Peptide Nucleic Acid Conjugates of Quinone Methide Precursors Alkylate Ribonucleic Acid after Activation with Light

• Published in: Bioconjugate chemistry 2020-03, Vol.31 (3), p.639-645
• Main Authors: Hornung, Jan-Erik, Hellwig, Nils, Göbel, Michael W
• Format: Article
• Language: English
• Subjects: Alkylation; Base Sequence; Crosslinking; Indolequinones - chemistry; Irradiation; Nucleic acids; Nucleotides; Peptide nucleic acids; Peptide Nucleic Acids - chemistry; Peptide Nucleic Acids - genetics; Peptides; Photochemical Processes; Precursors; Purines - chemistry; Quinones; Radiation; Reaction kinetics; Ribonucleic acid; RNA; RNA - chemistry; RNA - genetics
• ISSN: 1043-1802; 1520-4812
• DOI: 10.1021/acs.bioconjchem.9b00796

Quinone methide precursors 2 and 3 were protected with a photoreactive 2-nitrobenzyl group and conjugated to peptide nucleic acids (PNA) using a Huisgen click reaction. After brief irradiation at 365 nm, cross-linking with complementary RNA strands started and was analyzed with an ALFexpress sequencer. When this method was used, the gel temperature had a major influence on apparent rates. Quinone methides are known to form transient as well as stable bonds with nucleotides. Although both were detected at 25 °C, analysis at 57 °C only recorded the stable types of cross-links, suggesting much slower alkylation kinetics. Linker 11 allowed us to attach quinone methides to internal positions of the PNA/RNA duplex and to capture a model of miR-20a with good efficiency.