Nucleic acid sample storage is of paramount importance in forensic sciences and genetic laboratories. Very recently, hydrated ionic liquids (ILs) have been identified as ideal media for long-term DNA storage. Hence, understanding the binding characteristics and molecular mechanism of interactions of ILs with DNA is of both practical and fundamental interest. Here we employ a hybrid technique, combining molecular dynamics (MD) simulations and spectroscopic experiments to unravel the key factors that stabilize DNA in hydrated ILs. Both simulation and experimental data show that DNA maintains the native B-conformation. Simulation results further suggest that, apart from the electrostatic associations of IL cations to DNA backbone, groove binding of IL cations through hydrophobic and polar interactions contribute significantly to DNA stability. CD spectral measurements and fluorescent dye displacement assay confirm the intrusion of IL molecules into the DNA minor groove. Very interestingly, the IL cations were seen to disrupt the water cage around DNA, particularly the spine of hydration in the minor grove. We believe this partial dehydration of DNA by IL cations serves the basis of long-term DNA stability, as it prevents the hydrolytic reactions that denature DNA. The detailed understanding of IL-DNA interactions provided here could guide the future development of novel ILs, specific for nucleic acids solutes.

Groove binding mechanism of ionic liquids: A key factor in long term stability of DNA in hydrated ionic liquids

243rd National Meeting (2012)

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