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

0553491 - MBÚ 2023 RIV CH eng J - Journal Article
Fadaei, Fatemeh - Seifert, M. - Raymond, J. - Řeha, David - Kulik, Natalia - Minofar, Babak - Heitz, M.
Interactions between a dsDNA Oligonucleotide and Imidazolium Chloride Ionic Liquids: Effect of Alkyl Chain Length, Part I.
Molecules. Roč. 27, č. 1 (2022), č. článku 116. E-ISSN 1420-3049
R&D Projects: GA ČR(CZ) GA21-15936S
Institutional support: RVO:61388971
Keywords : molecular-dynamics * binding characteristics * initial configurations * dna * dapi * fluorescence * stability * 4'-6-diamidino-2-phenylindole * simulation * mechanism * dapi * DNA duplex * DNA oligonucleotide * imidazolium ionic liquids * fluorescence * fluorescence lifetime * molecular dynamics * radial distribution function
OECD category: Microbiology
Impact factor: 4.6, year: 2022
Method of publishing: Open access
https://www.mdpi.com/1420-3049/27/1/116

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 ([Im(n,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 pi-pi 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.
Permanent Link: http://hdl.handle.net/11104/0330410