Interactions between a dsDNA Oligonucleotide and Imidazolium Chloride Ionic Liquids: Effect of Alkyl Chain Length, Part I.

Fatemeh Fadaei,Natalia Kulik,Mark P. Heitz,David Řeha,Michelle Seifert,Joshua R. Raymond,Babak Minofar

doi:10.3390/molecules27010116

Abstract

Ionic liquids (ILs) have become nearly ubiquitous solvents and their interactions with biomolecules has been a focus of study. Here, we used the fluorescence emission of DAPI, a groove binding fluorophore, coupled with molecular dynamics (MD) simulations to report on interactions between imidazolium chloride ([Imn,1]+) ionic liquids and a synthetic DNA oligonucleotide composed entirely of T/A bases (7(TA)) to elucidate the effects ILs on a model DNA duplex. Spectral shifts on the order of 500–1000 cm−1, spectral broadening (~1000 cm−1), and excitation and emission intensity ratio changes combine to give evidence of an increased DAPI environment heterogeneity on added IL. Fluorescence lifetimes for DAPI/IL solutions yielded two time constants 0.15 ns (~80% to 60% contribution) and 2.36–2.71 ns for IL up to 250 mM. With DNA, three time constants were required that varied with added IL (0.33–0.15 ns (1–58% contribution), ~1.7–1.0 ns (~5% contribution), and 3.8–3.6 ns (94–39% contribution)). MD radial distribution functions revealed that π-π stacking interactions between the imidazolium ring were dominant at lower IL concentration and that electrostatic and hydrophobic interactions become more prominent as IL concentration increased. Alkyl chain alignment with DNA and IL-IL interactions also varied with IL. Collectively, our data showed that, at low IL concentration, IL was primarily bound to the DNA minor groove and with increased IL concentration the phosphate regions and major groove binding sites were also important contributors to the complete set of IL-DNA duplex interactions.

Highlights

Deoxyribonucleic acid (DNA), the most important of biomolecules, plays pivotal biological roles in the storing and carrying of genetic information for the growth, functioning, and reproduction of all known organisms
Initial measurements were performed to assess the binding of DAPI to a synthetic double stranded 7(TA) repeat sequence (14 base pairs per strand), B-DNA oligonucleotide to determine the optimal DAPI:DNA ratio be used in our experiments
We observed that the fluorescence intensity of DAPI increases upon binding to our 7(TA) DNA duplex and reached a maximum and decreased when the oligonucleotide had accommodated the maximum number DAPI molecules

Summary

Introduction

Deoxyribonucleic acid (DNA), the most important of biomolecules, plays pivotal biological roles in the storing and carrying of genetic information for the growth, functioning, and reproduction of all known organisms. The same group studied pyridinium ionic liquids for their DNA binding properties [5] In these examples, they investigated the interaction the synthesized ILs with DNA to determine the anticancer mechanism. Revathi et al [6] synthesized a new series of bio active Cu(II) and Zn(II) complexes They performed both experimental and theoretical study to investigate the possible interaction of them with DNA. Alraqa and coworkers [7] designed and synthesized the hybridization of benzotriazole and 1,2,3-triazoles with several functionalities, including amide, ketone, ester, and/or carboxylic acid According to their results, the compounds have good interaction with the minor grooves of DNA through hydrogen bonding and hydrophobic interactions. They suggest the reported molecules may be future anticancer agents

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