1
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Harding DP, Kingsley LJ, Spraggon G, Wheeler SE. Importance of model size in quantum mechanical studies of DNA intercalation. J Comput Chem 2020; 41:1175-1184. [PMID: 32011009 DOI: 10.1002/jcc.26164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/18/2019] [Accepted: 01/19/2020] [Indexed: 01/11/2023]
Abstract
The convergence of DFT-computed interaction energies with increasing binding site model size was assessed. The data show that while accurate intercalator interaction energies can be derived from binding site models featuring only the flanking nucleotides for uncharged intercalators that bind parallel to the DNA base pairs, errors remain significant even when including distant nucleotides for intercalators that are charged, exhibit groove-binding tails that engage in noncovalent interactions with distant nucleotides, or that bind perpendicular to the DNA base pairs. Consequently, binding site models that include at least three adjacent nucleotides are required to consistently predict converged binding energies. The computationally inexpensive HF-3c method is shown to provide reliable interaction energies and can be routinely applied to such large models.
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Affiliation(s)
- Drew P Harding
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia.,Department of Chemistry, Texas A&M University, College Station, Texas
| | - Laura J Kingsley
- Genomics Institute of the Novartis Research Foundation, San Diego, California
| | - Glen Spraggon
- Genomics Institute of the Novartis Research Foundation, San Diego, California
| | - Steven E Wheeler
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia
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2
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Maganti L, Bhattacharyya D. Sequence specificity in DNA–drug intercalation: MD simulation and density functional theory approaches. J Comput Aided Mol Des 2019; 34:83-95. [DOI: 10.1007/s10822-019-00268-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/29/2019] [Indexed: 12/14/2022]
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3
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Banerjee I, Aralaguppe SG, Lapins N, Zhang W, Kazemzadeh A, Sönnerborg A, Neogi U, Russom A. Microfluidic centrifugation assisted precipitation based DNA quantification. LAB ON A CHIP 2019; 19:1657-1664. [PMID: 30931470 DOI: 10.1039/c9lc00196d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nucleic acid amplification methods are increasingly being used to detect trace quantities of DNA in samples for various diagnostic applications. However, quantifying the amount of DNA from such methods often requires time consuming purification, washing or labeling steps. Here, we report a novel microfluidic centrifugation assisted precipitation (μCAP) method for single-step DNA quantification. The method is based on formation of a visible precipitate, which can be quantified, when an intercalating dye (GelRed) is added to the DNA sample and centrifuged for a few seconds. We describe the mechanism leading to the precipitation phenomenon. We utilize centrifugal microfluidics to precisely control the formation of the visible and quantifiable mass. Using a standard CMOS sensor for imaging, we report a detection limit of 45 ng μl-1. Furthermore, using an integrated lab-on-DVD platform we recently developed, the detection limit is lowered to 10 ng μl-1, which is comparable to those of current commercially available instruments for DNA quantification. As a proof of principle, we demonstrate the quantification of LAMP products for a HIV-1B type genome containing plasmid on the lab-on-DVD platform. The simple DNA quantification system could facilitate advanced point of care molecular diagnostics.
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Affiliation(s)
- I Banerjee
- Division of Nanobiotechnology, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Sweden.
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4
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Bera D, Verdonck L, Glassner M, Madder A, Hoogenboom R. Thermoresponsive DNA by Intercalation of dsDNA with Oligoethylene-Glycol-Functionalized Small-Molecule Intercalators. Macromol Rapid Commun 2019; 40:e1800900. [PMID: 30725517 DOI: 10.1002/marc.201800900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/21/2019] [Indexed: 11/05/2022]
Abstract
Thermoresponsive polymeric materials are important building blocks for smart materials. In this work, the transformation of dsDNA into a thermoresponsive polymer is reported by intercalation of short, oligoethylene-glycol-modified proflavine intercalators. The thermoresponsiveness of the dsDNA-intercalator complex originates from the heating-induced dehydration of the ethylene glycol side chains, which leads to aggregation of the intercalated dsDNA. This work demonstrates the possibility of designing small-molecule intercalators to prepare thermoresponsive dsDNA complexes with tunable lower critical solution temperature behavior.
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Affiliation(s)
- Debaditya Bera
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000, Ghent, Belgium
| | - Lars Verdonck
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000, Ghent, Belgium
| | - Mathias Glassner
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000, Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000, Ghent, Belgium
| | - Richard Hoogenboom
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000, Ghent, Belgium
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5
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Tandon R, Luxami V, Kaur H, Tandon N, Paul K. 1,8-Naphthalimide: A Potent DNA Intercalator and Target for Cancer Therapy. CHEM REC 2017; 17:956-993. [PMID: 28375569 DOI: 10.1002/tcr.201600134] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Indexed: 12/11/2022]
Abstract
The poor pharmacokinetics, side effects and particularly the rapid emergence of drug resistance compromise the efficiency of clinically used anticancer drugs. Therefore, the discovery of novel and effective drugs is still an extremely primary mission. Naphthalimide family is one of the highly active anticancer drug based upon effective intercalator with DNA. In this article, we review the discovery and development of 1,8-naphthalimide moiety, and, especially, pay much attention to the structural modifications and structure activity relationships. The review demonstrates how modulation of the moiety affecting naphthalimide compound for DNA binding that is achieved to afford a profile of antitumor activity. The DNA binding of imide and ring substitution at naphthalimide, bisnaphthalimide, naphthalimide-metal complexes is achieved by molecular recognition through intercalation mode. Thus, this synthetic/natural small molecule can act as a drug when activation or inhibition of DNA function, is required to cure or control the cancer disease. The present study is a review of the advances in 1,8-naphthalimide-related research, with a focus on how such derivatives are intercalated into DNA for their anticancer activities.
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Affiliation(s)
- Runjhun Tandon
- Department of Chemistry, School of Physical Sciences, Lovely, Professional University, Phagwara-, 144411, India
| | - Vijay Luxami
- School of Chemistry and Biochemistry, Thapar University, Patiala-, 147004, India
| | - Harsovin Kaur
- Department of Chemistry, School of Physical Sciences, Lovely, Professional University, Phagwara-, 144411, India
| | - Nitin Tandon
- Department of Chemistry, School of Physical Sciences, Lovely, Professional University, Phagwara-, 144411, India
| | - Kamaldeep Paul
- School of Chemistry and Biochemistry, Thapar University, Patiala-, 147004, India
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Duchemin N, Heath-Apostolopoulos I, Smietana M, Arseniyadis S. A decade of DNA-hybrid catalysis: from innovation to comprehension. Org Biomol Chem 2017; 15:7072-7087. [DOI: 10.1039/c7ob00176b] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Since the pioneering work of Roelfes and Feringa in the field of DNA-based asymmetric catalysis, the unique chirality of oligonucleotides has allowed the development of a variety of asymmetric synthetic transformations. This review offers a complete overview of the field.
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Affiliation(s)
- Nicolas Duchemin
- Queen Mary University of London
- School of Biological and Chemical Sciences
- London
- UK
| | | | - Michael Smietana
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
| | - Stellios Arseniyadis
- Queen Mary University of London
- School of Biological and Chemical Sciences
- London
- UK
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7
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Reyes-Rangel FJ, López-Rodríguez AK, Pastrana-Cancino LV, Loza-Mejía MA, Solano JD, Rodríguez-Sotres R, Lira-Rocha A. Synthesis, cytotoxic activity, DNA binding and molecular docking studies of novel 9-anilinothiazolo[5,4-b]quinoline derivatives. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1718-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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8
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Effect of intercalator substituent and nucleotide sequence on the stability of DNA- and RNA-naphthalimide complexes. Bioorg Med Chem 2015; 23:3586-91. [PMID: 25960324 DOI: 10.1016/j.bmc.2015.04.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/30/2015] [Accepted: 04/09/2015] [Indexed: 01/02/2023]
Abstract
DNA intercalators are commonly used as anti-cancer and anti-tumor agents. As a result, it is imperative to understand how changes in intercalator structure affect binding affinity to DNA. Amonafide and mitonafide, two naphthalimide derivatives that are active against HeLa and KB cells in vitro, were previously shown to intercalate into DNA. Here, a systematic study was undertaken to change the 3-substituent on the aromatic intercalator 1,8-naphthalimide to determine how 11 different functional groups with a variety of physical and electronic properties affect binding of the naphthalimide to DNA and RNA duplexes of different sequence compositions and lengths. Wavelength scans, NMR titrations, and circular dichroism were used to investigate the binding mode of 1,8-naphthalimide derivatives to short synthetic DNA. Optical melting experiments were used to measure the change in melting temperature of the DNA and RNA duplexes due to intercalation, which ranged from 0 to 19.4°C. Thermal stabilities were affected by changing the substituent, and several patterns and idiosyncrasies were identified. By systematically varying the 3-substituent, the binding strength of the same derivative to various DNA and RNA duplexes was compared. The binding strength of different derivatives to the same DNA and RNA sequences was also compared. The results of these comparisons shed light on the complexities of site specificity and binding strength in DNA-intercalator complexes. For example, the consequences of adding a 5'-TpG-3' or 5'-GpT-3' step to a duplex is dependent on the sequence composition of the duplex. When added to a poly-AT duplex, naphthalimide binding was enhanced by 5.6-11.5°C, but when added to a poly-GC duplex, naphthalimide binding was diminished by 3.2-6.9°C.
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9
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Zhu X, Wang X, He F, Tang F, Li L. Self-assembled nanocomposite film with tunable enhanced fluorescence for the detection of DNA. ACS APPLIED MATERIALS & INTERFACES 2015; 7:1334-1339. [PMID: 25539666 DOI: 10.1021/am507772e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this study, a simple and environmentally friendly, silver nanocomposite film was prepared via the in situ reduction of silver ions in self-assembled chitosan (CS)/sodium alginate film matrixes. Negatively charged DNA containing the fluorescent intercalator acriflavine (Acf) was assembled on the surface of the silver nanocomposite film, to facilitate the detection of DNA. A tunable fluorescence enhancement was achieved for the Acf in the silver nanocomposite film simply by changing the thickness of the interlayer between the DNA and the silver nanocomposite film. Using the interlayer prepared by an assembly of poly(acrylic acid) and CS, a significant enhancement in the fluorescence of Acf was obtained. Owing to the ability of Acf to intercalate into DNA, this hybrid system with an enhanced Acf fluorescence could be used to monitor the template-independent DNA elongation process in a facile, high-efficiency, label-free fashion.
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Affiliation(s)
- Xi Zhu
- School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, P. R. China
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10
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Verebová V, Adamcik J, Danko P, Podhradský D, Miškovský P, Staničová J. Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA and lengthen linear DNA. Biochem Biophys Res Commun 2014; 444:50-5. [PMID: 24434150 DOI: 10.1016/j.bbrc.2014.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/07/2014] [Indexed: 11/19/2022]
Abstract
The intercalating drugs possess a planar aromatic chromophore unit by which they insert between DNA bases causing the distortion of classical B-DNA form. The planar tricyclic structure of anthraquinones belongs to the group of chromophore units and enables anthraquinones to bind to DNA by intercalating mode. The interactions of simple derivatives of anthraquinone, quinizarin (1,4-dihydroxyanthraquinone) and danthron (1,8-dihydroxyanthraquinone), with negatively supercoiled and linear DNA were investigated using a combination of the electrophoretic methods, fluorescence spectrophotometry and single molecule technique an atomic force microscopy. The detection of the topological change of negatively supercoiled plasmid DNA, unwinding of negatively supercoiled DNA, corresponding to appearance of DNA topoisomers with the low superhelicity and an increase of the contour length of linear DNA in the presence of quinizarin and danthron indicate the binding of both anthraquinones to DNA by intercalating mode.
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Affiliation(s)
- Valéria Verebová
- Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia
| | - Jozef Adamcik
- Food and Soft Materials Science, Institute of Food, Nutrition & Health, ETH Zurich, Schmelzbergstrasse 9, CH-8092 Zürich, Switzerland
| | - Patrik Danko
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia
| | - Dušan Podhradský
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia
| | - Pavol Miškovský
- Department of Biophysics, Faculty of Sciences, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia; Center for Interdisciplinary Biosciences, Faculty of Sciences, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Jana Staničová
- Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia.
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11
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Ghosh D, Chattopadhyay N. Equilibrium and dynamic effects on ligand binding to biomacromolecules and biomimetic model systems. INT REV PHYS CHEM 2013. [DOI: 10.1080/0144235x.2013.782683] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Drug-DNA intercalation: from discovery to the molecular mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:1-62. [PMID: 23954098 DOI: 10.1016/b978-0-12-411636-8.00001-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The ability of small molecules to perturb the natural structure and dynamics of nucleic acids is intriguing and has potential applications in cancer therapeutics. Intercalation is a special binding mode where the planar aromatic moiety of a small molecule is inserted between a pair of base pairs, causing structural changes in the DNA and leading to its functional arrest. Enormous progress has been made to understand the nature of the intercalation process since its idealistic conception five decades ago. However, the biological functions were detected even earlier. In this review, we focus mainly on the acridine and anthracycline types of drugs and provide a brief overview of the development in the field through various experimental methods that led to our present understanding of the subject. Subsequently, we discuss the molecular mechanism of the intercalation process, free-energy landscapes, and kinetics that was revealed recently through detailed and rigorous computational studies.
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RIAHI SIAVASH, GANJALI MOHAMMADREZA, NOROUZI PARVIZ. QUANTUM MECHANICAL DESCRIPTION OF THE INTERACTIONS BETWEEN DNA AND 9,10-ANTHRAQUINONE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633608003770] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Molecular geometries of the 9,10-anthraquinone (AQ) and DNA bases (Adenine, Guanine, Cytosine, and Thymine) were optimized using B3LYP/6-31G** method. Properties of isolated intercalator (9,10-anthraquinone) and their stacking interactions with adenine ⋯ thymine (AT) and guanine ⋯ cytosine (GC) nucleic acid base pairs were investigated by means of DFTB method. DFTB method, an approximate version of the DFT method, was extended to cover London dispersion energy. AQ exhibits a large charge delocalization and it has no site with dominant charge. This intercalator has a large polarizability and is a good electron acceptor, while base pairs are good electron donors. B3LYP/6-31G** stabilization energies of intercalator ⋯ base pair complexes are large (-18.83 kcal/mol for AT ⋯ AQ and -15.69 kcal/mol for GC ⋯ AQ). It is concluded that, the dispersion energy predominantly contributes to the stability of intercalator ⋯ DNA base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation. The results showed that AQ changes the structure of DNA on bond length, bond angle, torsion angle, and charges.
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Affiliation(s)
- SIAVASH RIAHI
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, Iran
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, P. O. Box 14155-6455, Iran
| | - MOHAMMAD REZA GANJALI
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, P. O. Box 14155-6455, Iran
| | - PARVIZ NOROUZI
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, P. O. Box 14155-6455, Iran
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Langner KM, Janowski T, Góra RW, Dziekoński P, Sokalski WA, Pulay P. The Ethidium–UA/AU Intercalation Site: Effect of Model Fragmentation and Backbone Charge State. J Chem Theory Comput 2011; 7:2600-9. [DOI: 10.1021/ct200121f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Karol M. Langner
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Tomasz Janowski
- Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Robert W. Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Paweł Dziekoński
- Wrocław Center for Networking and Supercomputing, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - W. Andrzej Sokalski
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Peter Pulay
- Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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15
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Jiang Z, Zhang Y, Yu Y, Wang Z, Zhang X, Duan X, Wang S. Study on intercalations between double-stranded DNA and pyrene by single-molecule force spectroscopy: toward the detection of mismatch in DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:13773-13777. [PMID: 20698511 DOI: 10.1021/la102647p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Intercalation interactions between planar aromatic molecules and double-stranded DNA (dsDNA) relate to not only the structure of the guest molecules but also the structure of the dsDNA. In this letter, we have comparatively studied the intercalation between pyrene and fully matched or mismatched dsDNA using single-molecule force spectroscopy (SMFS). The significant difference in rupture forces, upon pyrene unbinding from 25-mer dsDNA with or without mismatches, is observed at the single-molecule level, indicating the influence of mismatches on the interaction between pyrene and dsDNA. In the analysis of the dynamic force spectra, two transition barriers are revealed for pyrene unbinding from matched sites in dsDNA and for pyrene unbinding from mismatched sites as well. These results suggest that SMFS is a useful single-molecule method for the detection of mismatches in dsDNA by the intercalation of pyrene.
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Affiliation(s)
- Zhenhua Jiang
- Key Lab of Organic Optoelectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, PR China
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16
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Prunkl C, Pichlmaier M, Winter R, Kharlanov V, Rettig W, Wagenknecht HA. Optical, Redox, and DNA-Binding Properties of Phenanthridinium Chromophores: Elucidating the Role of the Phenyl Substituent for Fluorescence Enhancement of Ethidium in the Presence of DNA. Chemistry 2010; 16:3392-402. [DOI: 10.1002/chem.200902823] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Neto BAD, Lapis AAM, Mancilha FS, Batista Jr. EL, Netz PA, Rominger F, Basso LA, Santos DS, Dupont J. On the selective detection of duplex deoxyribonucleic acids by 2,1,3-benzothiadiazole fluorophores. MOLECULAR BIOSYSTEMS 2010; 6:967-75. [DOI: 10.1039/b919155k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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18
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Ruiz R, García B, Ruisi G, Silvestri A, Barone G. Computational study of the interaction of proflavine with d(ATATATATAT)2 and d(GCGCGCGCGC)2. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.08.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Wheeler SE, Houk KN. Through-Space Effects of Substituents Dominate Molecular Electrostatic Potentials of Substituted Arenes. J Chem Theory Comput 2009; 5:2301-2312. [PMID: 20161573 DOI: 10.1021/ct900344g] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Model systems have been studied using density functional theory to assess the contributions of π-resonance and through-space effects on electrostatic potentials of substituted arenes. The results contradict the widespread assumption that changes in molecular ESPs reflect only local changes in the electron density. Substituent effects on the ESP above the molecular plane are commonly attributed to changes in the aryl π-system. We show that ESP changes for a collection of substituted benzenes and more complex aromatic systems can be accounted for mostly by through-space effects, with no change in the aryl π-electron density. Only when π-resonance effects are substantial do they influence changes in the ESP above the aromatic ring to any extent. Examples of substituted arenes studied here are taken from the fields of drug design, host-guest chemistry, and crystal engineering. These findings emphasize the potential pitfalls of assuming ESP changes reflect changes in the local electron density. Since ESP changes are frequently used to rationalize and predict intermolecular interactions, these findings have profound implications for our understanding of substituent effects in countless areas of chemistry and molecular biology. Specifically, in many non-covalent interactions there are significant, often neglected, through-space interactions with the substituents. Finally, the present results explain the perhaps unexpectedly good performance of many molecular mechanics force-fields applied to supramolecular assembly phenomena and π-π interactions in biological systems despite the neglect of the polarization of the aryl π-system by substituents.
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Affiliation(s)
- Steven E Wheeler
- Department of Chemistry and Biochemistry University of California, Los Angeles, CA 90095
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Recent developments in the chemistry of deoxyribonucleic acid (DNA) intercalators: principles, design, synthesis, applications and trends. Molecules 2009; 14:1725-46. [PMID: 19471193 PMCID: PMC6254398 DOI: 10.3390/molecules14051725] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Revised: 04/20/2009] [Accepted: 05/05/2009] [Indexed: 01/17/2023] Open
Abstract
In the present overview, we describe the bases of intercalation of small molecules (cationic and polar neutral compounds) in DNA. We briefly describe the importance of DNA structure and principles of intercalation. Selected syntheses, possibilities and applications are shown to exemplify the importance, drawbacks and challenges in this pertinent, new, and exciting research area. Additionally, some clinical applications (molecular processes, cancer therapy and others) and trends are described.
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21
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Kostjukov VV, Khomutova NM, Lantushenko AO, Evstigneev MP. Hydrophobic contribution to the free energy of complexation of aromatic ligands with DNA. ACTA ACUST UNITED AC 2009. [DOI: 10.7124/bc.0007d6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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22
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Loza-Mejía MA, Castillo R, Lira-Rocha A. Molecular modeling of tricyclic compounds with anilino substituents and their intercalation complexes with DNA sequences. J Mol Graph Model 2009; 27:900-7. [PMID: 19269869 DOI: 10.1016/j.jmgm.2009.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 01/28/2009] [Accepted: 02/02/2009] [Indexed: 10/21/2022]
Abstract
Although 9-anilinoacridines are among the best studied antitumoral intercalators, there are few studies about the effect of isosteric substitution of a benzene moiety for a heterocycle ring in the acridine framework. According to these studies, this approach may lead to effective cytotoxic agents, but good cytotoxic activity depends on structural requirements in the aniline ring which differ from those in 9-anilinoacridines. The present paper deals with molecular modeling studies of some 9-anilino substituted tricyclic compounds and their intercalation complexes (in various DNA sequences) resulting from docking the compounds into various DNA sequences. As expected, the isosteric substitution in 9-anilinoacridines influences the LUMO energy values and orbital distribution, the dipole moment, electrostatic charges and the conformation of the anilino ring. Other important differences are observed during the docking studies, for example, changes in the spatial arrangement of the tricyclic nucleus and the anilino ring at the intercalation site. Semiempirical calculations of the intercalation complexes show that the isosteric replacement of a benzene ring in the acridine nucleus affects not only DNA affinity but also base pair selectivity. These findings explain, at least partially, the different structural requirements observed in several 9-anilino substituted tricyclic compounds for cytotoxic activity. Thus, the data presented here may guide the rational design of new agents with different DNA binding properties and/or a cytotoxic profile by isosteric substitution of known intercalators.
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Affiliation(s)
- Marco A Loza-Mejía
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, 04510, Mexico
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Kostjukov VV, Khomytova NM, Davies DB, Evstigneev MP. Electrostatic contribution to the energy of binding of aromatic ligands with DNA. Biopolymers 2008; 89:680-90. [PMID: 18351582 DOI: 10.1002/bip.20985] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The method of solution of the nonlinear Poisson-Boltzmann equation was used to calculate electrostatic energy of binding of various aromatic ligands with DNA oligomers of different length. Analysis of the electrostatic contribution was made in terms of a two-step DNA binding process: formation of the intercalation cavity and insertion of the ligand. The total electrostatic energy was also partitioned into components: the energy of atom-atom coulombic interactions and the energy of interaction with surrounding water. The results indicate that electrostatic interactions are, as a whole, unfavorable to the intercalation process and that a correct analysis of structure-energy interrelation for Ligand-DNA interactions should only be accomplished at the level of the components rather than at the level of total electrostatic energy.
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Affiliation(s)
- V V Kostjukov
- Department of Physics, Sevastopol National Technical University, Sevastopol 99053, Crimea, Ukraine
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24
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Abstract
A stably-bound external binding site for ethidium cation in the major groove of B-form DNA is proposed. This complex is stabilized by hydrogen bonding between this ligand and the nucleophilic centers O6 and N7 of guanine, both of which are accessible via the major groove. This binding site is not the same as the well-characterized electrostatically-stabilized external binding site, but rather is seen to be a covalently bound complex which is stabilized by two hydrogen bonds between the ethidium ligand and guanine in the double stranded (ds) B-form DNA. This site [(1), R. Monaco, F. Hasheer. J Biomol Struct Dyn 10, 675 (1993)] can only exist at very low occupancy ratios. The existence of this binding site leads directly to the expectation that there will exist particular mechanistic steps along the pathway of interaction between ethidium and ds B-DNA at low and high ligand concentrations that involve this binding mode. This would not only explain observations published recently [for example, see (2-6), W. Wilson, I. Lopp. Biopolymers 18, 3025 (1979); L. Wakelin, M. Waring. J Mol Biol 144, 183-214 (1980); A. Karpetyan, N. Mehrabian, G. Terzikian, A. Antonian, P. Vardevanian, M. Frank-Kamenetshii. Proceedings of the 10th Conversation, SUNY Albany, 275 (1998); P. Vardevanyan, A. Antonyan, G. Manukyan, A. Karapetyan. Experimental and Molecular Medicine 33, 205 (2001); P. Vardevanyan, A. Antonyan, L. Minasbekan, A. Karapetyan. Proceedings of the 2002 Miami Nature Biotechnology Winter Symposium, 2(S1), 144 (2002)] but also give insight into discrepancies reported in the literature over the years by different workers studying the mechanism of interaction between ethidium and DNA. In this paper this novel binding interaction is discussed, and it is shown how the elucidation of this interaction led to the proposal of two distinct mechanisms of intercalation between ds B-DNA and ethidium cation for high and low concentrations of ligand. Modeling studies show the stability, configuration, and relative energies of this outside binding site. It is expected that this externally bound complex between ethidium cation and ds B-form DNA will be experimentally detectable using fluorescent polarization and/or linear and circular dichroism spectroscopic studies [(7, 8) E. Tuite, U. Sehlstedt, P. Hagmar, B. Norden, M. Takahashi. Euro J Biochem 243, 482-492 (1997); T. Hard. Biopolymers 26, 613-618 (1987)].
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Affiliation(s)
- R R Monaco
- Department of Environmental Chemistry, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.
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25
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Neto BAD, Lapis AAM, Mancilha FS, Vasconcelos IB, Thum C, Basso LA, Santos DS, Dupont J. New Sensitive Fluorophores for Selective DNA Detection. Org Lett 2007; 9:4001-4. [PMID: 17784767 DOI: 10.1021/ol701708y] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
4,7-Disubstituted benzothiadiazoles containing 1-arylethynyl and 4-methoxyphenyl groups are selective photoluminescent "light up" probes to duplex DNA with unprecedented sensibility in both spectrophotometric and spectrofluorimetric measurements.
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Affiliation(s)
- Brenno A D Neto
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Tecnopuc, PUC-RS, Brazil.
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26
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Langner KM, Kedzierski P, Sokalski WA, Leszczynski J. Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane. J Phys Chem B 2007; 110:9720-7. [PMID: 16686524 DOI: 10.1021/jp056836b] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.
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Affiliation(s)
- Karol M Langner
- Wroclaw University of Technology, Wyb.Wyspianskiego 27, 50-370 Wroclaw, Poland
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27
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Toczyłowski RR, Cybulski SM. An analysis of the electrostatic interaction between nucleic acid bases. J Chem Phys 2007; 123:154312. [PMID: 16252953 DOI: 10.1063/1.2069887] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Results from several commonly used approximate methods of evaluating electrostatic interactions have been compared to the rigorous, nonexpanded electrostatic energies at both uncorrelated and correlated levels of theory. We examined a number of energy profiles for both hydrogen bonded and stacked configurations of the nucleic acid base pairs. We found that the penetration effects play an extremely important role and the expanded electrostatic energies are significantly underestimated with respect to the ab initio values. Apart from the inability to reproduce the magnitudes of the ab initio electrostatic energy, there are other problems with the available approximate electrostatic models. For example, the distributed multipole analysis, one of the most advanced methods, is extremely sensitive to the basis set and level of theory used to evaluate the multipole moments. Detailed ab initio results are provided that other researchers could use to test their approximate models.
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Affiliation(s)
- Rafał R Toczyłowski
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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28
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Stability and structural features of DNA intercalation with ethidium bromide, acridine orange and methylene blue. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2006.05.004] [Citation(s) in RCA: 324] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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29
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Liu Y, Danielsson B. Rapid high throughput assay for fluorimetric detection of doxorubicin--application of nucleic acid-dye bioprobe. Anal Chim Acta 2007; 587:47-51. [PMID: 17386752 DOI: 10.1016/j.aca.2007.01.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 12/22/2006] [Accepted: 01/11/2007] [Indexed: 10/23/2022]
Abstract
A double stranded DNA based fluorescence bioprobe for anticancer agent (doxorubicin) detection is described. This method provides a new way for sensitive DNA/drug interaction study by a homogeneous assay. The probe employs the long-wavelength intercalating fluorophore TOTO-3 (TT3). The anticancer agent, doxorubicin, which interacts with the DNA-TT3 complex, was indirectly measured by the decrease in the fluorescence intensity. Various oligonucleotides with different sequences were examined. Doxorubicin has preference for the oligonucleotide 5'AGCACG3'. Enhanced fluorescence observed for the TT3 intercalation with this oligonucleotide makes the DNA-dye complex a suitable bioprobe for doxorubicin detection by competitive assay. A home-built CCD camera setup was applied along with 384 well plate assay format for high throughput fluorescence imaging. The detection limit can be as low as 25 ng mL(-1) with an upper limit of 100 microg mL(-1). The recovery test with spiked serum sample shows that this method can be a potential routine method for therapeutic drug monitoring (TDM).
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Affiliation(s)
- Yang Liu
- Pure and Applied Biochemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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30
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Sebestík J, Stibor I, Hlavácek J. New peptide conjugates with 9-aminoacridine: synthesis and binding to DNA. J Pept Sci 2006; 12:472-80. [PMID: 16506149 DOI: 10.1002/psc.752] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
New peptides-9-aminoacridine conjugates with an ethylene diamine linker-have been synthesized (both solution and solid phase methods were used) and their interactions with DNA have been studied. The affinity of H-Phe-Gln-Gly-Ile(2)-NHCH(2)CH(2)NH-Acr conjugate and of its extended analogue containing 6-aminohexanoic acid to DNA were lower than that of a standard H-Gly-NHCH(2)CH(2)NH-Acr conjugate. The results fit well into our concept of peptide conjugates with lowered binding activity to DNA, which could be capable of unlimited extravascular distribution. Moreover, new structures could be potentially useful as the mild tuners of DNA interaction with strong bis-acridine binders.
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Affiliation(s)
- Jaroslav Sebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
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31
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Abstract
The electronic structure of the common intercalating agent ethidium bromide (3,8-diamino-5-ethyl-6-phenylphenanthridinium bromide) is dominated by an interplay of electron donating and withdrawing effects mediated by its nitrogen atoms. X-ray crystallography, UV/Vis and IR absorption, fluorescence emission, and NMR spectroscopy are used to probe the electronic properties of the phenanthridinium "core" of ethidium as well as its exocyclic amines and 6-phenyl groups. Interestingly, despite its positive charge, most of ethidium's aromatic carbon and hydrogen atoms have high electron densities (compared to both 6-phenylphenanthridine and benzene). The data suggest that electron donation by ethidium's exocyclic amines dominates over the electron withdrawing effects of its endocyclic iminium in their combined influence on the electron densities of these atoms. Ethidium's nitrogen atoms are, conversely, electron deficient where the 5-position is the most electropositive, followed by the 3-amino, and lastly the 8-amino group. These results have been used to generate an empirically-based pi-electron density map of ethidium that may prove useful to understanding its nucleic acid binding specificity.
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Affiliation(s)
- Nathan W Luedtke
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA.
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32
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Setzer WN, Rozmus GF, Setzer MC, Schmidt JM, Vogler B, Reeb S, Jackes BR, Irvine AK. Bioactive principles in the bark of Pilidiostigma tropicum. J Mol Model 2006; 12:703-11. [PMID: 16601968 DOI: 10.1007/s00894-005-0047-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Accepted: 09/27/2005] [Indexed: 10/24/2022]
Abstract
The crude dichloromethane bark extract of Pilidiostigma tropicum (Myrtaceae) from north Queensland, Australia, shows antibacterial and cytotoxic activity. Bioactivity-directed separation led to the isolation of rhodomyrtoxin B and ursolic acid-3-p-coumarate as the biologically active materials. The structures of these compounds were elucidated on the basis of spectral analysis. The intercalation interaction of rhodomyrtoxin B with DNA was investigated using molecular mechanics and ab initio molecular-orbital techniques. A favorable pi-pi interaction between rhodomyrtoxin B and the cytosine-guanine base pair is predicted, but the orientation of the interaction cannot be predicted based on frontier molecular orbitals.
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Affiliation(s)
- William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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33
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Xiao X, Cushman M. Effect of E-Ring Modifications in Camptothecin on Topoisomerase I Inhibition: A Quantum Mechanics Treatment. J Org Chem 2005; 70:9584-7. [PMID: 16268636 DOI: 10.1021/jo0513360] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Camptothecins (CPTs) are the prototypical class of topoisomerase I (Top1) inhibitors with significant anticancer activities. Structure-activity relationship studies have demonstrated that inverting the stereochemistry at C-20 (R-CPT) or changing the E-ring lactone to a lactam (CPT-lactam) abolishes the Top1 inhibitory activity. The explanations that have been advanced for these effects are that there is either a failure of hydrogen bond formation involving the C-20 hydroxyl group of R-CPT or a failure of E-ring opening of the lactam, which have been proposed to be required for Top1 inhibition. We demonstrate here that the preferred conformation for the CPTs has the 20-Et pseudoaxial, while the 20-OH is pseudoequatorial, and therefore, the 20-OH groups in all the three CPT analogues (S-CPT, R-CPT, and CPT-lactam) are able to hydrogen bond with Asp533. The loss of the Top1 inhibitory activity by the latter two CPT analogues is attributed to the decreased pi-pi stacking interaction energy with the neighboring base pairs compared to the natural S-CPT. The differences in pi-pi stacking interaction energies are derived from the differential electrostatics on the E-ring.
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Affiliation(s)
- Xiangshu Xiao
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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34
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Xiao X, Antony S, Pommier Y, Cushman M. On the Binding of Indeno[1,2-c]isoquinolines in the DNA−Topoisomerase I Cleavage Complex. J Med Chem 2005; 48:3231-8. [PMID: 15857129 DOI: 10.1021/jm050017y] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An ab initio quantum mechanics calculation is reported which predicts the orientation of indenoisoquinoline 4 in the ternary cleavage complex formed from DNA and topoisomerase I (top1). The results of this calculation are consistent with the hypothetical structures previously proposed for the indenoisoquinoline-DNA-top1 ternary complexes based on molecular modeling, the crystal structure of a recently reported ternary complex, and the biological results obtained with a pair of diaminoalkyl-substituted indenoisoquinoline enantiomers. The results of these studies indicate that the pi-pi stacking interactions between the indenoisoquinolines and the neighboring DNA base pairs play a major role in determining binding orientation. The calculation of the electrostatic potential surface maps of the indenoisoquinolines and the adjacent DNA base pairs shows electrostatic complementarity in the observed binding orientation, leading to the conclusion that electrostatic attraction between the intercalators and the base pairs in the cleavage complex plays a major stabilizing role. On the other hand, the calculation of LUMO and HOMO energies of indenoisoquinoline 13b and neighboring DNA base pairs in conjunction with NBO analysis indicates that charge transfer complex formation plays a relatively minor role in stabilizing the ternary complexes derived from indenoisoquinolines, DNA, and top1. The results of these studies are important in understanding the existing structure-activity relationships for the indenoisoquinolines as top1 inhibitors and as anticancer agents, and they will be important in the future design of indenoisoquinoline-based top1 inhibitors.
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Affiliation(s)
- Xiangshu Xiao
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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Ihmels H, Faulhaber K, Vedaldi D, Dall'Acqua F, Viola G. Intercalation of Organic Dye Molecules into Double-stranded DNA. Part 2: The Annelated Quinolizinium Ion as a Structural Motif in DNA Intercalators†. Photochem Photobiol 2005; 81:1107-15. [PMID: 15934789 DOI: 10.1562/2005-01-25-ir-427] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
DNA intercalators represent an important class of compounds with a high potential as DNA-targeting drugs. In this review it is demonstrated that annelated quinolizinium derivatives such as coralyne and derivatives thereof intercalate into DNA and that this structural motif allows several variations of the substitution pattern without loss of intercalating properties. The commonly applied methods for the evaluation of the DNA association, mainly spectroscopic studies, are pointed out. In addition, studies on the biological activities of annelated quinolizinium derivatives, such as topoisomerase poisoning or cell toxicity, are highlighted.
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Affiliation(s)
- Heiko Ihmels
- Institute of Organic Chemistry, University of Siegen, Siegen, Germany.
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36
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Huber R, Amann N, Wagenknecht HA. Synthesis of DNA with phenanthridinium as an artificial DNA base. J Org Chem 2004; 69:744-51. [PMID: 14750800 DOI: 10.1021/jo0355404] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A phenanthridinium-containing DNA building block was synthesized as an ethidium nucleoside analogue starting from 3,8-diamino-6-phenyl-phenanthridine. Using this building block, oligonucleotides bearing the phenanthridinium moiety as an artificial DNA base were prepared via automated solid-phase phosphoramidite chemistry. The modified phenanthridinium-containing DNA duplexes were characterized by UV/vis absorption spectroscopy (including the melting behavior), CD spectroscopy, and steady-state fluorescence spectroscopy. These experiments reveal the expected similarity of the synthetic phenanthridinium moiety with noncovalently bound ethidium. More importantly, the results show clearly that the artificial phenanthridinium base is intercalated within the DNA base stack. The counterbase as part of the complementary strand seems to have only a minor influence on the intercalation properties of the phenanthridinium moiety.
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Affiliation(s)
- Robert Huber
- Institute for Organic Chemistry and Biochemistry, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany
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Trieb M, Rauch C, Wellenzohn B, Wibowo F, Loerting T, Mayer E, Liedl KR. Daunomycin Intercalation Stabilizes Distinct Backbone Conformations of DNA. J Biomol Struct Dyn 2004; 21:713-24. [PMID: 14769064 DOI: 10.1080/07391102.2004.10506961] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Daunomycin is a widely used antibiotic of the anthracycline family. In the present study we reveal the structural properties and important intercalator-DNA interactions by means of molecular dynamics. As most of the X-ray structures of DNA-daunomycin intercalated complexes are short hexamers or octamers of DNA with two drug molecules per doublehelix we calculated a self complementary 14-mer oligodeoxyribonucleotide duplex d(CGCGCGATCGCGCG)2 in the B-form with two putative intercalation sites at the 5'-CGA-3' step on both strands. Consequently we are able to look at the structure of a 1:1 complex and exclude crystal packing effects normally encountered in most of the X-ray crystallographic studies conducted so far. We performed different 10 to 20 ns long molecular dynamics simulations of the uncomplexed DNA structure, the DNA-daunomycin complex and a 1:2 complex of DNA-daunomycin where the two intercalator molecules are stacked into the two opposing 5'-CGA-3' steps. Thereby--in contrast to X-ray structures--a comparison of a complex of only one with a complex of two intercalators per doublehelix is possible. The chromophore of daunomycin is intercalated between the 5'-CG-3' bases while the daunosamine sugar moiety is placed in the minor groove. We observe a flexibility of the dihedral angle at the glycosidic bond, leading to three different positions of the ammonium group responsible for important contacts in the minor groove. Furthermore a distinct pattern of BI and BII around the intercalation site is induced and stabilized. This indicates a transfer of changes in the DNA geometry caused by intercalation to the DNA backbone.
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Affiliation(s)
- Michael Trieb
- Institute of General Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Hill G, Forde G, Hill N, Lester WA, Andrzej Sokalski W, Leszczynski J. Interaction energies in stacked DNA bases? How important are electrostatics? Chem Phys Lett 2003. [DOI: 10.1016/j.cplett.2003.09.076] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Cashman DJ, Scarsdale JN, Kellogg GE. Hydropathic analysis of the free energy differences in anthracycline antibiotic binding to DNA. Nucleic Acids Res 2003; 31:4410-6. [PMID: 12888500 PMCID: PMC169931 DOI: 10.1093/nar/gkg645] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Molecular models of six anthracycline antibiotics and their complexes with 32 distinct DNA octamer sequences were created and analyzed using HINT (Hydropathic INTeractions) to describe binding. The averaged binding scores were then used to calculate the free energies of binding for comparison with experimentally determined values. In parsing our results based on specific functional groups of doxorubicin, our calculations predict a free energy contribution of -3.6 +/- 1.1 kcal x mol(-1) (experimental -2.5 +/- 0.5 kcal x mol(-1)) from the groove binding daunosamine sugar. The net energetic contribution of removing the hydroxyl at position C9 is -0.7 +/- 0.7 kcal x mol(-1) (-1.1 +/- 0.5 kcal x mol(-1)). The energetic contribution of the 3' amino group in the daunosamine sugar (when replaced with a hydroxyl group) is -3.7 +/- 1.1 kcal x mol(-1) (-0.7 +/- 0.5 kcal x mol(-1)). We propose that this large discrepancy may be due to uncertainty in the exact protonation state of the amine. The energetic contribution of the hydroxyl group at C14 is +0.4 +/- 0.6 kcal x mol(-1) (-0.9 +/- 0.5 kcal x mol(-1)), largely due to unfavorable hydrophobic interactions between the hydroxyl oxygen and the methylene groups of the phosphate backbone of the DNA. Also, there appears to be considerable conformational uncertainty in this region. This computational procedure calibrates our methodology for future analyses where experimental data are unavailable.
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Affiliation(s)
- Derek J Cashman
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 East Leigh Street, Suite 212, PO Box 980540, Richmond, VA 23219-1540, USA
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Muravenko OV, Amosova AV, Samatadze TE, Popov KV, Poletaev AI, Zelenin AV. 9-Aminoacridine: an efficient reagent to improve human and plant chromosome banding patterns and to standardize chromosome image analysis. Cytometry A 2003; 51:52-7. [PMID: 12500305 DOI: 10.1002/cyto.a.10002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Successful automated chromosome analysis requires the development of new techniques to increase and standardize chromosome length and improve banding patterns. METHODS Human and plant cells were pretreated with the DNA intercalator 9-aminoacridine (9-AMA), and chromosomes were stained with GTG and aceto-orcein banding techniques and investigated by an image analysis system. RESULTS The human optimal chromosome spreads with the 850 G-band resolution level, suitable for image analysis, were obtained by 9-AMA pretreatment for 1 h at a final concentration of 0.5-1 microg/ml, as compared with 600-700 bands after ethidium bromide treatment and about 400 bands without pretreatment. The best results for plant chromosomes were obtained after pretreatment with 1-2 microg/ml of 9-AMA for 12-24 h. The chromosomes elongated approximately 1.5-fold, and the resolution of chromosome banding patterns increased, reaching approximately 140 bands per haploid set in the case of camomile. CONCLUSIONS 9-AMA is an efficient reagent for the standardization and increasing the resolution of chromosome banding patterns in human and plant chromosomes. It is extremely important for chromosome investigation in small plants.
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Affiliation(s)
- Olga V Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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42
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Reha D, Kabelác M, Ryjácek F, Sponer J, Sponer JE, Elstner M, Suhai S, Hobza P. Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study. J Am Chem Soc 2002; 124:3366-76. [PMID: 11916422 DOI: 10.1021/ja011490d] [Citation(s) in RCA: 271] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Properties of isolated intercalators (ethidium (E), daunomycin (D), ellipticine (EL), and 4,6'-diaminide-2-phenylindole (DAPI)) and their stacking interactions with adenine...thymine (AT) and guanine...cytosine (GC) nucleic acid base pairs were investigated by means of a nonempirical correlated ab initio method. All intercalators exhibit large charge delocalization, and none of them (including the DAPI dication) exhibits a site with dominant charge. All intercalators have large polarizability and are good electron acceptors, while base pairs are good electron donors. MP2/6-31G*(0.25) stabilization energies of intercalator...base pair complexes are large (E...AT, 22.4 kcal/mol; D...GC, 17.8 kcal/mol; EL...GC, 18.2 kcal/mol; DAPI...GC, 21.1 kcal/mol) and are well reproduced by modified AMBER potential (van der Waals radii of intercalator atoms are enlarged and their energy depths are increased). Standard AMBER potential underestimates binding, especially for DAPI-containing complexes. Because the DAPI dication is the best electron acceptor (among all intercalators studied), this difference is explained by the importance of the charge-transfer term, which is not included in the AMBER potential. For the neutral EL molecule, the standard AMBER force field provides correct results. The Hartree-Fock and DFT/B3LYP methods, not covering the dispersion energy, fail completely to reveal any energy minimum at the potential energy curve of the E...AT complex, and these methods thus cannot be recommended for a study of intercalation process. On the other hand, an approximate version of the DFT method, which was extended to cover London dispersion energy, yields for all complexes very good stabilization energies that are well comparable with referenced ab initio data. Besides the vertical dependence of the interaction, an energy twist dependence of the interaction energy was also investigated by a reference correlated ab initio method and empirical potentials. It is concluded that, despite the cationic (E +1, D +1, DAPI +2) or polar (EL) character of the intercalators investigated, it is the dispersion energy which predominantly contributes to the stability of intercalator...base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation.
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Affiliation(s)
- David Reha
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Systems and Biomolecules, Academy of Sciences of the Czech Republic, 182 23 Prague 8, Czech Republic
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