An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies
Molecular dynamics simulation and biophysical analysis were employed to reveal the characteristics and the influence of ionic liquids (ILs) on the structural properties of DNA. Both computational and experimental evidence indicate that DNA retains its native B-conformation in ILs. Simulation data sh...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Royal Society of Chemistry
2014
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| Online Access: | http://psasir.upm.edu.my/id/eprint/36417/ http://psasir.upm.edu.my/id/eprint/36417/1/An%20insight%20into%20structure%20and%20stability%20of%20DNA%20in%20ionic%20liquids%20from%20molecular%20dynamics%20simulation%20and%20experimental%20studies.pdf |
| _version_ | 1848848326302105600 |
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| author | Jumbri, K. Abdul Rahman, Mohd Basyaruddin Abd. Malek, Emilia Ahmad, Haslina Micaelo, Nuno M. |
| author_facet | Jumbri, K. Abdul Rahman, Mohd Basyaruddin Abd. Malek, Emilia Ahmad, Haslina Micaelo, Nuno M. |
| author_sort | Jumbri, K. |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Molecular dynamics simulation and biophysical analysis were employed to reveal the characteristics and the influence of ionic liquids (ILs) on the structural properties of DNA. Both computational and experimental evidence indicate that DNA retains its native B-conformation in ILs. Simulation data show that the hydration shells around the DNA phosphate group were the main criteria for DNA stabilization in this ionic media. Stronger hydration shells reduce the binding ability of ILs' cations to the DNA phosphate group, thus destabilizing the DNA. The simulation results also indicated that the DNA structure maintains its duplex conformation when solvated by ILs at different temperatures up to 373.15 K. The result further suggests that the thermal stability of DNA at high temperatures is related to the solvent thermodynamics, especially entropy and enthalpy of water. All the molecular simulation results were consistent with the experimental findings. The understanding of the properties of IL–DNA could be used as a basis for future development of specific ILs for nucleic acid technology. |
| first_indexed | 2025-11-15T09:32:43Z |
| format | Article |
| id | upm-36417 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T09:32:43Z |
| publishDate | 2014 |
| publisher | Royal Society of Chemistry |
| recordtype | eprints |
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| spelling | upm-364172015-10-05T01:15:43Z http://psasir.upm.edu.my/id/eprint/36417/ An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies Jumbri, K. Abdul Rahman, Mohd Basyaruddin Abd. Malek, Emilia Ahmad, Haslina Micaelo, Nuno M. Molecular dynamics simulation and biophysical analysis were employed to reveal the characteristics and the influence of ionic liquids (ILs) on the structural properties of DNA. Both computational and experimental evidence indicate that DNA retains its native B-conformation in ILs. Simulation data show that the hydration shells around the DNA phosphate group were the main criteria for DNA stabilization in this ionic media. Stronger hydration shells reduce the binding ability of ILs' cations to the DNA phosphate group, thus destabilizing the DNA. The simulation results also indicated that the DNA structure maintains its duplex conformation when solvated by ILs at different temperatures up to 373.15 K. The result further suggests that the thermal stability of DNA at high temperatures is related to the solvent thermodynamics, especially entropy and enthalpy of water. All the molecular simulation results were consistent with the experimental findings. The understanding of the properties of IL–DNA could be used as a basis for future development of specific ILs for nucleic acid technology. Royal Society of Chemistry 2014 Article PeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/36417/1/An%20insight%20into%20structure%20and%20stability%20of%20DNA%20in%20ionic%20liquids%20from%20molecular%20dynamics%20simulation%20and%20experimental%20studies.pdf Jumbri, K. and Abdul Rahman, Mohd Basyaruddin and Abd. Malek, Emilia and Ahmad, Haslina and Micaelo, Nuno M. (2014) An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies. Physical Chemistry Chemical Physics, 16 (27). pp. 14036-14046. ISSN 1463-9076; ESSN: 1463-9084 http://pubs.rsc.org/en/Content/ArticleLanding/2014/CP/c4cp01159g#!divAbstract 10.1039/C4CP01159G |
| spellingShingle | Jumbri, K. Abdul Rahman, Mohd Basyaruddin Abd. Malek, Emilia Ahmad, Haslina Micaelo, Nuno M. An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies |
| title | An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies |
| title_full | An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies |
| title_fullStr | An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies |
| title_full_unstemmed | An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies |
| title_short | An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies |
| title_sort | insight into structure and stability of dna in ionic liquids from molecular dynamics simulation and experimental studies |
| url | http://psasir.upm.edu.my/id/eprint/36417/ http://psasir.upm.edu.my/id/eprint/36417/ http://psasir.upm.edu.my/id/eprint/36417/ http://psasir.upm.edu.my/id/eprint/36417/1/An%20insight%20into%20structure%20and%20stability%20of%20DNA%20in%20ionic%20liquids%20from%20molecular%20dynamics%20simulation%20and%20experimental%20studies.pdf |