Nucleic Acid-Binding Fluorochromes and Nanoparticles: Structural Aspects of Binding Affinity and Fluorescence Intensity

Abstract

This study was conducted to determine the relationship between dye structure, particularly the structural charge and flexibility, and binding affinity. We also investigated the effect of multivalency on the maximum fluorescence intensity by conjugating varying numbers of monovalent fluorochromes on nanoparticles. Fluorochrome-conjugated nanoparticles were synthesized by conjugating N-hydroxysuccinimide ester of quinolinium,4-[(3-methyl-2(3H)-benzothiazolylidene)methyl]- 1-[3-(trimethylammonio)propyl]-,iodide (TO-PRO 1 NHS ester) into aminated nanoparticles. The half maximum effective concentration (EC50) of DNA-binding fluorochromes and fluorochrome-conjugated nanoparticles for double- stranded nucleic acid (dsDNA) was investigated by fluorescence. Two important factors regulating the binding characteristics of fluorochromes were studied: the number of positive charges and the structural flexibility. Positive charge enhancement of binding affinity was observed in various systems. TO-PRO 1, which has two positive charges, showed higher binding affinity than TO. Rigid structured dyes, propidium iodide and 4′,6-diamidino-2-phenylindole (DAPI), exhibited significantly lower maximum fluorescence than TO-PRO 1, even though they both have two positive charges. The dye with three positive charges, SYTOX Green, showed higher binding affinity than TO-PRO 1. TO-PRO 1 dimer (TO-TO), which has four positive charges, showed the highest binding affinity to DNA. Flexible dyes exhibited more than 1000-fold higher fluorescence upon binding to dsDNA. The multivalency of the fluorochromes on the nanoparticles revealed that a shorter distance between fluorochromes was related to higher maximum fluorescence intensity. The fluorescence intensity of multivalent fluorochromes was substantially dependent on the distance between the monovalent sites.