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Fadaei F, Tortora M, Gessini A, Masciovecchio C, Vigna J, Mancini I, Mele A, Vacek J, Minofar B, Rossi B. Local and cooperative structural transitions of double-stranded DNA in choline-based deep eutectic solvents. Int J Biol Macromol 2024; 256:128443. [PMID: 38035952 DOI: 10.1016/j.ijbiomac.2023.128443] [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: 08/25/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
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.
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Affiliation(s)
- Fatemeh Fadaei
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic
| | - Mariagrazia Tortora
- Area Science Park, Padriciano, 99, 34149 Trieste, Italy; Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy
| | | | - Jacopo Vigna
- Laboratory of Bioorganic Chemistry, Department of Physics, University of Trento, Via Sommarive, 14, 38123 Povo Trento, Italy
| | - Ines Mancini
- Laboratory of Bioorganic Chemistry, Department of Physics, University of Trento, Via Sommarive, 14, 38123 Povo Trento, Italy
| | - Andrea Mele
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15 Olomouc, Czech Republic
| | - Babak Minofar
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic.
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; Laboratory of Bioorganic Chemistry, Department of Physics, University of Trento, Via Sommarive, 14, 38123 Povo Trento, Italy.
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2
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Usmani Z, Sharma M, Tripathi M, Lukk T, Karpichev Y, Gathergood N, Singh BN, Thakur VK, Tabatabaei M, Gupta VK. Biobased natural deep eutectic system as versatile solvents: Structure, interaction and advanced applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163002. [PMID: 37003333 DOI: 10.1016/j.scitotenv.2023.163002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 03/18/2023] [Indexed: 06/01/2023]
Abstract
The increasing emphasis on the development of green replacements to traditional organic solvents and ionic liquids (ILs) can be attributed to the rising concerns over human health and detrimental impacts of conventional solvents towards the environment. A new generation of solvents inspired by nature and extracted from plant bioresources has evolved over the last few years, and are referred to as natural deep eutectic solvents (NADES). NADES are mixtures of natural constituents like sugars, polyalcohols, sugar-based alcohols, amino acids and organic acids. Interest in NADES has exponentially grown over the last eight years, which is evident from an upsurge in the number of research projects undertaken. NADES are highly biocompatible as they can be biosynthesized and metabolized by nearly all living organisms. These solvents pose several noteworthy advantages, such as easy synthesis, tuneable physico-chemical properties, low toxicity, high biodegradability, solute sustainability and stabilization and low melting point. Research on the applicability of NADES in diverse areas is gaining momentum, which includes as - media for chemical and enzymatic reactions; extraction media for essential oils; anti-inflammatory and antimicrobial agent; extraction of bioactive composites; as chromatographic media; preservatives for labile compounds and in drug synthesis. This review gives a complete overview of the properties, biodegradability and toxicity of NADES which we propose can assist in further knowledge generation on their significance in biological systems and usage in green and sustainable chemistry. Information on applications of NADES in biomedical, therapeutic and pharma-biotechnology fields is also highlighted in the current article along with the recent progress and future perspectives in novel applications of NADES.
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Affiliation(s)
- Zeba Usmani
- Department of Applied Biology, University of Science and Technology, Meghalaya 793101, India; Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Minaxi Sharma
- Haute Ecole Provinciale de Hainaut-Condorcet, 7800 ATH, Belgium
| | - Manikant Tripathi
- Biotechnology Program, Dr. Rammanohar Lohia Avadh University, Ayodhya, Uttar Pradesh 224001, India
| | - Tiit Lukk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Yevgen Karpichev
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Nicholas Gathergood
- School of Chemistry, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, Lincolnshire LN6 7DL, UK
| | - Brahma N Singh
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow-226001, Uttar Pradesh, India
| | - Vijay Kumar Thakur
- Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Meisam Tabatabaei
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Department of Biomaterials, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Chennai 600 077, India
| | - Vijai K Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
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Chang T, He S, Amini R, Li Y. Functional Nucleic Acids Under Unusual Conditions. Chembiochem 2021; 22:2368-2383. [PMID: 33930229 DOI: 10.1002/cbic.202100087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/24/2021] [Indexed: 02/06/2023]
Abstract
Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. Given the high chemical stability of nucleic acids and their ability to fold into diverse sequence-dependent structures, FNAs are suggested to be highly functional under unusual reaction conditions. This review will examine the progress of research on FNAs under conditions of low pH, high temperature, freezing conditions, and the inclusion of organic solvents and denaturants that are known to disrupt nucleic acid structures. The FNA species to be discussed include ribozymes, riboswitches, G-quadruplex-based peroxidase mimicking DNAzymes, RNA-cleaving DNAzymes, and aptamers. Research within this space has not only revealed the hidden talents of FNAs but has also laid important groundwork for pursuing these intriguing functional macromolecules for unique applications.
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Affiliation(s)
- Tianjun Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
- Department of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, Henan, P. R. China
| | - Sisi He
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
- School of Science, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen, 518055, Guangdong, P. R. China
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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Kist JA, Zhao H, Mitchell-Koch KR, Baker GA. The study and application of biomolecules in deep eutectic solvents. J Mater Chem B 2021; 9:536-566. [DOI: 10.1039/d0tb01656j] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Deep eutectic solvents offer stimulating possibilities for biomolecular stabilization and manipulation, biocatalysis, bioextraction, biomass processing, and drug delivery and therapy.
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Affiliation(s)
- Jennifer A. Kist
- Department of Chemistry
- University of Missouri-Columbia
- Columbia
- USA
| | - Hua Zhao
- Department of Chemistry and Biochemistry
- University of Northern Colorado
- Greeley
- USA
| | | | - Gary A. Baker
- Department of Chemistry
- University of Missouri-Columbia
- Columbia
- USA
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5
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Hansen BB, Spittle S, Chen B, Poe D, Zhang Y, Klein JM, Horton A, Adhikari L, Zelovich T, Doherty BW, Gurkan B, Maginn EJ, Ragauskas A, Dadmun M, Zawodzinski TA, Baker GA, Tuckerman ME, Savinell RF, Sangoro JR. Deep Eutectic Solvents: A Review of Fundamentals and Applications. Chem Rev 2020; 121:1232-1285. [PMID: 33315380 DOI: 10.1021/acs.chemrev.0c00385] [Citation(s) in RCA: 779] [Impact Index Per Article: 194.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Deep eutectic solvents (DESs) are an emerging class of mixtures characterized by significant depressions in melting points compared to those of the neat constituent components. These materials are promising for applications as inexpensive "designer" solvents exhibiting a host of tunable physicochemical properties. A detailed review of the current literature reveals the lack of predictive understanding of the microscopic mechanisms that govern the structure-property relationships in this class of solvents. Complex hydrogen bonding is postulated as the root cause of their melting point depressions and physicochemical properties; to understand these hydrogen bonded networks, it is imperative to study these systems as dynamic entities using both simulations and experiments. This review emphasizes recent research efforts in order to elucidate the next steps needed to develop a fundamental framework needed for a deeper understanding of DESs. It covers recent developments in DES research, frames outstanding scientific questions, and identifies promising research thrusts aligned with the advancement of the field toward predictive models and fundamental understanding of these solvents.
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Affiliation(s)
- Benworth B Hansen
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee37996-2200, United States
| | - Stephanie Spittle
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee37996-2200, United States
| | - Brian Chen
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Derrick Poe
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Yong Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jeffrey M Klein
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Alexandre Horton
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee37996-2200, United States
| | - Laxmi Adhikari
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - Tamar Zelovich
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Brian W Doherty
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Burcu Gurkan
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Edward J Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Arthur Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee37996-2200, United States
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37916, United States
| | - Thomas A Zawodzinski
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee37996-2200, United States
| | - Gary A Baker
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - Mark E Tuckerman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Robert F Savinell
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Joshua R Sangoro
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee37996-2200, United States
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6
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Pal S, Roy R, Paul S. Potential of a Natural Deep Eutectic Solvent, Glyceline, in the Thermal Stability of the Trp-Cage Mini-protein. J Phys Chem B 2020; 124:7598-7610. [DOI: 10.1021/acs.jpcb.0c03501] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Rituparna Roy
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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7
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Gao H, Zheng X, Yang T, Zhang Q, Yan C, Zhou X, Shao Y. A pH-triggered G-triplex switch with K + tolerance. Chem Commun (Camb) 2020; 56:7349-7352. [PMID: 32484186 DOI: 10.1039/d0cc02757j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A pH-triggered G-triplex (G3) switch is demonstrated to operate in K+ using a planar ligand enabling reversible iminium-alkanolamine conversion as the G3 structuring-destructuring initiator.
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Affiliation(s)
- Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
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8
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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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9
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El Achkar T, Fourmentin S, Greige-Gerges H. Deep eutectic solvents: An overview on their interactions with water and biochemical compounds. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111028] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Mbous YP, Hayyan M, Hayyan A, Wong WF, Hashim MA, Looi CY. Applications of deep eutectic solvents in biotechnology and bioengineering-Promises and challenges. Biotechnol Adv 2016; 35:105-134. [PMID: 27923764 DOI: 10.1016/j.biotechadv.2016.11.006] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/22/2016] [Accepted: 11/26/2016] [Indexed: 12/20/2022]
Abstract
Deep eutectic solvents (DESs) have been touted recently as potential alternatives to ionic liquids (ILs). Although they possess core characteristics that are similar to those of ILs (e.g., low volatility, non-flammability, low melting points, low vapor pressure, dipolar nature, chemical and thermal stability, high solubility, and tuneability), DESs are superior in terms of the availability of raw materials, the ease of storage and synthesis, and the low cost of their starting materials. As such, they have become the subject of intensive research in various sectors, notably the chemical, electrochemical, and biological sectors. To date, the applications of DESs have shown great promise, especially in the medical and biotechnological fields. In spite of these various achievements, the safety concern for these mixtures must be sufficiently addressed. Indeed, in order to exploit the vast array of opportunities that DESs offer to the biological industry, first, they must be established as safe mixtures. Hence, the biotechnological applications of DESs only can be implemented if they are proven to have negligible or low toxicity profiles. This review is the first of its kind, and it discusses two current aspects of DES-based research. First, it describes the properties of these mixtures with ample focus on their toxicity profiles. Second, it provides an overview of the breakthroughs that have occurred and the foreseeable prospects of the use of DESs in various biotechnological and biological applications.
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Affiliation(s)
- Yves Paul Mbous
- University of Malaya Centre for Ionic Liquids (UMCiL), University of Malaya, Kuala Lumpur 50603, Malaysia; Department of Chemical Engineering, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Maan Hayyan
- University of Malaya Centre for Ionic Liquids (UMCiL), University of Malaya, Kuala Lumpur 50603, Malaysia; Institute of Halal Research University of Malaya (IHRUM), Academy of Islamic Studies, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Adeeb Hayyan
- University of Malaya Centre for Ionic Liquids (UMCiL), University of Malaya, Kuala Lumpur 50603, Malaysia; Institute of Halal Research University of Malaya (IHRUM), Academy of Islamic Studies, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Won Fen Wong
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Mohd Ali Hashim
- University of Malaya Centre for Ionic Liquids (UMCiL), University of Malaya, Kuala Lumpur 50603, Malaysia; Department of Chemical Engineering, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Chung Yeng Looi
- Department of Pharmacology, University of Malaya, Kuala Lumpur 50603, Malaysia
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Kholiya F, Bhatt N, Rathod MR, Meena R, Prasad K. Fundamental studies on the feasibility of deep eutectic solvents for the selective partition of glaucarubinone present in the roots of Simarouba glauca. J Sep Sci 2015; 38:3170-3175. [DOI: 10.1002/jssc.201500470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/22/2015] [Accepted: 06/26/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Faisal Kholiya
- Process Design and Engineering Cell; CSIR-Central Salt and Marine Chemicals Research Institute; Bhavnagar Gujarat India
| | - Nidhi Bhatt
- Marine Biotechnology and Ecology Division; CSIR-Central Salt and Marine Chemicals Research Institute; Bhavnagar Gujarat India
| | - Meena R. Rathod
- Marine Biotechnology and Ecology Division; CSIR-Central Salt and Marine Chemicals Research Institute; Bhavnagar Gujarat India
| | - Ramavatar Meena
- Process Design and Engineering Cell; CSIR-Central Salt and Marine Chemicals Research Institute; Bhavnagar Gujarat India
- AcSIR-Central Salt and Marine Chemicals Research Institute; Bhavnagar Gujarat India
| | - Kamalesh Prasad
- Marine Biotechnology and Ecology Division; CSIR-Central Salt and Marine Chemicals Research Institute; Bhavnagar Gujarat India
- AcSIR-Central Salt and Marine Chemicals Research Institute; Bhavnagar Gujarat India
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13
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Lozano P, Bernal JM, Nieto S, Gomez C, Garcia-Verdugo E, Luis SV. Active biopolymers in green non-conventional media: a sustainable tool for developing clean chemical processes. Chem Commun (Camb) 2015; 51:17361-74. [DOI: 10.1039/c5cc07600e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
By understanding structure–function relationships of active biopolymers (e.g. enzymes and nucleic acids) in green non-conventional media, sustainable chemical processes may be developed.
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Affiliation(s)
- Pedro Lozano
- Departamento de Bioquímica y Biología Molecular “B” e Inmunología
- Facultad de Química
- Campus de Excelencia Internacional Mare Nostrum
- Universidad de Murcia
- Murcia
| | - Juana M. Bernal
- Departamento de Bioquímica y Biología Molecular “B” e Inmunología
- Facultad de Química
- Campus de Excelencia Internacional Mare Nostrum
- Universidad de Murcia
- Murcia
| | - Susana Nieto
- Departamento de Bioquímica y Biología Molecular “B” e Inmunología
- Facultad de Química
- Campus de Excelencia Internacional Mare Nostrum
- Universidad de Murcia
- Murcia
| | - Celia Gomez
- Departamento de Bioquímica y Biología Molecular “B” e Inmunología
- Facultad de Química
- Campus de Excelencia Internacional Mare Nostrum
- Universidad de Murcia
- Murcia
| | | | - Santiago V. Luis
- Departamento de Química Inorgánica y Orgánica
- Universidad Jaume I
- Castellón
- Spain
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Tateishi-Karimata H, Sugimoto N. Structure, stability and behaviour of nucleic acids in ionic liquids. Nucleic Acids Res 2014; 42:8831-44. [PMID: 25013178 PMCID: PMC4132699 DOI: 10.1093/nar/gku499] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Nucleic acids have become a powerful tool in nanotechnology because of their conformational polymorphism. However, lack of a medium in which nucleic acid structures exhibit long-term stability has been a bottleneck. Ionic liquids (ILs) are potential solvents in the nanotechnology field. Hydrated ILs, such as choline dihydrogen phosphate (choline dhp) and deep eutectic solvent (DES) prepared from choline chloride and urea, are 'green' solvents that ensure long-term stability of biomolecules. An understanding of the behaviour of nucleic acids in hydrated ILs is necessary for developing DNA materials. We here review current knowledge about the structures and stabilities of nucleic acids in choline dhp and DES. Interestingly, in choline dhp, A-T base pairs are more stable than G-C base pairs, the reverse of the situation in buffered NaCl solution. Moreover, DNA triplex formation is markedly stabilized in hydrated ILs compared with aqueous solution. In choline dhp, the stability of Hoogsteen base pairs is comparable to that of Watson-Crick base pairs. Moreover, the parallel form of the G-quadruplex is stabilized in DES compared with aqueous solution. The behaviours of various DNA molecules in ILs detailed here should be useful for designing oligonucleotides for the development of nanomaterials and nanodevices.
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Affiliation(s)
- Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojimaminamimachi, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojimaminamimachi, Kobe 650-0047, Japan Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojimaminamimachi, Kobe 650-0047, Japan
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15
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Mukesh C, Mondal D, Sharma M, Prasad K. Choline chloride–thiourea, a deep eutectic solvent for the production of chitin nanofibers. Carbohydr Polym 2014; 103:466-71. [DOI: 10.1016/j.carbpol.2013.12.082] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 12/25/2013] [Accepted: 12/28/2013] [Indexed: 10/25/2022]
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16
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Shing Ho P, Mergny JL. Nucleic acid structure: a continuing tradition. Methods 2013; 64:1-2. [PMID: 24160748 DOI: 10.1016/j.ymeth.2013.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, CO 80523-1870, USA.
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