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Athira KK, Mepperi J, Chandra Kotamarthi H, Gardas RL. Ionic liquid-based aqueous biphasic system as an alternative tool for enhanced bacterial DNA extraction. Anal Chim Acta 2024; 1321:343045. [PMID: 39155099 DOI: 10.1016/j.aca.2024.343045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/20/2024]
Abstract
BACKGROUND Developing an alternative and benign method for DNA extraction is imperative due to the high cost and potential harms associated with conventional techniques. Investigation of Ionic liquid (IL) as a solvent for DNA storage and stability revealed the ability of IL to assist DNA processes. IL-based aqueous biphasic system emerges as a comprehensive extraction platform capitalizing on the task-specificity of ILs and the wide applicability of ABS for biomolecule extractions. Therefore, it is beneficial to optimize an IL-based ABS specifically for DNA extraction, taking into account the fundamental interactions between the IL and DNA. RESULTS The primary objective was to design ABS consisting of Ammonium based ILs, and Potassium phosphate buffer as the salting-out agent for the partitioning of salmon sperm DNA. The analysis focused on optimizing biocompatible anions for the extraction. Moreover, the stability of the DNA in the IL rich phases was analysed to validate the method. The proposed process was then employed for extracting plasmid DNA from bacteria, demonstrating results comparable to those obtained with a commercially available kit. Further validation using agarose gel electrophoresis and transformation of the extracted DNA into E.coli were conducted, producing promising outcomes. Although there is room for improvement in terms of recovery of DNA and reusability of ABS, the described approach is comparable with the conventional one while being cost-effective, and showcases a noticeable and convincing link to eco-friendly processes. SIGNIFICANCE There is limited literature on IL-based ABS for DNA extraction, and the existing studies predominantly concentrate on systems derived from Cholinium ILs. However, their high hydrophilicity limits the choice of the second-phase forming component to polymers for the formation of ABS. Ammonium ILs efficiently form biphasic systems with various available salting-out agents, and biocompatible anions are introduced to mitigate the toxicity of the ILs.
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Affiliation(s)
- K K Athira
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Jijith Mepperi
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India
| | | | - Ramesh L Gardas
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India.
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2
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Olave B. DNA nanotechnology in ionic liquids and deep eutectic solvents. Crit Rev Biotechnol 2024; 44:941-961. [PMID: 37518062 DOI: 10.1080/07388551.2023.2229950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 08/01/2023]
Abstract
Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.
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Affiliation(s)
- Beñat Olave
- University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
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3
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Knanghat R, Senapati S. Toward Greater DNA Stability by Leveraging the Proton-Donating Ability of Protic Ionic Liquids. J Phys Chem B 2024. [PMID: 38682809 DOI: 10.1021/acs.jpcb.3c08479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Deoxyribonucleic acid (DNA) stability is a prerequisite in many applications, ranging from DNA-based vaccines and data storage to gene therapy. However, the strategies to enhance DNA stability are limited, and the underlying mechanisms are poorly understood. Ionic liquids (ILs), molten salts of organic cations and organic/inorganic anions, are showing tremendous prospects in myriads of applications. With a judicious choice of constituent ions, the protic nature of ILs can be tuned. In this work, we investigate the relative stability of full-length genomic DNA in aqueous IL solutions of increasing protic nature. Our experimental measurements show that the protic ionic liquids (PILs) enhance the DNA melting temperature significantly while unaltering its native B-conformation. Molecular dynamics simulations and quantum mechanical calculation results suggest that the intramolecular Watson-Crick H-bonding in DNA remains unaffected and, in addition, the PILs induce stronger H-bonding networks in solution through their ability to make multiple intermolecular H-bonds with the nucleobases and among its constituent ions, thus aiding greater DNA stability. The detailed understanding obtained from this study could bring about the much-awaited breakthrough in improved DNA stability for its sustained use in the aforesaid applications!
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Affiliation(s)
- Rajani Knanghat
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sanjib Senapati
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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4
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Zoli M. Twist-stretch relations in nucleic acids. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:641-650. [PMID: 37357224 DOI: 10.1007/s00249-023-01669-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/15/2023] [Accepted: 06/10/2023] [Indexed: 06/27/2023]
Abstract
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite twist-stretch patterns and stretching properties when overwound under a constant applied load. The key structural features of the A-form RNA and B-form DNA helices are here incorporated in a three-dimensional mesoscopic Hamiltonian model which accounts for the radial, bending and twisting fluctuations of the base pairs. Using path integral techniques which sum over the ensemble of the base pair fluctuations, I compute the average helical repeat of the molecules as a function of the load. The obtained twist-stretch relations and stretching properties, for short A- and B-helical fragments, are consistent with the opposite behaviors observed in kilo-base long molecules.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology, University of Camerino, 62032, Camerino, Italy.
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5
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Wilkinson RC, Meldrum K, Maggs CJ, Thomas NE, Thomas BR, De Mello N, Joyce N. Determining the efficacy of disinfectants at nucleic acid degradation. J Appl Microbiol 2023; 134:lxad244. [PMID: 37884448 DOI: 10.1093/jambio/lxad244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/06/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023]
Abstract
AIMS Nucleic acids, particularly antibiotic resistance genes, are commonly found on surfaces within healthcare environments, with levels not reducing following cleaning. Within the UK, there are no regulations for testing disinfectants against nucleic acids. METHODS AND RESULTS A series of commonplace in vitro methods were used to determine disinfectant-induced physical and functional damage to various nucleic acids; RNA (10 μg), genomic DNA (2 μg), and plasmids (1 μg). Using these methods, the optimal residence time (10 minutes) and working concentration (10%) were determined for a new disinfectant. Furthermore, comparison of disinfectants with different active ingredients including lactic acid (LA), sodium hydroxide (NaOH), chloroxylenol (PCMX), and quaternary ammonium compounds (QACs), were compared to controls. All disinfectants showed greater degradation by gel electrophoresis of genomic DNA and RNA than of purified plasmids. Functional analysis using quantitative polymerase chain reaction (qPCR) and polymerase chain reaction (PCR) demonstrated that no disinfectant tested (apart from control) could damage DNA to the level where PCR amplification was not possible, and only the NaOH reagent could achieve this for RNA. CONCLUSIONS The set of methods described herein provides a platform for future standardization and potential regulation regarding monitoring cleaning solutions for their activity against nucleic acids.
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Affiliation(s)
- Rachael C Wilkinson
- Healthcare Technology Centre, Swansea University Medical School, Swansea University, Swansea SA2 8PP, United Kingdom
| | - Kirsty Meldrum
- Healthcare Technology Centre, Swansea University Medical School, Swansea University, Swansea SA2 8PP, United Kingdom
| | - Caitlin J Maggs
- Healthcare Technology Centre, Swansea University Medical School, Swansea University, Swansea SA2 8PP, United Kingdom
| | - Nerissa E Thomas
- Healthcare Technology Centre, Swansea University Medical School, Swansea University, Swansea SA2 8PP, United Kingdom
| | - Bethan R Thomas
- Healthcare Technology Centre, Swansea University Medical School, Swansea University, Swansea SA2 8PP, United Kingdom
| | - Natalie De Mello
- Healthcare Technology Centre, Swansea University Medical School, Swansea University, Swansea SA2 8PP, United Kingdom
| | - Naomi Joyce
- Healthcare Technology Centre, Swansea University Medical School, Swansea University, Swansea SA2 8PP, United Kingdom
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6
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Chhetri KB, Dasgupta C, Maiti PK. Diameter Dependent Melting and Softening of dsDNA Under Cylindrical Confinement. Front Chem 2022; 10:879746. [PMID: 35586267 PMCID: PMC9108266 DOI: 10.3389/fchem.2022.879746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Carbon nanotubes (CNTs) are considered promising candidates for biomolecular confinement, including DNA encapsulation for gene delivery. Threshold values of diameters have been reported for double-stranded DNA (dsDNA) encapsulation inside CNTs. We have performed all-atom molecular dynamics (MD) simulations of dsDNAs confined inside single-walled CNTs (SWCNTs) at the physiologically relevant temperature of 300 K. We found that the dsDNA can be confined without being denatured only when the diameter of the SWCNT exceeds a threshold value. Below this threshold diameter, the dsDNA gets denatured and melts even at the temperature of 300 K. Our simulations using SWCNTs with chirality indices (20,20) to (30,30) at 300 K found the critical diameter to be 3.25 nm (corresponding to (24,24) chirality). Analyses of the hydrogen bonds (H-bonds), Van der Walls (VdW) energy, and other inter-base interactions show drastic reduction in the number of H-bonds, VdW energy, and electrostatic energies between the bases of dsDNA when it is confined in narrower SWCNTs (up to diameter of 3.12 nm). On the other hand, the higher interaction energy between the dsDNA and the SWCNT surface in narrower SWCNTs assists in the melting of the dsDNA. Electrostatic mapping and hydration status analyses show that the dsDNA is not adequately hydrated and the counter ion distribution is not uniform below the critical diameter of the SWCNT. As properly hydrated counter ions provide stability to the dsDNA, we infer that the inappropriate hydration of counter ions and their non-uniform distribution around the dsDNA cause the melting of the dsDNA inside SWCNTs of diameter below the critical value of 3.25 nm. For confined dsDNAs that do not get denatured, we computed their elastic properties. The persistence length of dsDNA was found to increase by a factor of about two and the torsional stiffness by a factor of 1.5 for confinement inside SWCNTs of diameters up to 3.79 nm, the stretch modulus also following nearly the same trend. Interestingly, for higher diameters of SWCNT, 3.79 nm and above, the dsDNA becomes more flexible, demonstrating that the mechanical properties of the dsDNA under cylindrical confinement depend non-monotonically on the confinement diameter.
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Affiliation(s)
- Khadka B. Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Pokhara, Nepal
| | - Chandan Dasgupta
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
| | - Prabal K. Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
- *Correspondence: Prabal K. Maiti,
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Tulsiyan K, Jena S, González-Viegas M, Kar RK, Biswal HS. Structural Dynamics of RNA in the Presence of Choline Amino Acid Based Ionic Liquid: A Spectroscopic and Computational Outlook. ACS CENTRAL SCIENCE 2021; 7:1688-1697. [PMID: 34729412 PMCID: PMC8554839 DOI: 10.1021/acscentsci.1c00768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Indexed: 05/03/2023]
Abstract
Ribonucleic acid (RNA) is exceedingly sensitive to degradation compared to DNA. The current protocol for storage of purified RNA requires freezing conditions below -20 °C. Recent advancements in biological chemistry have identified amino acid-based ionic liquids as suitable preservation media for RNA, even in the presence of degrading enzymes. However, the mechanistic insight into the interaction between ILs and RNA is unclear. To the best of our knowledge, no attempts are made so far to provide a molecular view. This work aims to establish a detailed understanding of how ILs enable structural stability to RNA sourced from Torula yeast. Herein, we manifest the hypothesis of multimodal binding of IL and its minimal perturbation to the macromolecular structure, with several spectroscopic techniques such as time-resolved fluorescence and fluorescence correlation spectroscopy (FCS) aided with molecular dynamics at microsecond time scales. Relevant structural and thermodynamic details from biophysical experiments confirm that even long-term RNA preservation with ILs is a possible alternative devoid of any structural deformation. These results establish a unifying mechanism of how ILs are maintaining conformational integrity and thermal stability. The atomistic insights are transferable for their potential applications in drug delivery and biomaterials by considering the advantages of having maximum structural retention and minimum toxicity.
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Affiliation(s)
- Kiran
Devi Tulsiyan
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - María González-Viegas
- Institut
für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany
| | - Rajiv K. Kar
- Faculty
II-Mathematics and Natural Sciences, Technische
Universität Berlin, Sekr. PC 14, Strasse des 17, Juni 135, D-10623 Berlin, Germany
| | - Himansu S. Biswal
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
- . Phone: +91-674-2494 185/186
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8
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Rahman MH, Senapati S. Effects of Ionic Liquids on Aqueous Urea Solutions: Insights into the Ionic Liquid-Assisted Protein Renaturation. J Phys Chem B 2021; 125:4808-4818. [PMID: 33914552 DOI: 10.1021/acs.jpcb.1c00586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ionic liquids (ILs) are designer solvents that find wide applications in various areas. Recently, ILs have been shown to induce the refolding of certain proteins that were previously denatured under the treatment of urea. A molecular-level understanding of the counteracting mechanism of ILs on urea-induced protein denaturation remains elusive. In this study, we employ atomistic molecular dynamics simulations to investigate the ternary urea-water-IL solution in comparison to the aqueous urea solution to understand how the presence of ILs can modulate the structure, energetics, and dynamics of urea-water solutions. Our results show that the ions of the IL used, ethylammonium nitrate (EAN), interact strongly with urea and disrupt the urea aggregates that were known to stabilize the unfolded state of the proteins. Results also suggest a disruption in urea-water interaction that releases more free water molecules in solution. We subsequently strengthened these findings by simulating a model peptide in the absence and presence of EAN, which showed broken versus intact secondary structure in urea solution. Analyses show that these changes were accomplished by the added IL, which enforced a gradual displacement of urea from the peptide surface by water. We propose that the ILs facilitate protein renaturation by breaking down the urea aggregates and increasing the amount of free water molecules around the protein.
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Affiliation(s)
- Mohammad Homaidur Rahman
- Department of Biotechnology, BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Sanjib Senapati
- Department of Biotechnology, BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
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9
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Sarkar S, Chandra Singh P. Anions of Ionic Liquids Are Important Players in the Rescue of DNA Damage. J Phys Chem Lett 2020; 11:10150-10156. [PMID: 33191753 DOI: 10.1021/acs.jpclett.0c03016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The non-targeted action of fungicides generates genotoxic effect in vertebrates by perturbing the structure of DNA, which impacts its replication and transcriptional process, leading to several serious gene associated diseases. Hence, finding a suitable medium that can reduce/reverse the structural perturbation of DNA induced by fungicide, viz. dodine, is essential. Spectroscopic as well as molecular dynamics simulation techniques have been implemented to understand the effect of ionic liquids (ILs) having a tetramethylguanidinium cation along with short and long hydrophobic chain anions mixed with fungicide. The addition of ILs possessing anions with long hydrophobic chain blocks the fungicide from binding in the groove region of DNA by forming micelle-like structure and reverses the structural change induced by the fungicide. The hydrophobicity of long hydrocarbon and fluorocarbon chains of anions is a key parameter for reversing the effect of fungicide as small anion based ILs are incapable of annulling the structural change of DNA.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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Pal S, Paul S. Understanding The Role of Reline, a Natural DES, on Temperature-Induced Conformational Changes of C-Kit G-Quadruplex DNA: A Molecular Dynamics Study. J Phys Chem B 2020; 124:3123-3136. [PMID: 32207949 DOI: 10.1021/acs.jpcb.0c00644] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The noncanonical guanine-rich DNAs have drawn particular attention to the scientific world due to their controllable diverse and polymorphic structures. Apart from biological and medical significance, G-quadruplex DNAs are widely used in various fields such as nanotechnology, nanomachine, biosensors, and biocatalyst. So far, the applications of the G-quadruplex DNA are mainly limited in the water medium. Recently, a new generation of solvent named deep eutectic solvent (DES) has become very popular and has been widely used as a reaction medium of biocatalytic reactions and long-term storage medium for nucleic acids, even at high temperature. Hence, it is essential to understand the role of DES on temperature-induced conformational changes of a G-quadruplex DNA. In this research work, we have explored the temperature-mediated conformational dynamics of c-kit oncogene promoter G-quadruplex DNA in reline medium in the temperature range of 300-500 K, using a total of 10 μs unbiased all-atom molecular dynamics simulation. Here, from RMSD, RMSF, Rg and principal component analyses, we notice that the c-kit G-quadruplex DNA is stable up to 450 K in reline medium. However, it unfolds in water medium at 450 K. It is found that the hydrogen bonding interactions between c-kit G-quadruplex DNA and reline play a key role in the stabilization of the G-quadruplex DNA even at high temperature. Furthermore, in this work we have observed a very interesting and distinctive phenomenon of the central cation of the G-quadruplex DNA. Its position was seen to fluctuate between the two tetrad cores, that is, the region between tetrad-1 and tetrad-2 and that between tetrad-2 and tetrad-3 and vice versa at 450 and 500 K in reline medium which is absent in water medium at 450 K. Moreover, the rate of its oscillation is increased when temperature is increased.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, India, 781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, India, 781039
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Pressure-Dependent Stability of Imidazolium-Based Ionic Liquid/DNA Materials Investigated by High-Pressure Infrared Spectroscopy. MATERIALS 2019; 12:ma12244202. [PMID: 31847290 PMCID: PMC6947093 DOI: 10.3390/ma12244202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022]
Abstract
1-Butyl-3-methylimidazolium hexafluorophosphate ([C4MIM][PF6])/DNA and 1-methyl-3-propylimidazolium hexafluorophosphate ([C3MIM][PF6])/DNA mixtures were prepared and characterized by high-pressure infrared spectroscopy. Under ambient pressure, the imidazolium C2-H and C4,5-H absorption bands of [C4MIM][PF6]/DNA mixture were red-shifted in comparison with those of pure [C4MIM][PF6]. This indicates that the C2-H and C4,5-H groups may have certain interactions with DNA that assist in the formation of the ionic liquid/DNA association. With the increase of pressure from ambient to 2.5 GPa, the C2-H and C4,5-H absorption bands of pure [C4MIM][PF6] displayed significant blue shifts. On the other hand, the imidazolium C-H absorption bands of [C4MIM][PF6]/DNA showed smaller frequency shift upon compression. This indicates that the associated [C4MIM][PF6]/DNA conformation may be stable under pressures up to 2.5 GPa. Under ambient pressure, the imidazolium C2-H and C4,5-H absorption bands of [C3MIM][PF6]/DNA mixture displayed negligible shifts in frequency compared with those of pure [C3MIM][PF6]. The pressure-dependent spectra of [C3MIM][PF6]/DNA mixture revealed spectral features similar to those of pure [C3MIM][PF6]. Our results indicate that the associated structures of [C4MIM][PF6]/DNA are more stable than those of [C3MIM][PF6]/DNA under high pressures.
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