleic acid oxidants with poor chemoselectivity that will negatively impact attempts at targeted oxidation of modified nucleotides in cells. Modifications of DNA/RNA impact their properties including susceptibility to oxidation. 5‐Methylcytosine and N6‐methyladenine were competed for photooxidation by riboflavin, anthraquinone, or Rose Bengal against dA, dG, dC, and dT in DNA. This confirmed dG is more oxidation prone, representing collateral damage during photosensitized probing for the base methylations.