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Sakthikumar K, Kabuyaya Isamura B, Krause RWM. Exploring the antioxidant, antimicrobial, cytotoxic and biothermodynamic properties of novel morpholine derivative bioactive Mn(ii), Co(ii) and Ni(ii) complexes - combined experimental and theoretical measurements towards DNA/BSA/SARS-CoV-2 3CL Pro. RSC Med Chem 2023; 14:1667-1697. [PMID: 37731703 PMCID: PMC10508264 DOI: 10.1039/d2md00394e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/07/2022] [Indexed: 09/22/2023] Open
Abstract
A novel class of bioactive complexes (1-3) [MII(L)2(bpy)], where, L = 2-(4-morpholinobenzylideneamino)phenol, bpy = 2,2'-bipyridine, MII = Mn (1), Co (2) or Ni (3), were assigned to octahedral geometry based on analytical and spectral measurements. Gel electrophoresis showed that complex (2) demonstrated significant DNA cleavage activity compared to the other complexes under the action of oxidation agent (H2O2). The DNA binding constant properties measured by various techniques were in the following sequence: (2) > (3) > (1) > (HL), which suggests that the complexes might intercalate DNA, a possibility that is also supported by their biothermodynamic characteristics. The binding constant results for BSA from electronic absorption and fluorometric titrations demonstrate that complex (2) exhibits the highest binding effectiveness among them all, which means that all the compounds could interact with BSA through a static approach, additionally supported by FRET measurements. DFT and docking calculations were employed to realize the electronic structure, reactivity, and interaction capability of all substances with DNA, BSA, and the SARS-CoV-2 main protease. These binding energies fell within the ranges -7.7 to -8.5, -8.2 to -10.1 and -6.7 to -9.3 kcal mol-1, respectively. The higher reactivity of the complexes than the ligand is supported by FMO theory. The in vitro antibacterial, cytotoxicity, and radical scavenging characteristics revealed that complexes (2-3) have better biological efficacy than the others. The cytotoxicity and binding properties also show good correlation with the partition coefficient (log P), which is encouraging because all of the experimental findings are closely correlated with the theoretical measurements.
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Affiliation(s)
- Karunganathan Sakthikumar
- Organic & Medicinal Chemistry, Department of Chemistry, Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa
| | - Bienfait Kabuyaya Isamura
- Organic & Medicinal Chemistry, Department of Chemistry, Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa
- Department of Chemistry, The University of Manchester Manchester M13 9PL UK
| | - Rui Werner Maçedo Krause
- Organic & Medicinal Chemistry, Department of Chemistry, Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa
- Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa +27 741622674 +27 46 603 7030
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2
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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3
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Lim JM, Tevatia R, Saraf RF. Quantitative PCR of Small Nucleic Acids: Size Matters. ChemistrySelect 2021; 6:2975-2979. [PMID: 36819227 PMCID: PMC9937448 DOI: 10.1002/slct.202100807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Quantitative dysregulation in small nucleic acids (NA), such as microRNA (miRNA), extracted from minimally invasive biopsies, such as, blood, stool, urine, nose, throat, are promising biomarker for diseases diagnosis and management. We quantify the effect of the extra step of poly(A) ligation for cDNA synthesis and small size of the NA on the limit of quantification (LOQ) of quantitative PCR (qPCR), the gold standard to measure copy number. It was discovered that for small NA, the cycle threshold, Ct that is proportional to -log[c], where [c] is the concentration of the target NA exhibits a sharp transition. The results indicate that although the limit of detection (LOD) of qPCR can be in femtomolar range, the LOQ is significantly reduced by well over three orders of magnitude, in picomolar range. Specifically, the study reveals that the PCR product length is the primary reason the limitation on LOQ and is explicitly shown to be an important consideration for primer design for qPCR in general.
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Affiliation(s)
- Jay Min Lim
- Vajra Instruments Inc., 8300 Cody Drive, Ste C, Lincoln, NE 68512, USA
| | - Rahul Tevatia
- Vajra Instruments Inc., 8300 Cody Drive, Ste C, Lincoln, NE 68512, USA
| | - Ravi F. Saraf
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln NE 68588, USA
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4
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Jiang Y, Feldman T, Bakx JA, Yang D, Wong WP. Stretching DNA to twice the normal length with single-molecule hydrodynamic trapping. LAB ON A CHIP 2020; 20:1780-1791. [PMID: 32301470 PMCID: PMC7239757 DOI: 10.1039/c9lc01028a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single-molecule force spectroscopy has brought many new insights into nanoscale biology, from the functioning of molecular motors to the mechanical response of soft materials within the cell. To expand the single-molecule toolbox, we have developed a surface-free force spectroscopy assay based on a high-speed hydrodynamic trap capable of applying extremely high tensions for long periods of time. High-speed single-molecule trapping is enabled by a rigid and gas-impermeable microfluidic chip, rapidly and inexpensively fabricated out of glass, double-sided tape and UV-curable adhesive. Our approach does not require difficult covalent attachment chemistries, and enables simultaneous force application and single-molecule fluorescence. Using this approach, we have induced a highly extended state with twice the contour length of B-DNA in regions of partially intercalated double-stranded (dsDNA) by applying forces up to 250 pN. This highly extended state resembles the hyperstretched state of dsDNA, which was initially discovered as a structure fully intercalated by dyes under high tension. It has been hypothesized that hyperstretched DNA could also be induced without the aid of intercalators if high-enough forces were applied, which matches our observation. Combining force application with single-molecule fluorescence imaging is critical for distinguishing hyperstretched DNA from single-stranded DNA that can result from peeling. High-speed hydrodynamic trapping is a powerful yet accessible force spectroscopy method that enables the mechanics of biomolecules to be probed in previously difficult to access regimes.
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Affiliation(s)
- Yan Jiang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Theodore Feldman
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- VA Boston Healthcare System, Boston, MA 02130, USA
| | - Julia A.M. Bakx
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Wesley P. Wong
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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5
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Surin M, Ulrich S. From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies. ChemistryOpen 2020; 9:480-498. [PMID: 32328404 PMCID: PMC7175023 DOI: 10.1002/open.202000013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel MaterialsCenter of Innovation and Research in Materials and Polymers (CIRMAP)University of Mons-UMONS7000MonsBelgium
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6
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Ji H, Johnson NP, von Hippel PH, Marcus AH. Local DNA Base Conformations and Ligand Intercalation in DNA Constructs Containing Optical Probes. Biophys J 2019; 117:1101-1115. [PMID: 31474304 PMCID: PMC6818173 DOI: 10.1016/j.bpj.2019.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/31/2019] [Accepted: 08/05/2019] [Indexed: 01/18/2023] Open
Abstract
Understanding local conformations of DNA at the level of individual nucleic acid bases and base pairs is important for elucidating molecular processes that depend on DNA sequence. Here, we apply linear absorption and circular dichroism measurements to the study of local DNA conformations, using the guanine base analog 6-methyl isoxanthopterin (6-MI) as a structural probe. We show that the spectroscopic properties of this probe can provide detailed information about the average local base and basepair conformations as a function of the surrounding DNA sequence. Based on these results we apply a simple theoretical model to calculate the circular dichroism spectra of 6-MI-substituted DNA constructs and show that our model can be used to extract information about how the local conformations of the 6-MI probe are influenced by the local base or basepair environment. We also use this probe to examine the pathway for the insertion (intercalation) of a tethered acridine ligand (9-amino-6-chloro methoxyacridine) into duplex DNA. We show that this model intercalator interacts with duplex DNA by a "displacement insertion intercalation" mechanism, whereby the acridine moiety is inserted into the DNA structure and displaces the base located opposite its attachment site. These findings suggest that site-specifically positioned base analog probes can be used to characterize the molecular and structural details of binding ligand effects on local base stacking and unstacking reactions in single- and double-stranded DNA and thus may help to define the molecular mechanisms of DNA-protein interactions that involve the site-specific intercalation of aromatic amino acid side chains into genomic DNA.
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Affiliation(s)
- Huiying Ji
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon
| | - Neil P Johnson
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon
| | - Peter H von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon; Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon.
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7
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Hormann J, Malina J, Lemke O, Hülsey MJ, Wedepohl S, Potthoff J, Schmidt C, Ott I, Keller BG, Brabec V, Kulak N. Multiply Intercalator-Substituted Cu(II) Cyclen Complexes as DNA Condensers and DNA/RNA Synthesis Inhibitors. Inorg Chem 2018; 57:5004-5012. [DOI: 10.1021/acs.inorgchem.8b00027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Hormann
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
| | - Jaroslav Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic
| | - Oliver Lemke
- Institut für Chemie und Biochemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Max J. Hülsey
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
- Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Stefanie Wedepohl
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Jan Potthoff
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
| | - Claudia Schmidt
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstr. 55, 38106 Braunschweig, Germany
| | - Ingo Ott
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstr. 55, 38106 Braunschweig, Germany
| | - Bettina G. Keller
- Institut für Chemie und Biochemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic
| | - Nora Kulak
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
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8
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Abstract
The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely used in biophysical/chemical assays and drug treatments. We present single-molecule experiments and a three-state statistical mechanical model that provide a quantitative understanding of the interplay between B-DNA, overstretched DNA and intercalated DNA. The predictions of this model include a hitherto unconfirmed hyperstretched state, twice the length of B-DNA. Our force-fluorescence experiments confirm this hyperstretched state and reveal its sequence dependence. These results pin down the physical principles that govern DNA mechanics under the influence of tension and biochemical reactions. A predictive understanding of the possibilities and limitations of DNA extension can guide refined exploitation of DNA in, e.g., programmable soft materials and DNA origami applications. The mechanics and structural transitions of DNA are important to many essential processes inside living cells. Here the authors combine theory and single-molecule experiments to show that intercalator binding stabilises a new structural state of DNA: hyperstretched DNA.
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9
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Ammar FF, Hobaika Z, Abdel-Azeim S, Zargarian L, Maroun RG, Fermandjian S. A targeted DNA substrate mechanism for the inhibition of HIV-1 integrase by inhibitors with antiretroviral activity. FEBS Open Bio 2016; 6:234-50. [PMID: 27239438 PMCID: PMC4821353 DOI: 10.1002/2211-5463.12025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/25/2015] [Accepted: 12/16/2015] [Indexed: 12/21/2022] Open
Abstract
We recently reported that viral DNA could be the primary target of raltegravir (RAL), an efficient anti‐HIV‐1 drug, which acts by inhibiting integrase. To elucidate this mechanism, we conducted a comparative analysis of RAL and TB11, a diketoacid abandoned as an anti‐HIV‐1 drug for its weak efficiency and marked toxicity, and tested the effects of the catalytic cofactor Mg2+ (5 mm) on drug‐binding properties. We used circular dichroism and fluorescence to determine drug affinities for viral DNA long terminal repeats (LTRs) and peptides derived from the integrase active site and DNA retardation assays to assess drug intercalation into DNA base pairs. We found that RAL bound more tightly to LTR ends than did TB11 (a diketo acid bearing an azido group) and that Mg2+ significantly increased the affinity of both RAL and TB11. We also observed a good relationship between drug binding with processed LTR and strand transfer inhibition. This unusual type of inhibition was caused by Mg2+‐assisted binding of drugs to DNA substrate, rather than to enzyme. Notably, while RAL bound exclusively to the cleavable/cleaved site, TB11 further intercalated into DNA base pairs and interacted with the integrase‐derived peptides. These unwanted binding sites explain the weaker bioavailability and higher toxicity of TB11 compared with the more effective RAL.
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Affiliation(s)
- Farah F Ammar
- Centre d'Analyses et de Recherche UR EGFEM Faculté des Sciences Université Saint-Joseph Beirut Lebanon; LBPA, UMR8113 du CNRS Ecole Normale Supérieure de Cachan Cedex Cachan France
| | - Zeina Hobaika
- Centre d'Analyses et de Recherche UR EGFEM Faculté des Sciences Université Saint-Joseph Beirut Lebanon
| | - Safwat Abdel-Azeim
- LBPA, UMR8113 du CNRS Ecole Normale Supérieure de Cachan Cedex Cachan France
| | - Loussinée Zargarian
- LBPA, UMR8113 du CNRS Ecole Normale Supérieure de Cachan Cedex Cachan France
| | - Richard G Maroun
- Centre d'Analyses et de Recherche UR EGFEM Faculté des Sciences Université Saint-Joseph Beirut Lebanon
| | - Serge Fermandjian
- LBPA, UMR8113 du CNRS Ecole Normale Supérieure de Cachan Cedex Cachan France; Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy UMR8601 CNRS Paris Cedex 06 France
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Yousuf M, Youn IS, Yun J, Rasheed L, Valero R, Shi G, Kim KS. Violation of DNA neighbor exclusion principle in RNA recognition. Chem Sci 2016; 7:3581-3588. [PMID: 29997851 PMCID: PMC6007354 DOI: 10.1039/c5sc03740a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 02/14/2016] [Indexed: 11/25/2022] Open
Abstract
DNA intercalation has been very useful for engineering DNA-based functional materials.
DNA intercalation has been very useful for engineering DNA-based functional materials. It is generally expected that the intercalation phenomenon in RNA would be similar to that in DNA. Here we note that the neighbor-exclusion principle is violated in RNA by naphthalene-based cationic probes, in contrast to the fact that it is usually valid in DNA. All the intercalation structures are responsible for the fluorescence, where small naphthalene moieties are intercalated in between bases via π–π interactions. The structure is aided by hydrogen bonds between the cationic moieties and the ribose-phosphate backbone, which results in specific selectivity for RNA over DNA. This experimentally observed mechanism is supported by computationally reproducing the fluorescence and CD data. MD simulations confirm the unfolding of RNA due to the intercalation of probes. Elucidation of the mechanism of selective sensing for RNA over DNA would be highly beneficial for dynamical observation of RNA which is essential for studying its biological roles.
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Affiliation(s)
- Muhammad Yousuf
- Pohang University of Science and Technology , Pohang 790-784 , Korea.,Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919 , Korea .
| | - Il Seung Youn
- Pohang University of Science and Technology , Pohang 790-784 , Korea.,Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919 , Korea .
| | - Jeonghun Yun
- Pohang University of Science and Technology , Pohang 790-784 , Korea.,Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919 , Korea .
| | - Lubna Rasheed
- Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919 , Korea .
| | - Rosendo Valero
- Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919 , Korea .
| | - Genggongwo Shi
- Pohang University of Science and Technology , Pohang 790-784 , Korea.,Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919 , Korea .
| | - Kwang S Kim
- Ulsan National Institute of Science and Technology (UNIST) , Ulsan 44919 , Korea .
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Cafferty BJ, Musetti C, Kim K, Horowitz ED, Krishnamurthy R, Hud NV. Small molecule-mediated duplex formation of nucleic acids with ‘incompatible’ backbones. Chem Commun (Camb) 2016; 52:5436-9. [DOI: 10.1039/c6cc00779a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A small molecule promotes duplex formation by nucleic acids with natural and non-natural backbones that otherwise do not form duplexes.
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Affiliation(s)
- Brian J. Cafferty
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Caterina Musetti
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Keunsoo Kim
- Department of Chemistry
- The Scripps Research Institute
- La Jolla
- USA
| | - Eric D. Horowitz
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | | | - Nicholas V. Hud
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
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12
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Colorimetric detection of clinical DNA samples using an intercalator-conjugated polydiacetylene sensor. Biosens Bioelectron 2015; 72:127-32. [DOI: 10.1016/j.bios.2015.04.093] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/03/2015] [Accepted: 04/29/2015] [Indexed: 01/03/2023]
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13
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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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14
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Vargiu AV, Magistrato A. Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations. ChemMedChem 2014; 9:1966-81. [DOI: 10.1002/cmdc.201402203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/19/2022]
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15
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Rescifina A, Zagni C, Varrica MG, Pistarà V, Corsaro A. Recent advances in small organic molecules as DNA intercalating agents: synthesis, activity, and modeling. Eur J Med Chem 2014; 74:95-115. [PMID: 24448420 DOI: 10.1016/j.ejmech.2013.11.029] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/26/2013] [Accepted: 11/28/2013] [Indexed: 11/28/2022]
Abstract
The interaction of small molecules with DNA plays an essential role in many biological processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study about the interaction of drug and DNA has a key role in pharmacology. Moreover, understanding the interactions of small molecules with DNA is of prime significance in the rational design of more powerful and selective anticancer agents. Two of the most important and promising targets in cancer chemotherapy include DNA alkylating agents and DNA intercalators. For these last the DNA recognition is a critical step in their anti-tumor action and the intercalation is not only one kind of the interactions in DNA recognition but also a pivotal step of several clinically used anti-tumor drugs such as anthracyclines, acridines and anthraquinones. To push clinical cancer therapy, the discovery of new DNA intercalators has been considered a practical approach and a number of intercalators have been recently reported. The intercalative binding properties of such molecules can also be harnessed as diagnostic probes for DNA structure in addition to DNA-directed therapeutics. Moreover, the problem of intercalation site formation in the undistorted B-DNA of different length and sequence is matter of tremendous importance in molecular modeling studies and, nowadays, three models of DNA intercalation targets have been proposed that account for the binding features of intercalators. Finally, despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. Therefore, a default protocol to identify DNA binding modes which uses a modified canonical DNA as receptor is needed.
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Affiliation(s)
- Antonio Rescifina
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
| | - Chiara Zagni
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Maria Giulia Varrica
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Venerando Pistarà
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Antonino Corsaro
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
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Greschner AA, Bujold KE, Sleiman HF. Intercalators as Molecular Chaperones in DNA Self-Assembly. J Am Chem Soc 2013; 135:11283-8. [PMID: 23829631 DOI: 10.1021/ja404402b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea A. Greschner
- Department of Chemistry
and Center for Self-Assembled
Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Katherine E. Bujold
- Department of Chemistry
and Center for Self-Assembled
Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Hanadi F. Sleiman
- Department of Chemistry
and Center for Self-Assembled
Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
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17
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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: 58] [Impact Index Per Article: 5.3] [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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18
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Hosseini SS, Bhadbhade M, Clarke RJ, Rutledge PJ, Rendina LM. Synthesis, carbohydrate- and DNA-binding studies of cationic 2,2′:6′,2′′-terpyridineplatinum(ii) complexes containing N- and S-donor boronic acid ligands. Dalton Trans 2011; 40:506-13. [DOI: 10.1039/c0dt00892c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Horowitz ED, Lilavivat S, Holladay BW, Germann MW, Hud NV. Solution structure and thermodynamics of 2',5' RNA intercalation. J Am Chem Soc 2009; 131:5831-8. [PMID: 19309071 DOI: 10.1021/ja810068e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As a means to explore the influence of the nucleic acid backbone on the intercalative binding of ligands to DNA and RNA, we have determined the solution structure of a proflavine-bound 2',5'-linked octamer duplex with the sequence GCCGCGGC. This structure represents the first NMR structure of an intercalated RNA duplex, of either backbone structural isomer. By comparison with X-ray crystal structures, we have identified similarities and differences between intercalated 3',5' and 2',5'-linked RNA duplexes. First, the two forms of RNA have different sugar pucker geometries at the intercalated nucleotide steps, yet have the same interphosphate distances. Second, as in intercalated 3',5' RNA, the phosphate backbone angle zeta at the 2',5' RNA intercalation site prefers to be in the trans conformation, whereas unintercalated 2',5' and 3',5' RNA prefer the -gauche conformation. These observations provide new insights regarding the transitions required for intercalation of a phosphodiester-ribose backbone and suggest a possible contribution of the backbone to the origin of the nearest-neighbor exclusion principle. Thermodynamic studies presented for intercalation of both structural RNA isomers also reveal a surprising sensitivity of intercalator binding enthalpy and entropy to the details of RNA backbone structure.
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Affiliation(s)
- Eric D Horowitz
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, School of Chemistry and Biochemistry, Atlanta, Georgia 30332-0400, USA
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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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Blaney JM, Dixon JS. Distance Geometry in Molecular Modeling. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125823.ch6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Yang Q, Xu J, Sun Y, Li Z, Li Y, Qian X. Hydrolysis of plasmid DNA and RNA by amino alkyl naphthalimide as metal-free artificial nuclease. Bioorg Med Chem Lett 2006; 16:803-6. [PMID: 16314096 DOI: 10.1016/j.bmcl.2005.11.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 10/23/2005] [Accepted: 11/08/2005] [Indexed: 10/25/2022]
Abstract
A strategy of dimethylamino alkyldiimide conjugated with an intercalator of naphthalimide for hydrolysis of DNA was suggested and evaluated. 4 can hydrolyze 4 kb plasmid DNA into 2 kb fragments with GC and GG selectivity, which represents a novel example of sequence- or site-selective metal-free DNA artificial nuclease. Results also show it could hydrolyze RNA efficiently.
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Affiliation(s)
- Qing Yang
- Department of Bioscience and Biotechnology, Dalian University of Technology, Dalian 116024, China.
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23
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Sandeep P, Bisht PB. Concentration sensing based on radiative rate enhancement from a single microcavity. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.08.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Gençaslan S, Sheldrick WS. Bifunctional Bioorganometallic Iridium(III)-Platinum(II) Complexes Incorporating Both Intercalative and Covalent DNA Binding Capabilities. Eur J Inorg Chem 2005. [DOI: 10.1002/ejic.200500223] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Trieb M, Rauch C, Wibowo FR, Wellenzohn B, Liedl KR. Cooperative effects on the formation of intercalation sites. Nucleic Acids Res 2004; 32:4696-703. [PMID: 15342790 PMCID: PMC516060 DOI: 10.1093/nar/gkh788] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Daunomycin is one of the most important agents used in anticancer chemotherapy. It interacts with DNA through intercalation of its planar chromophore between successive base pairs. The effect of intercalation on structure, dynamics and energetics is the topic of a wealth of scientific studies. In the present study, we report a computational examination of the energetics of the intercalation process. In detail, we concentrate on the energetic penalty that intercalation of daunomycin introduces into DNA by disturbing it from its unbound conformation. For these means, we are analyzing already published molecular dynamics simulations of daunomycin-DNA complexes and present novel simulations of a bisdaunomycin-DNA and a 9-dehydroxydaunomycin-DNA intercalated complex using the MM-GBSA module implemented in the AMBER suite of programs. Using this molecular dynamics based, continuum solvent method we were able to calculate the energy required to form an intercalation site. Consequently, we compare the free energy of the duplex d(CGCGCGATCGCGCG)(2) in the B-form conformation with the respective conformations when intercalated with daunomycin and a bisintercalating analog. Our results show that the introduction of one single intercalation site costs approximately 32 kcal/mol. For double intercalation, or intercalation of the bisintercalator, the respective value for one intercalation site decreases to 27 and 24 kcal/mol, respectively, at a theoretical salt concentration of 0.15 M. This proposes that at least in these cases, a synergistic effect takes place. Although it is well known that intercalation leads to substantial disturbance of the DNA conformation, already performed investigations suggest a lower energetic penalty. Nevertheless to the best of our knowledge the calculations presented here are the most complete ones and consider hydration effects for the first time. The interaction energy between the ligand and the DNA certainly over-compensates this penalty for introducing the intercalation site and thus favors complexation. Such analyses are helpful for the description of allosteric effects in protein ligand binding.
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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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26
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Shaikh SA, Ahmed SR, Jayaram B. A molecular thermodynamic view of DNA–drug interactions: a case study of 25 minor-groove binders. Arch Biochem Biophys 2004; 429:81-99. [PMID: 15288812 DOI: 10.1016/j.abb.2004.05.019] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2004] [Revised: 05/27/2004] [Indexed: 11/20/2022]
Abstract
Developing a molecular view of the thermodynamics of DNA recognition is essential to the design of ligands for regulating gene expression. In a first comprehensive attempt at sketching an atlas of DNA-drug energetics, we present here a detailed thermodynamic view of minor-groove recognition by small molecules via a computational study on 25 DNA-drug complexes. The studies are configured in the MMGBSA (Molecular Mechanics-Generalized Born-Solvent Accessibility) framework at the current state of the art and facilitate a structure-energy component correlation. Analyses were conducted on both energy minimized structures of DNA-drug complexes and molecular dynamics trajectories developed for the purpose of this study. While highlighting the favorable role of packing, shape complementarity, and van der Waals and hydrophobic interactions of the drugs in the minor groove in conformity with experiment, the studies reveal an interesting annihilation of favorable electrostatics by desolvation. Structural modifications attempted on the ligands point to the requisite physico-chemical factors for obtaining improved binding energies. Hydrogen bonds predicted to be important for specificity based on structural considerations do not always turn out to be significant to binding in post facto analyses of molecular dynamics trajectories, which treat thermal averaging, solvent, and counterion effects rigorously. The strength of the hydrogen bonds retained between the DNA and drug during the molecular dynamics simulations is approximately 1kcal/mol. Overall, the study reveals the compensatory nature of the diverse binding free energy components, possible threshold limits for some of these properties, and the availability of a computationally viable free energy methodology which could be of value in drug-design endeavors.
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Affiliation(s)
- Saher Afshan Shaikh
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
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27
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Zacharias M, Sklenar H. Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex. J Comput Chem 1999. [DOI: 10.1002/(sici)1096-987x(199902)20:3<287::aid-jcc1>3.0.co;2-h] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Kapur A, Beck JL, Sheil MM. Observation of daunomycin and nogalamycin complexes with duplex DNA using electrospray ionisation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 1999; 13:2489-2497. [PMID: 10589098 DOI: 10.1002/(sici)1097-0231(19991230)13:24<2489::aid-rcm816>3.0.co;2-f] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The noncovalent binding of the antitumour drugs daunomycin and nogalamycin to duplex DNA has been studied using electrospray ionisation mass spectrometry (ESI-MS). The conditions for the preparation of drug/duplex DNA complexes and for their detection by ESI-MS have been optimised. Ions corresponding to these complexes were most abundant relative to free DNA when prepared in the pH range 8-9, and using gentle ESI interface conditions. Self-complementary oligonucleotides, 5'-d(GGCTAGCC)-3' or 5'-d(CGGCGCCG)-3', annealed in the presence of a 5-fold molar excess of either nogalamycin or daunomycin gave ESI mass spectra in which the most intense ions corresponded to three molecules of drug bound to duplex DNA, with some evidence for four drug molecules bound. For binding to 5'-d(TGAGCTAGCTCA)(2)-3', complexes containing up to four nogalamycin and six daunomycin molecules were observed. These data are consistent with the neighbour exclusion principle whereby intercalation occurs between every other base pair such that up to four bound drugs would be expected for the 8 mers and up to six for the 12 mer. Competition experiments involving a single drug in an equimolar mixture of two oligonucleotides (5'-d(TGAGCTAGCTCA)(2)-3' with either 5'-d(CGGCGCCG)(2)-3' or 5'-d(GGCTAGCC)(2)-3') showed ions arising from complexes of drug/5'-d(CGGCGCCG)(2)-3' were more intense than complexes of drug/5'-d(GGCTAGCC)(2)-3', relative to those from the 12 mer in each mixture. While this suggests ESI-MS has the potential to detect differences in sequence selectivity, more detailed experiments involving a comparison of the relative ionisation efficiency of different oligonucleotides and a wider range of intercalators are required to establish this definitively. ESI mass spectra from experiments in which both drugs were reacted with the same oligonucleotide were more complex, such that a clear preference for one drug could not be established.
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Affiliation(s)
- A Kapur
- Department of Chemistry, University of Wollongong, New South Wales 2522, Australia
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29
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Ha Duong T, Zakrzewska K. Influence of drug binding on DNA flexibility: a normal mode analysis. J Biomol Struct Dyn 1997; 14:691-701. [PMID: 9195338 DOI: 10.1080/07391102.1997.10508172] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
DNA-drug complexes are important because of their pharmacological interest but, in addition, they provide a useful model to study the essential aspects of DNA recognition processes. In order to investigate the influence of ligand binding on the dynamic properties of DNA we have carried out normal mode analysis for complexes with drugs of two types: a typical intercalator, 9-aminoacridine, and a typical groove binder, netropsin. Normal modes are analysed in terms of helicoidal parameter variations with special attention being paid to global deformations of the double helix. The results show that the influence of these two drugs is very different. Intercalation of 9-aminoacridine leads to an increase in the flexibility of the intercalated dinucleotide step, with notably larger vibrational amplitudes for both roll and twist parameters compared to free DNA. In contrast, the groove binding of netropsin induces a stiffening of the DNA segment which is in contact with the drug reflected by decreased vibrational amplitudes for backbone angles and inter base pair helicoidal parameters and an increase in vibrations for adjacent base pairs in terms of buckle and propeller twist.
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Affiliation(s)
- T Ha Duong
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, Paris, France
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30
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Heller DP, Greenstock CL. Fluorescence lifetime analysis of DNA intercalated ethidium bromide and quenching by free dye. Biophys Chem 1994; 50:305-12. [PMID: 8011950 DOI: 10.1016/0301-4622(93)e0101-a] [Citation(s) in RCA: 143] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The fluorescence characteristics of ethidium bromide (Eb) complexed to calf thymus DNA have been examined using fluorescence lifetime analysis for a range of DNA (effective nucleotide concentration) to Eb molar ratios. Control of both temperature and ion concentration is necessary for reproducible analyses. Eb complexed to double stranded DNA has a maximum fluorescence lifetime of 23 ns and is easily distinguishable from a fluorescence lifetime value of 1.67 ns corresponding to unbound Eb. In a solution of calf thymus DNA containing excess EB a binding equilibrium is reached, and this corresponds to one Eb molecule for every five nucleotides. With increasing amounts of unbound Eb, the fluorescence lifetime of the DNA-Eb complex decreases with a concomitant drop in the steady state fluorescence intensity, without a change in the amount of Eb bound to DNA. It is concluded that unbound Eb, acting via a quenching mechanism, shortens the fluorescence lifetime of bound Eb and consequently decreases the overall fluorescence intensity. This means that a different approach is necessary: time-resolved fluorescence spectroscopy directly distinguishes between a decrease in fluorescence intensity due to quenching by an excess of unbound Eb from that due to a decrease in Eb binding to double-stranded DNA. These studies suggest that techniques which measure total steady state fluorescence intensity of bound Eb in order to infer relative amounts of double-stranded DNA must be interpreted with caution. For such assays to be valid it is essential that no unbound Eb be present: otherwise a variable correction factor is required to account for unbound Eb.
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Affiliation(s)
- D P Heller
- Medical Physics Department, Ottawa Regional Cancer Center, Ontario, Canada
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31
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Tidor B, Karplus M. The contribution of cross-links to protein stability: a normal mode analysis of the configurational entropy of the native state. Proteins 1993; 15:71-9. [PMID: 7680808 DOI: 10.1002/prot.340150109] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The vibrational entropy of native BPTI, with three disulfide bonds, was determined by use of normal mode calculations and compared with that of folded variants having either one less disulfide bond or lacking a peptide bond at the trypsin-reactive site. Favorable contributions to the free energy of 2.5-5.1 kcal/mol at 300 K were calculated for the reduction of disulfide bonds in the folded state, whereas no favorable contribution was found for the hydrolysis of the peptide bond cleaved by trypsin. This is on the order of the effect of disulfides in the unfolded state. The implications of these results for the stabilization of a folded protein by the introduction of cross-links are discussed.
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Affiliation(s)
- B Tidor
- Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138
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32
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Abstract
Molecular dynamics simulations have been undertaken for a B-form dodecanucleotide duplex in solution with and without an intercalated proflavine molecule between the central C.G base pairs. The introduction of this simple intercalator affects both the conformational features and dynamic properties of the oligonucleotide double helix. Changes are seen in the rms atomic fluctuations and anisotropy of phosphate, sugar and base atoms. The backbone conformation is slightly changed on average and more sugars adopt the C3' endo conformation in the simulation of the complex compared with the simulation of the oligonucleotide alone. Both major and minor grooves becomes wider on average with the addition of the intercalating drug. Flanking A.T base pairs on both sides of the intercalation site have undergone an increase in flexibility, with the base pairs, especially at the 5' side, having the N1...N3 hydrogen bonds being broken.
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Affiliation(s)
- P Herzyk
- Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, UK
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33
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Herzyk P, Goodfellow JM, Neidle S. Molecular dynamics simulations of dinucleoside and dinucleoside-drug crystal hydrates. J Biomol Struct Dyn 1991; 9:363-86. [PMID: 1741968 DOI: 10.1080/07391102.1991.10507918] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molecular dynamics simulations have been performed on the dinucleoside monophosphates rGpC and dCpG, the latter in its intercalation complex with the acridine drug proflavine. The simulations were performed on the crystal structures, with crystallographically-located solvent molecules. It was found that satisfactory results were best obtained with restraints placed on the movements of the water molecules. Motions of individual atoms have been examined in terms of rms fluctuations and anisotropy and correlation functions. Relative motions of groups (phosphates, sugars, bases and proflavine molecules) have been analysed.
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Affiliation(s)
- P Herzyk
- Department of Crystallography, Birkbeck College, London, U.K
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34
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Rye HS, Quesada MA, Peck K, Mathies RA, Glazer AN. High-sensitivity two-color detection of double-stranded DNA with a confocal fluorescence gel scanner using ethidium homodimer and thiazole orange. Nucleic Acids Res 1991; 19:327-33. [PMID: 2014172 PMCID: PMC333598 DOI: 10.1093/nar/19.2.327] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Ethidium homodimer (EthD; lambda Fmax 620 nm) at EthD:DNA ratios up to 1 dye:4-5 bp forms stable fluorescent complexes with double-stranded DNA (dsDNA) which can be detected with high sensitivity using a confocal fluorescence gel scanner (Glazer, A.N., Peck, K. & Mathies, R.A. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 3851-3855). However, on incubation with unlabeled DNA partial migration of EthD takes place from its complex with dsDNA to the unlabeled DNA. It is shown here that this migration is dependent on the fractional occupancy of intercalating sites in the original dsDNA-EthD complex and that there is no detectable transfer from dsDNA-EthD complexes formed at 50 bp: 1 dye. The monointercalator thiazole orange (TO; lambda Fmax 530 nm) forms readily dissociable complexes with dsDNA with a large fluorescence enhancement on binding (Lee, L.G., Chen, C. & Liu, L.A. (1986) Cytometry 7, 508-517). However, a large molar excess of TO does not displace EthD from its complex with dsDNA. When TO and EthD are bound to the same dsDNA molecule, excitation of TO leads to efficient energy transfer from TO to EthD. This observation shows the practicability of 'sensitizing' EthD fluorescence with a second intercalating dye having a very high absorption coefficient and efficient energy transfer characteristics. Electrophoresis on agarose gels, with TO in the buffer, of preformed linearized M13mp18 DNA-EthD complex together with unlabeled linearized pBR322 permits sensitive fluorescence detection in the same lane of pBR322 DNA-TO complex at 530 nm and of M13mp18 DNA-EthD complex at 620 nm. These observations lay the groundwork for the use of stable DNA-dye intercalation complexes carrying hundreds of chromophores in two-color applications such as the physical mapping of chromosomes.
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Affiliation(s)
- H S Rye
- Division of Biochemistry and Molecular Biology, University of California, Berkeley 94720
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35
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Veal JM, Li Y, Zimmerman SC, Lamberson CR, Cory M, Zon G, Wilson WD. Interaction of a macrocyclic bisacridine with DNA. Biochemistry 1990; 29:10918-27. [PMID: 2271691 DOI: 10.1021/bi00501a009] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The binding of the macrocycle SDM to DNA was investigated by visible spectroscopy, stopped-flow kinetics, and NMR spectroscopy. SDM is composed of two 9-aminoacridines linked via the amino groups by a spermine side chain and via the 4-positions by a N,N'-[(methylthio)ethyl]succinamide side chain [Zimmerman, S. C., Lamberson, C. R., Cory, M., & Fairley, T. A. (1989) J. Am. Chem. Soc. 111, 6805-6809]. The visible spectrum of SDM bound to poly[d(A-T)]2 or poly[d(G-C)]2 is red-shifted relative to the spectrum of SDM alone and displays considerable hypochromicity. Results from titrations of SDM with polymer indicate a binding site size of three base pairs per macrocycle. The dissociation constant for SDM bound to either poly[d(A-T)]2 or poly[d(G-C)]2 is an order of magnitude lower than that for a similar bisacridine linked only by a spermine side chain. In addition, the dependence of the dissociation constant on ionic strength is significantly reduced. NMR studies of SDM complexes with poly[d(A-T)]2 or a tetramer, d(CGCG)2, show that intercalation is the mode of binding. The magnitudes of the chemical shift differences for SDM aromatic protons in the free and bound states support intercalation with the acridine ring systems essentially parallel to the long axis of the base pairs. Cross peaks from NOESY spectra of the SDM complex with d(CGCG)2 further support this mode of binding and provide information on the structure of the complex. The results are analyzed for consistency with each of three binding models: (i) bisintercalation with the two side chains in the same groove; (ii) bisintercalation according to the neighbor-exclusion principle with the two side chains in opposite grooves; and (iii) bisintercalation with two side chains in opposite grooves but with violation of the neighbor-exclusion principle. Model i is found to be unlikely on the basis of all evidence obtained, including preliminary modeling studies. Both models ii and iii can be reconciled with the experimental evidence and from a modeling standpoint are energetically feasible.
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Affiliation(s)
- J M Veal
- Department of Chemistry, Georgia State University, Atlanta 30303-3083
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36
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Xodo LE, Manzini G, Ruggiero J, Quadrifoglio F. On the interaction of daunomycin with synthetic alternating DNAs: sequence specificity and polyelectrolyte effects on the intercalation equilibrium. Biopolymers 1988; 27:1839-57. [PMID: 3233335 DOI: 10.1002/bip.360271112] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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