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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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2
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Varona M, Eor P, Ferreira Neto LC, Merib J, Anderson JL. Metal-containing and magnetic ionic liquids in analytical extractions and gas separations. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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3
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Egorova KS, Posvyatenko AV, Larin SS, Ananikov V. Ionic liquids: prospects for nucleic acid handling and delivery. Nucleic Acids Res 2021; 49:1201-1234. [PMID: 33476366 PMCID: PMC7897475 DOI: 10.1093/nar/gkaa1280] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
Operations with nucleic acids are among the main means of studying the mechanisms of gene function and developing novel methods of molecular medicine and gene therapy. These endeavours usually imply the necessity of nucleic acid storage and delivery into eukaryotic cells. In spite of diversity of the existing dedicated techniques, all of them have their limitations. Thus, a recent notion of using ionic liquids in manipulations of nucleic acids has been attracting significant attention lately. Due to their unique physicochemical properties, in particular, their micro-structuring impact and tunability, ionic liquids are currently applied as solvents and stabilizing media in chemical synthesis, electrochemistry, biotechnology, and other areas. Here, we review the current knowledge on interactions between nucleic acids and ionic liquids and discuss potential advantages of applying the latter in delivery of the former into eukaryotic cells.
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Affiliation(s)
- Ksenia S Egorova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow 119991, Russia
| | - Alexandra V Posvyatenko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow 119991, Russia
- Molecular Immunology Laboratory, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samory Mashela St 1, Moscow 117997, Russia
| | - Sergey S Larin
- Molecular Immunology Laboratory, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samory Mashela St 1, Moscow 117997, Russia
| | - Valentine P Ananikov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow 119991, Russia
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4
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Nucleic acid extraction: Fundamentals of sample preparation methodologies, current advancements, and future endeavors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115985] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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5
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Bowers AN, Trujillo-Rodríguez MJ, Farooq MQ, Anderson JL. Extraction of DNA with magnetic ionic liquids using in situ dispersive liquid-liquid microextraction. Anal Bioanal Chem 2019; 411:7375-7385. [PMID: 31655857 DOI: 10.1007/s00216-019-02163-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/15/2019] [Accepted: 09/20/2019] [Indexed: 12/29/2022]
Abstract
A new class of magnetic ionic liquids (MILs) with metal-containing cations was applied in in situ dispersive liquid-liquid microextraction (DLLME) for the extraction of long and short double-stranded DNA. For developing the method, MILs comprised of N-substituted imidazole ligands (with butyl-, benzyl-, or octyl-groups as substituents) coordinated to different metal centers (Ni2+, Mn2+, or Co2+) as cations, and chloride anions were investigated. These water-soluble MILs were reacted with the bis[(trifluoromethyl)sulfonyl]imide anion during the extraction to generate a water-immiscible MIL capable of preconcentrating DNA. The feasibility of combining the extraction methodology with anion-exchange high-performance liquid chromatography with diode array detection (HPLC-DAD) or fluorescence spectroscopy was studied. The method with the Ni2+- and Co2+-based MILs was easily combined with fluorescence spectroscopy and provided a faster and more sensitive method than HPLC-DAD for the determination of DNA. In addition, the method was compared to conventional DLLME using analogous water-immiscible MILs. The developed in situ MIL-DLLME method required only 3 min for DNA extraction and yielded 1.1-1.5 times higher extraction efficiency (EFs) than the conventional MIL-DLLME method. The in situ MIL-DLLME method was also compared to the trihexyl(tetradecyl)phosphonium tris(hexafluorocetylaceto)nickelate(II) MIL, which has been used in previous DNA extraction studies. EFs of 42-99% were obtained using the new generation of MILs, whereas EFs of only 20-38% were achieved with the phosphonium MIL. This new class of MILs is simple and inexpensive to prepare. In addition, the MILs present operational advantages such as easier manipulation in comparison to hydrophobic MILs, which can have high viscosities. These MILs are a promising new class of DNA extraction solvents that can be manipulated using an external magnetic field. Graphical abstract Magnetic ionic liquids with metal-containing cations are applied in in situ dispersive liquid-liquid microextraction for the extraction of long and short double-stranded DNA.
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Affiliation(s)
- Ashley N Bowers
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, USA
| | | | - Muhammad Q Farooq
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, USA
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, USA.
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6
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Marcinkowska R, Konieczna K, Marcinkowski Ł, Namieśnik J, Kloskowski A. Application of ionic liquids in microextraction techniques: Current trends and future perspectives. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.07.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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7
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Marengo A, Emaus MN, Bertea CM, Bicchi C, Rubiolo P, Cagliero C, Anderson JL. Arabidopsis thaliana ITS sequence-specific DNA extraction by ion-tagged oligonucleotides coupled with a magnetic ionic liquid. Anal Bioanal Chem 2019; 411:6583-6590. [PMID: 31422433 DOI: 10.1007/s00216-019-02054-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/18/2019] [Accepted: 07/26/2019] [Indexed: 12/28/2022]
Abstract
This study reports a follow-up investigation on the capture of specific DNA sequences using ion-tagged oligonucleotides (ITOs) and magnetic ionic liquids (MIL). Five allylimidazolium salts bearing octyl substituents ([AOIM+]-ITOs) were used for the selective extraction of the internal transcribed spacer region (ITS) from Arabidopsis thaliana. In this work, the ability of the [AOIM+]-ITOs to enhance the extraction of longer target sequences (~ 700 bp) of plant origin was shown. Moreover, the independence of the probe binding position and the importance of complementarity to the target region for the extraction performance were demonstrated. To test the specificity of the ITOs, the same experiments were performed using the ITS region from another plant species, with a lower target capture for the probes which were specific for the A. thaliana sequence. Finally, extraction in the presence of interferences (heterogenous DNA, primary and secondary metabolites, proteins) provided interesting and insightful results. This work illustrates the feasibility and versatility of these probes when coupled to MILs for rapid, cost-effective, and environmentally sensitive sample preparation in the extraction of specific target sequences from different origins. Graphical abstract.
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Affiliation(s)
- Arianna Marengo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125, Turin, Italy
| | - Miranda N Emaus
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, USA
| | - Cinzia M Bertea
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Unità di Fisiologia Vegetale, Università di Torino, via Quarello 15/A, 10135, Turin, Italy
| | - Carlo Bicchi
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125, Turin, Italy
| | - Patrizia Rubiolo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125, Turin, Italy
| | - Cecilia Cagliero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125, Turin, Italy.
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, USA
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Clark KD, Zhu C, Anderson JL. Maximizing Ion-Tagged Oligonucleotide Loading on Magnetic Ionic Liquid Supports for the Sequence-Specific Extraction of Nucleic Acids. Anal Chem 2019; 91:5945-5952. [PMID: 30995833 DOI: 10.1021/acs.analchem.9b00350] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Targeted nucleic acid analysis requires the highly selective extraction of desired DNA fragments in order to minimize interferences from samples with abundant heterogeneous sequences. We previously reported a method based on functionalized oligonucleotide probes known as ion-tagged oligonucleotides (ITOs) that hybridize with complementary DNA targets for subsequent capture using a hydrophobic magnetic ionic liquid (MIL) support. Although the ITO-MIL approach enriched specific DNA sequences in quantities comparable to a commercial magnetic bead-based method, the modest affinity of the ITO for the hydrophobic MIL limited the yield of DNA targets, particularly when stringent wash conditions were applied to remove untargeted DNA. Here, we report the synthesis and characterization of a series of ITOs in which functional groups were installed within the cation and anion components of the tag moiety in order to facilitate loading of the ITO to the MIL support phase. In addition to hydrophobic interactions, we demonstrate that π-π stacking and fluorophilic interactions can be exploited for loading oligonucleotide probes onto MILs. Using a disubstituted ion-tagged oligonucleotide (DTO) possessing two linear C8 groups, nearly quantitative loading of the probe onto the MIL support was achieved. The enhanced stability of the DTO within the MIL solvent permitted successive wash steps without the loss of the DNA target compared to a monosubstituted ITO with a single C8 group that was susceptible to increased loss of analyte. Furthermore, the successful capture of a 120 bp KRAS fragment from human plasma samples followed by real-time quantitative polymerase chain reaction (qPCR) amplification is demonstrated.
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Affiliation(s)
- Kevin D Clark
- Department of Chemistry , Iowa State University , 1605 Gilman Hall , Ames , Iowa 50011 , United States
| | - Chenghui Zhu
- Department of Chemistry , Iowa State University , 1605 Gilman Hall , Ames , Iowa 50011 , United States
| | - Jared L Anderson
- Department of Chemistry , Iowa State University , 1605 Gilman Hall , Ames , Iowa 50011 , United States
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9
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Emaus MN, Varona M, Anderson JL. Sequence-specific preconcentration of a mutation prone KRAS fragment from plasma using ion-tagged oligonucleotides coupled to qPCR compatible magnetic ionic liquid solvents. Anal Chim Acta 2019; 1068:1-10. [PMID: 31072469 DOI: 10.1016/j.aca.2019.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 01/22/2023]
Abstract
Circulating tumor DNA (ctDNA) is a source of mutant DNA found in plasma and holds great promise in guiding cancer diagnostics, prognostics, and treatment. However, ctDNA fragments are challenging to detect in plasma due to their low abundance compared to wild-type DNA. In this study, a series of ion-tagged oligonucleotides (ITO) were synthesized using thiol-ene click chemistry and designed to selectively anneal target DNA. The ITO-DNA duplex was subsequently captured using a hydrophobic magnetic ionic liquid (MIL) as a liquid support. Extracted target DNA was quantified by adding the DNA-enriched MIL to the quantitative polymerase chain reaction (qPCR) buffer to streamline the extraction procedure. Clinically relevant concentrations of the mutation prone KRAS fragment, which has been linked to colorectal, lung, and bladder cancer, were preconcentrated using the ITO-MIL strategy allowing for enrichment factors as high as 19.49 ± 1.44 from pure water and 4.02 ± 0.50 from 10-fold diluted plasma after a 1 min extraction. Preconcentration could only be achieved when adding the ITO probe to the sample validating the selectivity of the ITO in the capture process. In addition, the amplification efficiency of qPCR was not affected when performing extractions from a diluted-plasma matrix demonstrating that the ITO-MIL approach coupled to direct-qPCR can be used to quantitate DNA from complex matrices. In comparison, commercially available steptavidin-coated magnetic beads were observed to lose selectivity when performing extractions from a 10-fold diluted plasma matrix. The selectivity of the ITO-MIL method, coupled with the ability to rapidly preconcentrate clinically relevant concentrations of target DNA from 10-fold diluted plasma, suggests that this method has the potential to be applied towards the extraction of ctDNA fragments from clinical samples.
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Affiliation(s)
- Miranda N Emaus
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, United States
| | - Marcelino Varona
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, United States
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, United States.
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10
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Marengo A, Cagliero C, Sgorbini B, Anderson JL, Emaus MN, Bicchi C, Bertea CM, Rubiolo P. Development of an innovative and sustainable one-step method for rapid plant DNA isolation for targeted PCR using magnetic ionic liquids. PLANT METHODS 2019; 15:23. [PMID: 30899320 PMCID: PMC6408755 DOI: 10.1186/s13007-019-0408-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/02/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bottleneck in the bioanalytical workflow. New opportunities have been created by the use of magnetic ionic liquids (MILs) thanks to their affinity for nucleic acids. RESULTS In the present study, a MIL-based magnet-assisted dispersive liquid-liquid microextraction (maDLLME) method was optimized for the extraction of genomic DNA from Arabidopsis thaliana (L.) Heynh leaves. MILs containing different metal centers were tested and the extraction method was optimized in terms of MIL volume and extraction time for purified DNA and crude lysates. The proposed approach yielded good extraction efficiency and is compatible with both quantitative analysis through fluorimetric-based detection and qualitative analysis as PCR amplification of multi and single locus genes. The protocol was successfully applied to a set of plant species and tissues. CONCLUSIONS The developed MIL-based maDLLME approach exhibits good enrichment of nucleic acids for extraction of template suitable for targeted PCR; it is very fast, sustainable and potentially automatable thereby representing a powerful tool for screening plants rapidly using DNA-based methods.
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Affiliation(s)
- Arianna Marengo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | - Cecilia Cagliero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | - Barbara Sgorbini
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | | | - Miranda N. Emaus
- Department of Chemistry, Iowa State University, Ames, IA 50011 USA
| | - Carlo Bicchi
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | - Cinzia M. Bertea
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Unità di Fisiologia Vegetale, Università di Torino, via Quarello 15/A, 10135 Turin, Italy
| | - Patrizia Rubiolo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
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11
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Trujillo-Rodríguez MJ, Anderson JL. In situ generation of hydrophobic magnetic ionic liquids in stir bar dispersive liquid-liquid microextraction coupled with headspace gas chromatography. Talanta 2018; 196:420-428. [PMID: 30683387 DOI: 10.1016/j.talanta.2018.12.071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 11/17/2022]
Abstract
For the first time, an in situ stir bar dispersive liquid-liquid microextraction approach has been developed and coupled with headspace gas chromatography-mass spectrometry for the determination of a group of organic pollutants. The method exploits a new generation of magnetic ionic liquids (MILs) that contain paramagnetic cations based on Ni2+ or Co2+ metal centers coordinated with either N-butylimidazole or N-octylimidazole ligands and chloride anions. The reactants are added to an aqueous solution containing a high field neodymium rod magnet, followed by the addition of the bis[(trifluoromethyl)sulfonyl]imide anion that promotes a metathesis reaction for the in situ generation of a hydrophobic MIL. Concurrently, a high stirring rate is maintained to exceed the magnetic field of the rod magnet and disperse the generated MIL in the sample solution. When stirring is stopped, the MIL coats the rod magnet due to its paramagnetic nature, facilitating the MIL transfer and subsequent desorption and analysis. Under optimum conditions, the method required a 2.5-18% (w/v) aqueous solution of sodium chloride, 10 mL of sample, 20 or 30 mg of MIL, the addition of a small volume of dispersive solvent, and stirring for 5-7.5 min, depending on the MIL. The method provided limits of detection (LODs) down to 10 μg L-1, adequate reproducibility (with relative standard deviation values lower than 10% for a spiked level of 80 μg L-1), and relative recoveries between 72.5% and 102%. Furthermore, the method was successfully applied in the analysis of tap and mineral water.
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Affiliation(s)
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
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12
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Trujillo-Rodríguez MJ, Nan H, Varona M, Emaus MN, Souza ID, Anderson JL. Advances of Ionic Liquids in Analytical Chemistry. Anal Chem 2018; 91:505-531. [PMID: 30335970 DOI: 10.1021/acs.analchem.8b04710] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - He Nan
- Department of Chemistry , Iowa State University , 1605 Gilman Hall, Ames , Iowa 50011 , United States
| | - Marcelino Varona
- Department of Chemistry , Iowa State University , 1605 Gilman Hall, Ames , Iowa 50011 , United States
| | - Miranda N Emaus
- Department of Chemistry , Iowa State University , 1605 Gilman Hall, Ames , Iowa 50011 , United States
| | - Israel D Souza
- Department of Chemistry , Iowa State University , 1605 Gilman Hall, Ames , Iowa 50011 , United States
| | - Jared L Anderson
- Department of Chemistry , Iowa State University , 1605 Gilman Hall, Ames , Iowa 50011 , United States
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