New Fluorescent Analogs of Nucleotides Based on 3-Hydroxychromone for Recording Conformational Changes of DNA

Abstract

It has recently been found that derivatives of nucleotides containing а 3-hydroxychromone fluorescent dye can be used as sensitive markers of conformational changes of DNA. In this work, a comparative analysis of two fluorescent nucleotide derivatives—3-hydroxychromone a (3HC) and 3HC-modified uridine (FCU)—was performed during the study of protein–nucleic acid interactions for several human DNA repair enzymes, removing damaged nucleotides: DNA glycosylases AAG, OGG1, UNG2, and MBD4 and AP endonuclease APE1. The changes of fluorescence intensity significantly depended on the nature of neighbor nucleotides and may be opposite in direction for different cases. The FCU residue located in the complementary strand opposite to damaged nucleotide or in the same strand moved by few nucleotides, is very sensitive to processes induced by DNA glycosylases in the course of formation of enzyme–substrate complexes, which include local melting and bending of the DNA chain, as well as eversion of the damaged nucleotide from DNA double helix and insertion of amino acids of the active site into the void.