1
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Olave B. DNA nanotechnology in ionic liquids and deep eutectic solvents. Crit Rev Biotechnol 2023:1-21. [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] [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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2
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López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Chen D, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, Chan AH, Simanshu DK, Nissley DV, Streitz FH, Stephen AG, Turbyville TJ, Lightstone FC, Gnanakaran S, Ingólfsson HI, Neale C. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. J Chem Theory Comput 2022; 18:5025-5045. [PMID: 35866871 DOI: 10.1021/acs.jctc.2c00168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. Here, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (∼98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ∼1.5 million atoms is discussed in the context of MuMMI.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Fikret Aydin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N Van
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Lara A Patel
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Violetta Burns
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tyler J E Reddy
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Francesco Di Natale
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Albert H Chan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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3
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Wang Y, He H, Wang C, Lu Y, Dong K, Huo F, Zhang S. Insights into Ionic Liquids: From Z-Bonds to Quasi-Liquids. JACS AU 2022; 2:543-561. [PMID: 35373210 PMCID: PMC8965826 DOI: 10.1021/jacsau.1c00538] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Indexed: 05/26/2023]
Abstract
Ionic liquids (ILs) hold great promise in the fields of green chemistry, environmental science, and sustainable technology due to their unique properties, such as a tailorable structure, the various types available, and their environmentally friendly features. On the basis of multiscale simulations and experimental characterizations, two unique features of ILs are as follows: (1) strong coupling interactions between the electrostatic forces and hydrogen bonds, namely in the Z-bond, and (2) the unique semiordered structure and properties of ultrathin films, specifically regarding the quasi-liquid. In accordance with the aforementioned theoretical findings, many cutting-edge applications have been proposed: for example, CO2 capture and conversion, biomass conversion and utilization, and energy storage materials. Although substantial progress has been made recently in the field of ILs, considerable challenges remain in understanding the nature of and devising applications for ILs, especially in terms of e.g. in situ/real-time observation and highly precise multiscale simulations of the Z-bond and quasi-liquid. In this Perspective, we review recent developments and challenges for the IL research community and provide insights into the nature and function of ILs, which will facilitate future applications.
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Affiliation(s)
- Yanlei Wang
- Beijing
Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory
of Multiphase Complex Systems, CAS Key Laboratory of Green Process
and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- University
of Chinese Academy of Sciences, Beijing 100049, People’s
Republic of China
| | - Hongyan He
- Beijing
Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory
of Multiphase Complex Systems, CAS Key Laboratory of Green Process
and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- University
of Chinese Academy of Sciences, Beijing 100049, People’s
Republic of China
| | - Chenlu Wang
- Beijing
Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory
of Multiphase Complex Systems, CAS Key Laboratory of Green Process
and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- University
of Chinese Academy of Sciences, Beijing 100049, People’s
Republic of China
| | - Yumiao Lu
- Beijing
Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory
of Multiphase Complex Systems, CAS Key Laboratory of Green Process
and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Kun Dong
- Beijing
Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory
of Multiphase Complex Systems, CAS Key Laboratory of Green Process
and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Feng Huo
- Beijing
Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory
of Multiphase Complex Systems, CAS Key Laboratory of Green Process
and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Suojiang Zhang
- Beijing
Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory
of Multiphase Complex Systems, CAS Key Laboratory of Green Process
and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- University
of Chinese Academy of Sciences, Beijing 100049, People’s
Republic of China
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4
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Patel R, Clark AK, DeStefano G, DeStefano I, Gogoj H, Gray E, Patel AY, Hauner JT, Caputo GA, Vaden TD. Sequence-specific destabilization of azurin by tetramethylguanidinium-dipeptide ionic liquids. Biochem Biophys Rep 2022; 30:101242. [PMID: 35280523 PMCID: PMC8907678 DOI: 10.1016/j.bbrep.2022.101242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/18/2022] [Accepted: 03/02/2022] [Indexed: 12/01/2022] Open
Abstract
The thermal unfolding of the copper redox protein azurin was studied in the presence of four different dipeptide-based ionic liquids (ILs) utilizing tetramethylguanidinium as the cation. The four dipeptides have different sequences including the amino acids Ser and Asp: TMG-AspAsp, TMG-SerSer, TMG-SerAsp, and TMG-AspSer. Thermal unfolding curves generated from temperature-dependent fluorescence spectroscopy experiments showed that TMG-AspAsp and TMG-SerSer have minor destabilizing effects on the protein while TMG-AspSer and TMG-SerAsp strongly destabilize azurin. Red-shifted fluorescence signatures in the 25 °C correlate with the observed protein destabilization in the solutions with TMG-AspSer and TMG-SerAsp. These signals could correspond to interactions between the Asp residue in the dipeptide and the azurin Trp residue in the unfolded state. These results, supported by appropriate control experiments, suggest that dipeptide sequence-specific interactions lead to selective protein destabilization and motivate further studies of TMG-dipeptide ILs. Four different dipeptide-based ionic liquids were prepared with TMG as cation. The dipeptides included all four sequences containing Asp and Ser. The ionic liquids destabilizing effects on the protein azurin were measured. Different dipeptide sequences have different effects on the protein stability.
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Affiliation(s)
- Roshani Patel
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Austin K Clark
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Gabriella DeStefano
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Isabella DeStefano
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Hunter Gogoj
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Erin Gray
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Aashka Y Patel
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Joshua T Hauner
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
| | - Timothy D Vaden
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028, USA
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5
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Sarkar S, Singh PC. The combined action of cations and anions of ionic liquids modulates the formation and stability of G-quadruplex DNA. Phys Chem Chem Phys 2021; 23:24497-24504. [PMID: 34700329 DOI: 10.1039/d1cp03730g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
G-Quadruplex (Gq) formation and stabilization by any molecule is an essential requirement for its application in therapy, especially in oncology. Metal cations have shown higher propensity of the formation of the Gq structure and its stabilization. In this study, the role of both cations and anions of ionic liquids (ILs) on the Gq formation of human telomere (hTeloG) and its stability was investigated using spectroscopic and molecular dynamics simulation techniques. Irrespective of the nature of anions of ILs, tetramethylguanidinium (TMG) cations associated with different anions can form an antiparallel Gq structure in hTeloG. However, the propensity of the formation of an antiparallel Gq structure and its stability depend on the chain length of anions of ILs. Gq is significantly less stable in ILs having longer hydrocarbon chain anions compared to the short chain anions suggesting that the hydrophobicity of the anion plays a critical role in the stability and formation of the Gq structure by ILs. The data indicate that longer hydrocarbon chain anions of ILs preferably interact in the loop region of Gq through hydrophobic interaction which enhances the overall binding of the cation of ILs with Gq causing a decrease in the stacking energy between the G-quartets as well as Hoogsteen hydrogen bonds between the guanine bases leading to the destabilization of the antiparallel Gq structure.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, India, 700032.
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, India, 700032.
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6
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Shukla SK, Mikkola JP. Use of Ionic Liquids in Protein and DNA Chemistry. Front Chem 2020; 8:598662. [PMID: 33425856 PMCID: PMC7786294 DOI: 10.3389/fchem.2020.598662] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Ionic liquids (ILs) have been receiving much attention as solvents in various areas of biochemistry because of their various beneficial properties over the volatile solvents and ILs availability in myriad variants (perhaps as many as 108) owing to the possibility of paring one cation with several anions and vice-versa as well as formulations as zwitterions. Their potential as solvents lies in their tendency to offer both directional and non-directional forces toward a solute molecule. Because of these forces, ionic liquids easily undergo intermolecular interactions with a range of polar/non-polar solutes, including biomolecules such as proteins and DNA. The interaction of genomic species in aqueous/non-aqueous states assists in unraveling their structure and functioning, which have implications in various biomedical applications. The charge density of ionic liquids renders them hydrophilic and hydrophobic, which retain intact over long-range of temperatures. Their ability in stabilizing or destabilizing the 3D-structure of a protein or the double-helical structure of DNA has been assessed superior to the water and volatile organic solvents. The aptitude of an ion in influencing the structure and stability of a native protein depends on their ranking in the Hofmeister series. However, at several instances, a reverse Hofmeister ordering of ions and specific ion-solute interaction has been observed. The capability of an ionic liquid in terms of the tendency to promote the coiling/uncoiling of DNA structure is noted to rely on the basicity, electrostatic interaction, and hydrophobicity of the ionic liquid in question. Any change in the DNA's double-helical structure reflects a change in its melting temperature (T m), compared to a standard buffer solution. These changes in DNA structure have implications in biosensor design and targeted drug-delivery in biomedical applications. In the current review, we have attempted to highlight various aspects of ionic liquids that influence the structure and properties of proteins and DNA. In short, the review will address the issues related to the origin and strength of intermolecular interactions, the effect of structural components, their nature, and the influence of temperature, pH, and additives on them.
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Affiliation(s)
- Shashi Kant Shukla
- Technical Chemistry, Department of Chemistry, Chemical-Biological Centre, Umeå University, Umeå, Sweden
| | - Jyri-Pekka Mikkola
- Technical Chemistry, Department of Chemistry, Chemical-Biological Centre, Umeå University, Umeå, Sweden
- Industrial Chemistry and Reaction Engineering, Department of Chemical Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland
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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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