Exploring nucleic acid stability in ionic liquids: Measurements and mechanisms.

Abstract

The stability and integrity of nucleic acids, DNA and RNA, are vital in biotechnological applications. Conventionally, nucleic acids are stored under refrigeration for short and long-term applications as they are not stable at room temperature. Repeated freeze-thaw cycles are detrimental to the stability of nucleic acids and also remain a cost ineffective way of preservation. Ionic liquids (ILs), composed of organic cations and organic/inorganic anions, are shown to be promising solvent media for preservation of several biomolecules. Previously, we have shown that groove binding of IL cations through combined hydrophobic and polar interactions contribute significantly to the DNA stability.In this work, we attempt to understand the role of different class of ionic liquids in stabilizing DNA through experimental methods and explore their mechanism through molecular dynamic (MD) simulations. The ionic liquids of different class that are chosen involve ethyl ammonium nitrate [EAN] as protic, [BMIM]] [chloride] as a borderline between protic and aprotic, and [BMIM][acetate] as the aprotic IL. We employed UV-visible absorption spectroscopy and CD spectroscopy to investigate the interaction pattern between DNA and ILs and measure the structural integrity. The melting values (Tm) were recorded as a measure of stability. Further, we performed MD simulations and quantum calculations to understand the mechanism of interaction of ILs with DNA. Our findings show the significance of protic IL, [EAN] in stabilizing DNA to a greater extent with highest Tm value and a free energy of stabilization by −10.36 kcal/mol.