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Cinar M, Martinez-Medina L, Puvvula PK, Arakelyan A, Vardarajan BN, Anthony N, Nagaraju GP, Park D, Feng L, Sheff F, Mosunjac M, Saxe D, Flygare S, Alese OB, Kaufman JL, Lonial S, Sarmiento JM, Lossos IS, Vertino PM, Lopez JA, El-Rayes B, Bernal-Mizrachi L. Transposon DNA sequences facilitate the tissue-specific gene transfer of circulating tumor DNA between human cells. Nucleic Acids Res 2024:gkae427. [PMID: 38783375 DOI: 10.1093/nar/gkae427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/01/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
The exchange of genes between cells is known to play an important physiological and pathological role in many organisms. We show that circulating tumor DNA (ctDNA) facilitates cell-specific gene transfer between human cancer cells and explain part of the mechanisms behind this phenomenon. As ctDNA migrates into the nucleus, genetic information is transferred. Cell targeting and ctDNA integration require ERVL, SINE or LINE DNA sequences. Chemically manufactured AluSp and MER11C sequences replicated multiple myeloma (MM) ctDNA cell targeting and integration. Additionally, we found that ctDNA may alter the treatment response of MM and pancreatic cancer models. This study shows that retrotransposon DNA sequences promote cancer gene transfer. However, because cell-free DNA has been detected in physiological and other pathological conditions, our findings have a broader impact than just cancer. Furthermore, the discovery that transposon DNA sequences mediate tissue-specific targeting will open up a new avenue for the delivery of genes and therapies.
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Affiliation(s)
- Munevver Cinar
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | | | | | - Arsen Arakelyan
- Bioinformatics group, Institute of Molecular Biology NAS RA, Yerevan, Armenia
| | | | - Neil Anthony
- Integrated Cellular Imaging Core, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Ganji P Nagaraju
- Division of hematology and oncology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dongkyoo Park
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Lei Feng
- Kodikaz Therapeutic Solutions, Inc, New York, NY, USA
| | - Faith Sheff
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Marina Mosunjac
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Debra Saxe
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Steven Flygare
- Department of Computational Biology/ Genetics, The University of Utah, Salt Lake City, UT, USA
| | - Olatunji B Alese
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Jonathan L Kaufman
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Juan M Sarmiento
- Department of Surgery, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Izidore S Lossos
- Department of Medicine, Division of Hematology-Oncology and Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Paula M Vertino
- Department of Biomedical Genetics and the Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Jose A Lopez
- Bloodworks Northwest Research Institute, Division of Hematology, University of Washington School of Medicine, Seattle, WA, USA
| | - Bassel El-Rayes
- Division of hematology and oncology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leon Bernal-Mizrachi
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
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Mathur D, Medintz IL. The Growing Development of DNA Nanostructures for Potential Healthcare-Related Applications. Adv Healthc Mater 2019; 8:e1801546. [PMID: 30843670 PMCID: PMC9285959 DOI: 10.1002/adhm.201801546] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/17/2019] [Indexed: 12/21/2022]
Abstract
DNA self-assembly has proven to be a highly versatile tool for engineering complex and dynamic biocompatible nanostructures from the bottom up with a wide range of potential bioapplications currently being pursued. Primary among these is healthcare, with the goal of developing diagnostic, imaging, and drug delivery devices along with combinatorial theranostic devices. The path to understanding a role for DNA nanotechnology in biomedical sciences is being approached carefully and systematically, starting from analyzing the stability and immune-stimulatory properties of DNA nanostructures in physiological conditions, to estimating their accessibility and application inside cellular and model animal systems. Much remains to be uncovered but the field continues to show promising results toward developing useful biomedical devices. This review discusses some aspects of DNA nanotechnology that makes it a favorable ingredient for creating nanoscale research and biomedical devices and looks at experiments undertaken to determine its stability in vivo. This is presented in conjugation with examples of state-of-the-art developments in biomolecular sensing, imaging, and drug delivery. Finally, some of the major challenges that warrant the attention of the scientific community are highlighted, in order to advance the field into clinically relevant applications.
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Affiliation(s)
- Divita Mathur
- Center for Bio/Molecular Science and Engineering U.S. Naval Research Laboratory Code 6910 Washington DC 20375 USA
- College of Science George Mason University Fairfax VA 22030 USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering U.S. Naval Research Laboratory Code 6907 Washington DC 20375 USA
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3
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Klecka M, Thybo C, Macaubas C, Solov'yov I, Simard J, Balboni IM, Fox E, Voss A, Mellins ED, Astakhova K. Autoantibody Profiling in Lupus Patients using Synthetic Nucleic Acids. Sci Rep 2018; 8:5554. [PMID: 29615791 PMCID: PMC5883037 DOI: 10.1038/s41598-018-23910-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/19/2018] [Indexed: 02/08/2023] Open
Abstract
Autoantibodies to nuclear components of cells (antinuclear antibodies, ANA), including DNA (a-DNA), are widely used in the diagnosis and subtyping of certain autoimmune diseases, including systemic lupus erythematosus (SLE). Despite clinical use over decades, precise, reproducible measurement of a-DNA titers remains difficult, likely due to the substantial sequence and length heterogeneity of DNA purified from natural sources. We designed and tested a panel of synthetic nucleic acid molecules composed of native deoxyribonucleotide units to measure a-DNA. ELISA assays using these antigens show specificity and reproducibility. Applying the ELISA tests to serological studies of pediatric and adult SLE, we identified novel clinical correlations. We also observed preferential recognition of a specific synthetic antigen by antibodies in SLE sera. We determined the probable basis for this finding using computational analyses, providing valuable structural information for future development of DNA antigens. Synthetic nucleic acid molecules offer the opportunity to standardize assays and to dissect antibody-antigen interactions.
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Affiliation(s)
- Martin Klecka
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800, Kgs, Lyngby, Denmark
| | - Christina Thybo
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Claudia Macaubas
- Department of Pediatrics, Program in Immunology, Stanford University School of Medicine, 269 Campus Drive, Stanford, California, 94305, USA
| | - Ilia Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Julia Simard
- Department of Health and Research Policy, Stanford University School of Medicine, 150 Governor's Lane, Stanford, California, 94305, USA
| | - Imelda Maria Balboni
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, Stanford University, 700 Welch Rd. Suite 301, Stanford, California, 94304, USA
| | - Emily Fox
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, Stanford University, 700 Welch Rd. Suite 301, Stanford, California, 94304, USA
| | - Anne Voss
- Department of Rheumatology, Odense University Hospital, J. B. Winsløws Vej 19, 2, 5000, Odense C, Denmark
| | - Elizabeth D Mellins
- Department of Pediatrics, Program in Immunology, Stanford University School of Medicine, 269 Campus Drive, Stanford, California, 94305, USA.
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800, Kgs, Lyngby, Denmark.
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Greenstein PD, Casabianca LB. Interplay Between π-Stacking and Hydrogen Bonding in the Self-Association of Different Isomers of Naphthalenedicarboxylic Acid. J Phys Chem B 2017; 121:5086-5093. [PMID: 28489376 DOI: 10.1021/acs.jpcb.7b01465] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using proton and carbon chemical shifts, we investigated the self-association of three isomers of naphthalenedicarboxylic acid, a model for the aggregation of asphaltenes. Experimental proton chemical shifts of each isomer were measured as a function of concentration in an aprotic solvent. Several potential structures of the monomer and dimer of each naphthalenedicarboxylic acid were considered, and calculated proton chemical shifts for the potential monomer and dimer structures were compared to the experimental chemical shifts to find the weighted average structure that best fit the experimental shifts. Calculated carbon chemical shifts were also compared to experimental values. The chemical shift comparison and calculated energies indicate that π-stacked dimers are not likely to contribute significantly to the dimer structure of any of the three naphthalenedicarboxylic acid isomers studied.
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Affiliation(s)
- Paul D Greenstein
- Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States
| | - Leah B Casabianca
- Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States
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Domljanovic I, Carstens A, Okholm A, Kjems J, Nielsen CT, Heegaard NHH, Astakhova K. Complexes of DNA with fluorescent dyes are effective reagents for detection of autoimmune antibodies. Sci Rep 2017; 7:1925. [PMID: 28507286 PMCID: PMC5432514 DOI: 10.1038/s41598-017-02214-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/06/2017] [Indexed: 11/29/2022] Open
Abstract
To date, there are multiple assays developed that detect and quantify antibodies in biofluids. Nevertheless, there is still a lack of simple approaches that specifically detect autoimmune antibodies to double-stranded DNA. Herein we investigate the potential of novel nucleic acid complexes as targets for these antibodies. This is done in a simple, rapid and specific immunofluorescence assay. Specifically, employing 3D nanostructures (DNA origami), we present a new approach in the detection and study of human antibodies to DNA. We demonstrate the detection of anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We tested the most potent non-covalent pairs of DNA and fluorescent dyes. Several complexes showed specific recognition of autoimmune antibodies in human samples of lupus patients using a simple one-step immunofluorescence method. This makes the novel assay developed herein a promising tool for research and point-of-care monitoring of anti-DNA antibodies. Using this method, we for the first time experimentally confirm that the disease-specific autoimmune antibodies are sensitive to the 3D structure of nucleic acids and not only to the nucleotide sequence, as was previously thought.
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Affiliation(s)
- Ivana Domljanovic
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark
| | - Annika Carstens
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark
| | - Anders Okholm
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, 8000, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, 8000, Denmark
| | - Christoffer Tandrup Nielsen
- Copenhagen Lupus and Vasculitis Clinic, Centre for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, 2100, Denmark
| | - Niels H H Heegaard
- Department of Autoimmunology and Biomarkers, Statens Serum Institute, DK-2300, Copenhagen S, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, University of Southern Denmark, DK-5000, Odense C, Denmark
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark.
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Samuelsen SV, Solov'yov IA, Balboni IM, Mellins E, Nielsen CT, Heegaard NHH, Astakhova K. Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies. Sci Rep 2016; 6:35827. [PMID: 27775006 PMCID: PMC5075775 DOI: 10.1038/srep35827] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/05/2016] [Indexed: 01/11/2023] Open
Abstract
New techniques to detect and quantify antibodies to nucleic acids would provide a significant advance over current methods, which often lack specificity. We investigate the potential of novel antigens containing locked nucleic acids (LNAs) as targets for antibodies. Particularly, employing molecular dynamics we predict optimal nucleotide composition for targeting DNA-binding antibodies. As a proof of concept, we address a problem of detecting anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We test the best oligonucleotide binders in surface plasmon resonance studies to analyze binding and kinetic aspects of interactions between antigens and target DNA. These DNA and LNA/DNA sequences showed improved binding in enzyme-linked immunosorbent assay using human samples of pediatric lupus patients. Our results suggest that the novel method is a promising tool to create antigens for research and point-of-care monitoring of anti-DNA antibodies.
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Affiliation(s)
- Simone V Samuelsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark
| | - Imelda M Balboni
- Department of Pediatrics, Division of Allergy, Immunology and Rheumatology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Elizabeth Mellins
- Department of Pediatrics, Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Christoffer Tandrup Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institute, DK-2300 Copenhagen S, Denmark.,Copenhagen Lupus and Vasculitis Clinic, Centre for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, 2100, Denmark
| | - Niels H H Heegaard
- Department of Autoimmunology and Biomarkers, Statens Serum Institute, DK-2300 Copenhagen S, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, University of Southern Denmark, DK-5000 Odense C, Denmark
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark
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An electrochemical aptasensor for multiplex antibiotics detection based on metal ions doped nanoscale MOFs as signal tracers and RecJ f exonuclease-assisted targets recycling amplification. Talanta 2016; 161:867-874. [PMID: 27769495 DOI: 10.1016/j.talanta.2016.09.051] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/17/2016] [Accepted: 09/21/2016] [Indexed: 12/13/2022]
Abstract
An ultrasensitive electrochemical aptasensor for simultaneous detection of oxytetracycline (OTC) and kanamycin (KAN) has been developed based on metal ions doped metal organic frame materials (MOFs) as signal tracers and RecJf exonuclease-catalyzed targets recycling amplification. The aptasensor consists of capture beads (the anti-single-stranded DNA Antibody, as anti-ssDNA Ab, labeled on Dynabeads) and nanoscale MOF (NMOF) based signal tracers (simplified as Apts-MNM, the NMOF labeled with metal ions and the aptamers). Particularly, the MOF (UiO-66-NH2), with large internal surface areas, ultrahigh porosity and abundant amine groups in the pores, was employed as substrates to carry plenty of metal ions (Pb2+ or Cd2+) and label aptamers of OTC or KAN. Thus, the aptasensor is formed by the specific recognition between anti-ssDNA Ab and aptamers. In the presence of targets (OTC and KAN), aptamers prefer to form targets-Apts-MNM complexes in lieu of anti-ssDNA Ab-aptamer complexes, which results in the dissociation of Apts-MNM from capture beads. With the employment of RecJf exonuclease, targets-Apts-MNM in supernatant was digested into mononucleotides and liberated the target, which can further participate in the next reaction cycling to produce more signal tracers. After magnetic separation, the enhanced square wave voltammetry (SWV) signals were produced from signal tracers. The aptasensor exhibited a linear correlation in the range from 0.5pM to 50nM, with detection limits of 0.18pM and 0.15pM (S/N=3) toward OTC and KAN respectively. This strategy provides specificity and sensitive approach for multiplex antibiotics detection and has promising applications in food analysis.
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An Y, Bloom JWG, Wheeler SE. Quantifying the π-Stacking Interactions in Nitroarene Binding Sites of Proteins. J Phys Chem B 2015; 119:14441-50. [DOI: 10.1021/acs.jpcb.5b08126] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yi An
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Jacob W. G. Bloom
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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Wilson KA, Wetmore SD. A Survey of DNA–Protein π–Interactions: A Comparison of Natural Occurrences and Structures, and Computationally Predicted Structures and Strengths. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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10
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Contribution of phenylalanine side chain intercalation to the TATA-box binding protein–DNA interaction: molecular dynamics and dispersion-corrected density functional theory studies. J Mol Model 2014; 20:2499. [DOI: 10.1007/s00894-014-2499-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/13/2014] [Indexed: 10/24/2022]
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Wheeler SE, Bloom JWG. Toward a more complete understanding of noncovalent interactions involving aromatic rings. J Phys Chem A 2014; 118:6133-47. [PMID: 24937084 DOI: 10.1021/jp504415p] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Noncovalent interactions involving aromatic rings, which include π-stacking interactions, anion-π interactions, and XH-π interactions, among others, are ubiquitous in chemical and biochemical systems. Despite dramatic advances in our understanding of these interactions over the past decade, many aspects of these noncovalent interactions have only recently been uncovered, with many questions remaining. We summarize our computational studies aimed at understanding the impact of substituents and heteroatoms on these noncovalent interactions. In particular, we discuss our local, direct interaction model of substituent effects in π-stacking interactions. In this model, substituent effects are dominated by electrostatic interactions of the local dipoles associated with the substituents and the electric field of the other ring. The implications of the local nature of substituent effects on π-stacking interactions in larger systems are discussed, with examples given for complexes with carbon nanotubes and a small graphene model, as well as model stacked discotic systems. We also discuss related issues involving the interpretation of electrostatic potential (ESP) maps. Although ESP maps are widely used in discussions of noncovalent interactions, they are often misinterpreted. Next, we provide an alternative explanation for the origin of anion-π interactions involving substituted benzenes and N-heterocycles, and show that these interactions are well-described by simple models based solely on charge-dipole interactions. Finally, we summarize our recent work on the physical nature of substituent effects in XH-π interactions. Together, these results paint a more complete picture of noncovalent interactions involving aromatic rings and provide a firm conceptual foundation for the rational exploitation of these interactions in a myriad of chemical contexts.
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Affiliation(s)
- Steven E Wheeler
- Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
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