Local and cooperative structural transitions of double-stranded DNA in choline-based deep eutectic solvents

• Published in: International journal of biological macromolecules Vol. 256; no. Pt 2; p. 128443
• Main Authors: Fadaei, Fatemeh, Tortora, Mariagrazia, Gessini, Alessandro, Masciovecchio, Claudio, Vigna, Jacopo, Mancini, Ines, Mele, Andrea, Vacek, Jan, Minofar, Babak, Rossi, Barbara
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2024
• Subjects: Circular Dichroism; Deep eutectic solvents; Molecular dynamics simulation; Nucleic acids; Synchrotron UV Resonance Raman; Nucleic acids; Molecular dynamics simulation; Synchrotron UV Resonance Raman; Deep eutectic solvents; Circular Dichroism
• ISSN: 0141-8130; 1879-0003
• DOI: 10.1016/j.ijbiomac.2023.128443

The possibility of using deep eutectic solvents (DESs) as co-solvents for stabilizing and preserving the native structure of DNA provides an attractive opportunity in the field of DNA biotechnology. The rationale of this work is a systematic investigation of the effect of hydrated choline-based DES on the structural stability of a 30-base-pair double-stranded DNA model via a combination of spectroscopic experiments and MD simulations. UV absorption and CD experiments provide evidence of a significant contribution of DESs to the stabilization of the double-stranded canonical (B-form) DNA structure. Multi-wavelength synchrotron UV Resonance Raman (UVRR) measurements indicate that the hydration shell of adenine-thymine pairs is strongly perturbed in the presence of DESs and that the preferential interaction between H-bond sites of guanine residues and DESs is significantly involved in the stabilization of the dsDNA. Finally, MD calculations show that the minor groove of DNA is significantly selective for the choline part of the investigated DESs compared to the major groove. This finding is likely to have a significant impact not only in terms of thermal stability but also in the modulation of ligand-DNA interactions. •The effect of choline-based DES on stability of double-stranded DNA is investigated.•DES improve the thermal stabilization of double-stranded canonical DNA structure.•Hydration shell of AT pairs is strongly perturbed in the presence of DES.•Preferential interaction between HB sites of guanine residues and DES is detected.•Minor groove of DNA is significantly selective for the choline part of DES.