Effect of Fluorescent Labels on DNA Affinity for Gold Nanoparticles.

Anna V Epanchintseva,Elena I Ryabchikova,Inna A Pyshnaya,Ekaterina A Gorbunova,Dmitrii V Pyshnyi

doi:10.3390/nano11051178

Abstract

Fluorophore (FD) labeling is widely used for detection and quantification of various compounds bound to nanocarriers. The systems, composed of gold nanoparticles (GNPs) and oligonucleotides (ONs) labeled with FDs, have wide applications. Our work was aimed at a systemic study of how FD structure (in composition of ON-FDs) influenced the efficiency of their non-covalent associates’ formation with GNPs (ON-FD/GNPs). We examined ONs of different length and nucleotide composition, and corresponding ON-FDs (FDs from a series of xanthene, polymethine dyes; dyes based on polycyclic aromatic hydrocarbons). Methods: fluorometry, dynamic light scattering, high performance liquid chromatography, gel electrophoresis, molecular modeling and methods of thermodynamic and statistical analysis. We observed significant, differing several times, changes in surface density and Langmuir constant values of ON-FDs vs. ONs, evidence for the critical significance of FD nature for binding of ON-FDs with GNPs. Surface density of ON-FD/GNPs; hydrophobicity and total charge of ON or ON-FD; and charge and surface area of FDs were revealed as key factors determining affinity (Langmuir constant) of ON or ON-FDs for GNPs. These factors compose a specific set, which makes possible the highly reliable prediction of efficiency of ONs and ON-FDs binding with GNPs. The principal possibility of creating an algorithm for predictive calculation of efficiency of ONs and GNPs interaction was demonstrated. We proposed a hypothetical model that described the mechanism of contact interaction between negatively charged nano-objects, such as citrate-stabilized GNPs, and ONs or ON-FDs.

Highlights

For the first time, a systemic study concerning the effect of fluorophore dyes (FDs) structure on the efficiency of the formation of their non-covalent associates with gold nanoparticles (GNPs)
Having considered all the factors that determine the initial state of interacting components in the system of ON-FD and GNP, we can make an assumption about the mechanism of the formation of non-covalent associates of ON-FD/GNP type, and about the role of the FD in this process
Our study revealed that the presence of FD residues containing aromatic systems is a factor that largely determines the affinity of ON-FD

Summary

Introduction

A wide range of compounds, bound with different nanocarriers, are increasingly used in bioscience and biomedicine [1]. Quantification of these compounds binding to the carrier is necessary in many cases, and it can be carried out by methods without the use of labels, or using labels, which are mainly fluorophore dyes (FDs) [2,3,4,5,6,7,8]. Standard deviation is repreFluorescent labels of ONs are widely used to assess the efficiency of ON adsorption sented on graphs as error bars. A question arises: could a structure of FDs influence the adsorption of labeled ONs to the surface of GNPs?

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