1
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Jabak AA, Bryden N, Westerlund F, Lincoln P, McCauley MJ, Rouzina I, Williams MC, Paramanathan T. Left versus right: Exploring the effects of chiral threading intercalators using optical tweezers. Biophys J 2022; 121:3745-3752. [PMID: 35470110 PMCID: PMC9617076 DOI: 10.1016/j.bpj.2022.04.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/27/2022] [Accepted: 04/20/2022] [Indexed: 11/02/2022] Open
Abstract
Small-molecule DNA-binding drugs have shown promising results in clinical use against many types of cancer. Understanding the molecular mechanisms of DNA binding for such small molecules can be critical in advancing future drug designs. We have been exploring the interactions of ruthenium-based small molecules and their DNA-binding properties that are highly relevant in the development of novel metal-based drugs. Previously we have studied the effects of the right-handed binuclear ruthenium threading intercalator ΔΔ-[μ-bidppz(phen)4Ru2]4+, or ΔΔ-P for short, which showed extremely slow kinetics and high-affinity binding to DNA. Here we investigate the left-handed enantiomer ΛΛ-[μ-bidppz(phen)4Ru2]4+, or ΛΛ-P for short, to study the effects of chirality on DNA threading intercalation. We employ single-molecule optical trapping experiments to understand the molecular mechanisms and nanoscale structural changes that occur during DNA binding and unbinding as well as the association and dissociation rates. Despite the similar threading intercalation binding mode of the two enantiomers, our data show that the left-handed ΛΛ-P complex requires increased lengthening of the DNA to thread, and it extends the DNA more than double the length at equilibrium compared with the right-handed ΔΔ-P. We also observed that the left-handed ΛΛ-P complex unthreads three times faster than ΔΔ-P. These results, along with a weaker binding affinity estimated for ΛΛ-P, suggest a preference in DNA binding to the chiral enantiomer having the same right-handed chirality as the DNA molecule, regardless of their common intercalating moiety. This comparison provides a better understanding of how chirality affects binding to DNA and may contribute to the development of enhanced potential cancer treatment drug designs.
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Affiliation(s)
- Adam A Jabak
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts
| | - Nicholas Bryden
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Micah J McCauley
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, Massachusetts.
| | - Thayaparan Paramanathan
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts.
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2
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Andrezálová L, Országhová Z. Covalent and noncovalent interactions of coordination compounds with DNA: An overview. J Inorg Biochem 2021; 225:111624. [PMID: 34653826 DOI: 10.1016/j.jinorgbio.2021.111624] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/30/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022]
Abstract
Deoxyribonucleic acid plays a central role in crucial cellular processes, and many drugs exert their effects through binding to DNA. Since the discovery of cisplatin and its derivatives considerable attention of researchers has been focused on the development of novel anticancer metal-based drugs. Transition metal complexes, due to their great diversity in size and structure, have a big potential to modify DNA through diverse types of interactions, making them the prominent class of compounds for DNA targeted therapy. In this review we describe various binding modes of metal complexes to duplex DNA based on covalent and noncovalent interactions or combination of both. Specific examples of each binding mode as well as possible cytotoxic effects of metal complexes in tumor cells are presented.
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Affiliation(s)
- Lucia Andrezálová
- Institute of Medical Chemistry, Biochemistry and Clinical Biochemistry, Faculty of Medicine, Comenius University, Sasinkova 2, 813 72 Bratislava, Slovakia; Department of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Zuzana Országhová
- Institute of Medical Chemistry, Biochemistry and Clinical Biochemistry, Faculty of Medicine, Comenius University, Sasinkova 2, 813 72 Bratislava, Slovakia
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3
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Obitz D, Miller RG, Metzler-Nolte N. Synthesis and DNA interaction studies of Ru(II) cell penetrating peptide (CPP) bioconjugates. Dalton Trans 2021; 50:13768-13777. [PMID: 34549219 DOI: 10.1039/d1dt01776d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The synthesis of the first bioconjugates of a set of ruthenium(II) dipyridophenazine complexes with two different cell penetrating peptides (CPPs) is described. The CPPs, an arginine rich TAT-9 (RKKRRQRRR) sequence and the Xentry peptide (LCLRPVG), were synthesized using standard SPPS protocols, and the bioconjugates were obtained by the microwave-assisted coupling of the HOBt/TBTU preactivated metal complexes with the respective peptides on Wang resin. The racemic metal complexes were obtained by modified literature procedures. The bioconjugates were cleaved from the resin, purified by semi-preparative HPLC and characterized by analytical HPLC, high resolution mass spectrometry (HR-MS), and NMR spectroscopy. Despite the bioconjugation of the peptides to the dppz ligand, DNA intercalation was observed by CD spectroscopy, viscometry and the characteristic switch-on fluorescence of this class of compounds. Furthermore, the cellular uptake of the Xentry bioconjugates was confirmed by live cell imaging. Like the parent metal complexes, the bioconjugates show low in vitro cytotoxicity (IC50 > 80 μM), which is similar to the respective metal complexes alone.
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Affiliation(s)
- Daniel Obitz
- Inorganic Chemistry I - Bioinorganic Chemistry, Ruhr-University Bochum, Universitaetsstrasse 150, 44780 Bochum, Germany.
| | - Reece G Miller
- Inorganic Chemistry I - Bioinorganic Chemistry, Ruhr-University Bochum, Universitaetsstrasse 150, 44780 Bochum, Germany.
| | - Nils Metzler-Nolte
- Inorganic Chemistry I - Bioinorganic Chemistry, Ruhr-University Bochum, Universitaetsstrasse 150, 44780 Bochum, Germany.
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4
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Feng B, Sundin E, Lincoln P, Mårtensson AKF. DNA threading intercalation of enantiopure [Ru(phen) 2bidppz] 2+ induced by hydrophobic catalysis. Phys Chem Chem Phys 2021; 23:2238-2244. [PMID: 33439155 DOI: 10.1039/d0cp00845a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The enantiomers of a novel mononuclear ruthenium(ii) complex [Ru(phen)2bidppz]2+ with an elongated dppz moiety were synthesized. Surprisingly, the complex showed no DNA intercalating capability in an aqueous environment. However, by the addition of water-miscible polyethylene glycol ether PEG-400, self-aggregation of the hydrophobic ruthenium(ii) complexes was counter-acted, thus strongly promoting the DNA intercalation binding mode. This mild alteration of the environment surrounding the DNA polymer does not damage or alter the DNA structure but instead enables more efficient binding characterization studies of potential DNA binding drugs.
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Affiliation(s)
- Bobo Feng
- Department of Chemistry and Chemical Engineering, Kemigården 4, SE-412 96 Gothenburg, Sweden.
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5
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Li G, Zhu D, Wang X, Su Z, Bryce MR. Dinuclear metal complexes: multifunctional properties and applications. Chem Soc Rev 2020; 49:765-838. [DOI: 10.1039/c8cs00660a] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Dinuclear metal complexes have enabled breakthroughs in OLEDs, photocatalytic water splitting and CO2reduction, DSPEC, chemosensors, biosensors, PDT and smart materials.
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Affiliation(s)
- Guangfu Li
- Department of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
| | - Dongxia Zhu
- Department of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
| | - Xinlong Wang
- Department of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
| | - Zhongmin Su
- Department of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
- School of Chemistry and Environmental Engineering
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6
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Fairbanks SD, Robertson CC, Keene FR, Thomas JA, Williamson MP. Structural Investigation into the Threading Intercalation of a Chiral Dinuclear Ruthenium(II) Polypyridyl Complex through a B-DNA Oligonucleotide. J Am Chem Soc 2019; 141:4644-4652. [PMID: 30799603 DOI: 10.1021/jacs.8b12280] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we report the separation of the three stereoisomers of the DNA light-switch compound [{Ru(bpy)2}2(tpphz)]4+ (tpphz = tetrapyrido[3,2-a:2',3'-c:3″,2″-h:2‴,3‴-j]phenazine) by column chromatography and the characterization of each stereoisomer by X-ray crystallography. The interaction of these compounds with a DNA octanucleotide d(GCATATCG).d(CGATATGC) has been studied using NMR techniques. Selective deuteration of the bipyridyl rings was needed to provide sufficient spectral resolution to characterize structures. NMR-derived structures for these complexes show a threading intercalation binding mode with slow and chirality-dependent rates. This represents the first solution structure of an intercalated bis-ruthenium ligand. Intriguingly, we find that the binding site selectivity is dependent on the nature of the stereoisomer employed, with Λ RuII centers showing a better intercalation fit.
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Affiliation(s)
- Simon D Fairbanks
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , U.K.,Department of Molecular Biology and Biotechnology , University of Sheffield , Western Bank , Sheffield , S10 2TN , U.K
| | - Craig C Robertson
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , U.K
| | - F Richard Keene
- Department of Chemistry, School of Physical Sciences , University of Adelaide , Adelaide , SA 5005 , Australia
| | - Jim A Thomas
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , U.K
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology , University of Sheffield , Western Bank , Sheffield , S10 2TN , U.K
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7
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Mårtensson AKF, Bergentall M, Tremaroli V, Lincoln P. Diastereomeric bactericidal effect of Ru(phenanthroline) 2 dipyridophenazine. Chirality 2018; 28:713-720. [PMID: 27791316 PMCID: PMC5248623 DOI: 10.1002/chir.22656] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/05/2016] [Accepted: 09/21/2016] [Indexed: 01/30/2023]
Abstract
Metal susceptibility assays and spot plating were used to investigate the antimicrobial activity of enantiopure [Ru(phen)2 dppz]2+ (phen =1,10-phenanthroline and dppz = dipyrido[3,2-a:2´,3´-c]phenazine) and [μ-bidppz(phen)4 Ru2 ]4+ (bidppz =11,11´-bis(dipyrido[3,2-a:2´,3´-c]phenazinyl)), on Gram-negative Escherichia coli and Gram-positive Bacillus subtilis as bacterial models. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) were determined for both complexes: while [μ-bidppz(phen)4 Ru2 ]4+ only showed a bactericidal effect at the highest concentrations tested, the antimicrobial activity of [Ru(phen)2 dppz]2+ against B. subtilis was comparable to that of tetracyline. In addition, the Δ-enantiomer of [Ru(phen)2 dppz]2+ showed a 2-fold higher bacteriostatic and bactericidal effect compared to the Λ-enantiomer. This was in accordance with the enantiomers relative binding affinity for DNA, thus strongly indicating DNA binding as the mode of action.
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Affiliation(s)
- Anna K F Mårtensson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Mattias Bergentall
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Valentina Tremaroli
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
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8
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Clark AG, Naufer MN, Westerlund F, Lincoln P, Rouzina I, Paramanathan T, Williams MC. Reshaping the Energy Landscape Transforms the Mechanism and Binding Kinetics of DNA Threading Intercalation. Biochemistry 2018; 57:614-619. [PMID: 29243480 DOI: 10.1021/acs.biochem.7b01036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecules that bind DNA via threading intercalation show high binding affinity as well as slow dissociation kinetics, properties ideal for the development of anticancer drugs. To this end, it is critical to identify the specific molecular characteristics of threading intercalators that result in optimal DNA interactions. Using single-molecule techniques, we quantify the binding of a small metal-organic ruthenium threading intercalator (Δ,Δ-B) and compare its binding characteristics to a similar molecule with significantly larger threading moieties (Δ,Δ-P). The binding affinities of the two molecules are the same, while comparison of the binding kinetics reveals significantly faster kinetics for Δ,Δ-B. However, the kinetics is still much slower than that observed for conventional intercalators. Comparison of the two threading intercalators shows that the binding affinity is modulated independently by the intercalating section and the binding kinetics is modulated by the threading moiety. In order to thread DNA, Δ,Δ-P requires a "lock mechanism", in which a large length increase of the DNA duplex is required for both association and dissociation. In contrast, measurements of the force-dependent binding kinetics show that Δ,Δ-B requires a large DNA length increase for association but no length increase for dissociation from DNA. This contrasts strongly with conventional intercalators, for which almost no DNA length change is required for association but a large DNA length change must occur for dissociation. This result illustrates the fundamentally different mechanism of threading intercalation compared with conventional intercalation and will pave the way for the rational design of therapeutic drugs based on DNA threading intercalation.
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Affiliation(s)
- Andrew G Clark
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - M Nabuan Naufer
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - Thayaparan Paramanathan
- Department of Physics, Bridgewater State University , Bridgewater, Massachusetts 02325, United States
| | - Mark C Williams
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
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9
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Lindberg DJ, Wenger A, Sundin E, Wesén E, Westerlund F, Esbjörner EK. Binding of Thioflavin-T to Amyloid Fibrils Leads to Fluorescence Self-Quenching and Fibril Compaction. Biochemistry 2017; 56:2170-2174. [DOI: 10.1021/acs.biochem.7b00035] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David J. Lindberg
- Division
of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Anna Wenger
- Division
of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Elin Sundin
- Division
of Chemistry and Biochemistry, Department of Chemistry and Chemical
Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Emelie Wesén
- Division
of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Fredrik Westerlund
- Division
of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Elin K. Esbjörner
- Division
of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
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10
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Almaqwashi AA, Andersson J, Lincoln P, Rouzina I, Westerlund F, Williams MC. Dissecting the Dynamic Pathways of Stereoselective DNA Threading Intercalation. Biophys J 2016; 110:1255-63. [PMID: 27028636 DOI: 10.1016/j.bpj.2016.02.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/01/2016] [Accepted: 02/08/2016] [Indexed: 02/07/2023] Open
Abstract
DNA intercalators that have high affinity and slow kinetics are developed for potential DNA-targeted therapeutics. Although many natural intercalators contain multiple chiral subunits, only intercalators with a single chiral unit have been quantitatively probed. Dumbbell-shaped DNA threading intercalators represent the next order of structural complexity relative to simple intercalators, and can provide significant insights into the stereoselectivity of DNA-ligand intercalation. We investigated DNA threading intercalation by binuclear ruthenium complex [μ-dppzip(phen)4Ru2](4+) (Piz). Four Piz stereoisomers are defined by the chirality of the intercalating subunit (Ru(phen)2dppz) and the distal subunit (Ru(phen)2ip), respectively, each of which can be either right-handed (Δ) or left-handed (Λ). We used optical tweezers to measure single DNA molecule elongation due to threading intercalation, revealing force-dependent DNA intercalation rates and equilibrium dissociation constants. The force spectroscopy analysis provided the zero-force DNA binding affinity, the equilibrium DNA-ligand elongation Δxeq, and the dynamic DNA structural deformations during ligand association xon and dissociation xoff. We found that Piz stereoisomers exhibit over 20-fold differences in DNA binding affinity, from a Kd of 27 ± 3 nM for (Δ,Λ)-Piz to a Kd of 622 ± 55 nM for (Λ,Δ)-Piz. The striking affinity decrease is correlated with increasing Δxeq from 0.30 ± 0.02 to 0.48 ± 0.02 nm and xon from 0.25 ± 0.01 to 0.46 ± 0.02 nm, but limited xoff changes. Notably, the affinity and threading kinetics is 10-fold enhanced for right-handed intercalating subunits, and 2- to 5-fold enhanced for left-handed distal subunits. These findings demonstrate sterically dispersed transition pathways and robust DNA structural recognition of chiral intercalators, which are critical for optimizing DNA binding affinity and kinetics.
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Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Johanna Andersson
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden; Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, Massachusetts.
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11
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Kenney RM, Buxton KE, Glazier S. Investigating the impacts of DNA binding mode and sequence on thermodynamic quantities and water exchange values for two small molecule drugs. Biophys Chem 2016; 216:9-18. [PMID: 27322498 DOI: 10.1016/j.bpc.2016.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/02/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
Abstract
Doxorubicin and nogalamycin are antitumor antibiotics that interact with DNA via intercalation and threading mechanisms, respectively. Because the importance of water, particularly its impact on entropy changes, has been established in other biological processes, we investigated the role of water in these two drug-DNA binding events. We used the osmotic stress method to calculate the number of water molecules exchanged (Δnwater), and isothermal titration calorimetry to measure Kbinding, ΔH, and ΔS for two synthetic DNAs, poly(dA·dT) and poly(dG·dC), and calf thymus DNA (CT DNA). For nogalamycin, Δnwater<0 for CT DNA and poly(dG·dC). For doxorubicin, Δnwater>0 for CT DNA and Δnwater<0 for poly(dG·dC). For poly(dA·dT), Δnwater~0 with both drugs. Net enthalpy changes were always negative, but net entropy changes depended on the drug. The effect of water exchange on the overall sign of entropy change appears to be smaller than other contributions.
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Affiliation(s)
- Rachael M Kenney
- Department of Chemistry, St. Lawrence University, 23 Romoda Drive, Canton, NY, USA; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Katherine E Buxton
- Department of Chemistry, St. Lawrence University, 23 Romoda Drive, Canton, NY, USA; Department of Chemistry, University of Wisconsin, Madison, WI, USA.
| | - Samantha Glazier
- Department of Chemistry, St. Lawrence University, 23 Romoda Drive, Canton, NY, USA.
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12
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Liu P, Wu BY, Liu J, Dai YC, Wang YJ, Wang KZ. DNA Binding and Photocleavage Properties, Cellular Uptake and Localization, and in-Vitro Cytotoxicity of Dinuclear Ruthenium(II) Complexes with Varying Lengths in Bridging Alkyl Linkers. Inorg Chem 2016; 55:1412-22. [DOI: 10.1021/acs.inorgchem.5b01934] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ping Liu
- Beijing Key Laboratory of Energy Conversion and Storage Materials,
and Key Laboratory of Radiopharmaceuticals, Ministry of Education,
College of Chemistry, and ‡College of Life Sciences, Beijing Normal University, Beijing 100875, P.R. China
| | - Bao-Yan Wu
- Beijing Key Laboratory of Energy Conversion and Storage Materials,
and Key Laboratory of Radiopharmaceuticals, Ministry of Education,
College of Chemistry, and ‡College of Life Sciences, Beijing Normal University, Beijing 100875, P.R. China
| | - Jin Liu
- Beijing Key Laboratory of Energy Conversion and Storage Materials,
and Key Laboratory of Radiopharmaceuticals, Ministry of Education,
College of Chemistry, and ‡College of Life Sciences, Beijing Normal University, Beijing 100875, P.R. China
| | - Yong-Cheng Dai
- Beijing Key Laboratory of Energy Conversion and Storage Materials,
and Key Laboratory of Radiopharmaceuticals, Ministry of Education,
College of Chemistry, and ‡College of Life Sciences, Beijing Normal University, Beijing 100875, P.R. China
| | - You-Jun Wang
- Beijing Key Laboratory of Energy Conversion and Storage Materials,
and Key Laboratory of Radiopharmaceuticals, Ministry of Education,
College of Chemistry, and ‡College of Life Sciences, Beijing Normal University, Beijing 100875, P.R. China
| | - Ke-Zhi Wang
- Beijing Key Laboratory of Energy Conversion and Storage Materials,
and Key Laboratory of Radiopharmaceuticals, Ministry of Education,
College of Chemistry, and ‡College of Life Sciences, Beijing Normal University, Beijing 100875, P.R. China
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13
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Almaqwashi AA, Paramanathan T, Lincoln P, Rouzina I, Westerlund F, Williams MC. Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex. Nucleic Acids Res 2014; 42:11634-41. [PMID: 25245944 PMCID: PMC4191423 DOI: 10.1093/nar/gku859] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ‐bidppz‐(phen)4Ru2]4+ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation Kd is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes.
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Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Thayaparan Paramanathan
- Department of Physics, Northeastern University, Boston, MA 02115, USA Department of Physics, Bridgewater State University, Bridgewater, MA 02324, USA
| | - Per Lincoln
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Fredrik Westerlund
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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14
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Hadadzadeh H, Daryanavard M, Morshedi M. Interaction of mononuclear nickel(II) enantiomers, Δ- and Λ-bis(1,10-phenanthroline) (dipyrido[3,2-a:2′,3′-c]phenazine)nickel(II) chloride, with calf thymus DNA. Inorganica Chim Acta 2013. [DOI: 10.1016/j.ica.2013.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Johansson JR, Wang Y, Eng MP, Kann N, Lincoln P, Andersson J. Bridging ligand length controls at selectivity and enantioselectivity of binuclear ruthenium threading intercalators. Chemistry 2013; 19:6246-56. [PMID: 23576496 DOI: 10.1002/chem.201300483] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Indexed: 11/09/2022]
Abstract
The slow dissociation of DNA threading intercalators makes them interesting as model compounds in the search for new DNA targeting drugs, as there appears to be a correlation between slow dissociation and biological activity. Thus, it would be of great value to understand the mechanisms controlling threading intercalation, and for this purpose we have investigated how the length of the bridging ligand of binuclear ruthenium threading intercalators affects their DNA binding properties. We have synthesised a new binuclear ruthenium threading intercalator with slower dissociation kinetics from ct-DNA than has ever been observed for any ruthenium complex with any type of DNA, a property that we attribute to the increased distance between the ruthenium centres of the new complex. By comparison with previously studied ruthenium complexes, we further conclude that elongation of the bridging ligand reduces the sensitivity of the threading interaction to DNA flexibility, resulting in a decreased AT selectivity for the new complex. We also find that the length of the bridging ligand affects the enantioselectivity with increasing preference for the ΔΔ enantiomer as the bridging ligand becomes longer.
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Affiliation(s)
- Johan R Johansson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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16
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Wu L, Reymer A, Persson C, Kazimierczuk K, Brown T, Lincoln P, Nordén B, Billeter M. Initial DNA interactions of the binuclear threading intercalator Λ,Λ-[μ-bidppz(bipy)4Ru2]4+: an NMR study with [d(CGCGAATTCGCG)]2. Chemistry 2013; 19:5401-10. [PMID: 23447081 PMCID: PMC3743166 DOI: 10.1002/chem.201203175] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 11/26/2012] [Indexed: 11/12/2022]
Abstract
Binuclear polypyridine ruthenium compounds have been shown to slowly intercalate into DNA, following a fast initial binding on the DNA surface. For these compounds, intercalation requires threading of a bulky substituent, containing one RuII, through the DNA base-pair stack, and the accompanying DNA duplex distortions are much more severe than with intercalation of mononuclear compounds. Structural understanding of the process of intercalation may greatly gain from a characterisation of the initial interactions between binuclear RuII compounds and DNA. We report a structural NMR study on the binuclear RuII intercalator Λ,Λ-B (Λ,Λ-[μ-bidppz(bipy)4Ru2]4+; bidppz=11,11′-bis(dipyrido[3,2-a:2′,3′-c]phenazinyl, bipy = 2,2′-bipyridine) mixed with the palindromic DNA [d(CGCGAATTCGCG)]2. Threading of Λ,Λ-B depends on the presence and length of AT stretches in the DNA. Therefore, the latter was selected to promote initial binding, but due to the short stretch of AT base pairs, final intercalation is prevented. Structural calculations provide a model for the interaction: Λ,Λ-B is trapped in a well-defined surface-bound state consisting of an eccentric minor-groove binding. Most of the interaction enthalpy originates from electrostatic and van der Waals contacts, whereas intermolecular hydrogen bonds may help to define a unique position of Λ,Λ-B. Molecular dynamics simulations show that this minor-groove binding mode is stable on a nanosecond scale. To the best of our knowledge, this is the first structural study by NMR spectroscopy on a binuclear Ru compound bound to DNA. In the calculated structure, one of the positively charged Ru2+ moieties is near the central AATT region; this is favourable in view of potential intercalation as observed by optical methods for DNA with longer AT stretches. Circular dichroism (CD) spectroscopy suggests that a similar binding geometry is formed in mixtures of Λ,Λ-B with natural calf thymus DNA. The present minor-groove binding mode is proposed to represent the initial surface interactions of binuclear RuII compounds prior to intercalation into AT-rich DNA.
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Affiliation(s)
- Lisha Wu
- Department of Chemical and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
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17
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Hanczyc P, Lincoln P, Norden B. Interactions of binuclear ruthenium(II) complexes with oligonucleotides in hydrogel matrix: enantioselective threading intercalation into GC context. J Phys Chem B 2013; 117:2947-54. [PMID: 23406277 DOI: 10.1021/jp311952x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A stretched poly(vinyl alcohol) (PVA) film provides a unique matrix that enables also short DNA oligonucleotide duplex to be oriented and studied by linear dichroism (LD). This matrix further allows controlling DNA secondary structure by proper hydration (A or B form), and such humid films could potentially also mimic the molecular crowding in cellular contexts. However, early attempts to study intercalators and groove binders for probing DNA in PVA failed due to competitive matrix binding. Here we report the successful orientation in PVA of DNA oligonucleotide duplex hairpins with thread-intercalated binuclear complex [μ-(11,11'-bidppz)(phen)4Ru2](4+), and how LD depends on oligonucleotide sequence and metal center chirality. Opposite enantiomers of the ruthenium complex, ΔΔ and ΛΛ, were investigated with respect to enantioselectivity toward GC stretches as long as 22 bp. LD, supported by emission kinetics, reveals that threading intercalation occurs only with ΔΔ whereas ΛΛ remains externally bound, probably in either or both of the grooves of the GC-DNA. Enantioselective binding properties of sterically rigid DNA probes such as the ruthenium complexes could find applications for targeting nucleic acids, e.g., to inhibit transcription in therapeutic context such as treatment of malaria or cancer.
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Affiliation(s)
- Piotr Hanczyc
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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18
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Zhao XL, Li ZS, Zheng ZB, Zhang AG, Wang KZ. pH luminescence switch, DNA binding and photocleavage, and cytotoxicity of a dinuclear ruthenium complex. Dalton Trans 2013; 42:5764-77. [DOI: 10.1039/c3dt33116d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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19
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Ali Ezadyar S, Kumbhar AS, Kumbhar AA, Khan A. Binuclear ruthenium(II) polypyridyl complexes: DNA cleavage and mitochondria mediated apoptosis induction. Polyhedron 2012. [DOI: 10.1016/j.poly.2012.01.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Andersson J, Lincoln P. Stereoselectivity for DNA Threading Intercalation of Short Binuclear Ruthenium Complexes. J Phys Chem B 2011; 115:14768-75. [DOI: 10.1021/jp2062767] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johanna Andersson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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21
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McKinley AW, Lincoln P, Tuite EM. Environmental effects on the photophysics of transition metal complexes with dipyrido[2,3-a:3′,2′-c]phenazine (dppz) and related ligands. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2011.06.012] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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Kogan M, Nordén B, Lincoln P, Nordell P. Transition state of rare event base pair opening probed by threading into looped DNA. Chembiochem 2011; 12:2001-6. [PMID: 21739556 DOI: 10.1002/cbic.201100182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Indexed: 01/25/2023]
Affiliation(s)
- Maxim Kogan
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, 412 96 Göteborg, Sweden
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23
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Li M, Lincoln P, Andersson J. Slow Threading Intercalation of Monomeric Ru(II) Complexes with 10,13-Diarylsubstituted dppz Ligands. J Phys Chem B 2011; 115:7923-31. [DOI: 10.1021/jp1117618] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Minna Li
- School of Chemical Biology and Pharmaceutical Sciences, Capital Medical University, Beijing 100069, PR China
| | - Per Lincoln
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Johanna Andersson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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24
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25
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Bencini A, Lippolis V. 1,10-Phenanthroline: A versatile building block for the construction of ligands for various purposes. Coord Chem Rev 2010. [DOI: 10.1016/j.ccr.2010.04.008] [Citation(s) in RCA: 288] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Wilhelmsson LM, Kingi N, Bergman J. Interactions of Antiviral Indolo[2,3-b]quinoxaline Derivatives with DNA. J Med Chem 2008; 51:7744-50. [PMID: 19053744 DOI: 10.1021/jm800787b] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. Marcus Wilhelmsson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, Unit for Organic Chemistry, Department of Biosciences and Nutrition, Karolinska Institute, SE-14157, Huddinge, Sweden, and Drug Development, Vironova AB, Smedjegatan 6, SE-13134 Nacka, Sweden
| | - Ngarita Kingi
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, Unit for Organic Chemistry, Department of Biosciences and Nutrition, Karolinska Institute, SE-14157, Huddinge, Sweden, and Drug Development, Vironova AB, Smedjegatan 6, SE-13134 Nacka, Sweden
| | - Jan Bergman
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, Unit for Organic Chemistry, Department of Biosciences and Nutrition, Karolinska Institute, SE-14157, Huddinge, Sweden, and Drug Development, Vironova AB, Smedjegatan 6, SE-13134 Nacka, Sweden
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27
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Westerlund F, Nordell P, Blechinger J, Santos TM, Nordén B, Lincoln P. Complex DNA Binding Kinetics Resolved by Combined Circular Dichroism and Luminescence Analysis. J Phys Chem B 2008; 112:6688-94. [DOI: 10.1021/jp711116z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fredrik Westerlund
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Pär Nordell
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Julia Blechinger
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Teresa M. Santos
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Bengt Nordén
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Per Lincoln
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Department of Chemistry, CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
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28
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Biver T, Secco F, Venturini M. Mechanistic aspects of the interaction of intercalating metal complexes with nucleic acids. Coord Chem Rev 2008. [DOI: 10.1016/j.ccr.2007.10.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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29
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Brodie CR, Aldrich-Wright JR. Synthesis of Flexible Bis-Intercalating Ruthenium(II) Complexes. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200700079] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Westerlund F, Nordell P, Nordén B, Lincoln P. Kinetic Characterization of an Extremely Slow DNA Binding Equilibrium. J Phys Chem B 2007; 111:9132-7. [PMID: 17608412 DOI: 10.1021/jp072126p] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We here exploit the recently reported thermodynamic preference for poly(dAdT)(2) over mixed-sequence calf thymus (ct) DNA of two binuclear ruthenium complexes, DeltaDelta-[mu-bidppz(bipy)4Ru2](4+) (B) and DeltaDelta-[mu-bidppz(phen)(4)Ru(2)](4+) (P), that bind to DNA by threading intercalation, to determine their intrinsic dissociation rates. After adding poly(dAdT)(2) as a sequestering agent to B or P bound to ct-DNA, the observed rate of change in luminescence upon binding to the polynucleotide reflects the rate of dissociation from the mixed sequence. The activation parameters for the threading and dissociation rate constants allow us for the first time to characterize the thermodynamics of the exceedingly slow threading intercalation equilibrium of B and P with ct-DNA. The equilibrium is found to be endothermic by 33 and 76 kJ/mol, respectively, and the largest part of the enthalpy difference between the complexes originates from the forward threading step. At physiological temperature (37 degrees C) B and P have dissociation half-lives of 18 and 38 h, respectively. This is to our knowledge the slowest dissociating noncovalently bound DNA-drug reported. SDS sequestration is the traditional method for determination of rate constants for cationic drugs dissociating from DNA. However, the rates may be severely overestimated for slowly dissociating molecules due to unwanted catalysis by the SDS monomers and micelles. Having determined the intrinsic dissociation rates with poly(dAdT)(2) as sequestering agent, we find that the catalytic effect of SDS on the dissociation rate may be up to a factor of 60, and that the catalysis is entropy driven. A simple kinetic model for the SDS concentration dependence of the apparent dissociation rate suggests an intermediate that involves both micelles and DNA-threaded complex.
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Affiliation(s)
- Fredrik Westerlund
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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31
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Corradini R, Sforza S, Tedeschi T, Marchelli R. Chirality as a tool in nucleic acid recognition: principles and relevance in biotechnology and in medicinal chemistry. Chirality 2007; 19:269-94. [PMID: 17345563 DOI: 10.1002/chir.20372] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The understanding of the interaction of chiral species with DNA or RNA is very important for the development of new tools in biology and of new drugs. Several cases in which chirality is a crucial point in determining the DNA binding mode are reviewed and discussed, with the aim of illustrating how chirality can be considered as a tool for improving the understanding of mechanisms and the effectiveness of nucleic acid recognition. The review is divided into two parts: the former describes examples of chiral species interacting with DNA: intercalators, metal complexes, and groove binders; the latter part is dedicated to chirality in DNA analogs, with discussion of phosphate stereochemistry and chirality of ribose substitutes, in particular of peptide nucleic acids (PNAs) for which a number of works have been published recently dealing with the effect of chirality in DNA recognition. The discussion is intended to show how enantiomeric recognition originates at the molecular level, by exploiting the enormous progresses recently achieved in the field of structural characterization of complexes formed by nucleic acid with their ligands by crystallographic and spectroscopic methods. Examples of application of the DNA binding molecules described and the role of chirality in DNA recognition relevant for biotechnology or medicinal chemistry are reported.
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Affiliation(s)
- Roberto Corradini
- Dipartimento di Chimica Organica e Industriale, Università di Parma, I-4310 Parma, Italy.
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32
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Westerlund F, Lincoln P. AT-dependent luminescence of DNA-threading ruthenium complexes. Biophys Chem 2007; 129:11-7. [PMID: 17531370 DOI: 10.1016/j.bpc.2007.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 04/25/2007] [Indexed: 11/28/2022]
Abstract
Whereas the emission from the ruthenium complex deltadelta-[mu-bidppz(phen)4Ru2]4+ (P) is five times larger when intercalated into poly(dAdT)2 than when intercalated into ct-DNA, the homologue deltadelta-[mu-bidppz(bipy)4Ru2]4+ (B) has a smaller quantum yield and a red-shifted emission. The origin of this difference is here investigated by studying intercalation into oligonucleotides containing a central AT-tract. Increasing the length of the AT-tract increases the emission quantum yield for P but decreases it for B. However, not even four helix turns of AT base pairs is enough to mimic poly(dAdT)2. B and P thus use the increased flexibility with increasing length of the AT-tract in opposite ways, whereas B gets more prone to quenching by water, P gets more protected from quenching. The earlier reported gradual increase of the intercalation rate with AT-stretch length is thus paralleled by a gradual change in the equilibrium properties of the intercalated state.
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Affiliation(s)
- Fredrik Westerlund
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
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33
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Nordell P, Westerlund F, Wilhelmsson L, Nordén B, Lincoln P. Kinetic Recognition of AT-Rich DNA by Ruthenium Complexes. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604294] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Nordell P, Westerlund F, Wilhelmsson LM, Nordén B, Lincoln P. Kinetic Recognition of AT-Rich DNA by Ruthenium Complexes. Angew Chem Int Ed Engl 2007; 46:2203-6. [PMID: 17310483 DOI: 10.1002/anie.200604294] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pär Nordell
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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35
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Westerlund F, Eng MP, Winters MU, Lincoln P. Binding Geometry and Photophysical Properties of DNA-Threading Binuclear Ruthenium Complexes. J Phys Chem B 2006; 111:310-7. [PMID: 17201453 DOI: 10.1021/jp065871v] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA binding conformation and the photophysical properties of the semiflexible binuclear ruthenium complex [micro-bidppz(phen)4Ru2]4+ (2) were studied with optical spectroscopy and compared to the rigid, planar homologue in syn conformation [micro-dtpf(phen)4Ru2]4+ (3) and the parent "light-switch" complex [Ru(phen)2dppz]2+ (1). Comparison of calculated and observed absorption bands of the bridging ligand, bidppz, confirm earlier suggestions that 2 is significantly nonplanar, both free in solution and when intercalated into poly(dAdT)2, but the conclusion that the intercalated conformation is an anti rotamer is not substantiated by comparison of linear and circular dichroism spectra of 2 and 3. The behavior of the emission quantum yield as a function of temperature is similar for the two binuclear complexes 2 and 3 in different protic solvents, and a quantitative analysis suggests that, in solution, the solvent is more strongly hydrogen bonded to the excited state of 2 than to 1. However, the observation that for 2 the radiative rate constant increases to a value similar to 1 upon intercalation into DNA suggests that the difference between 1 and 2 in accepting hydrogen bonds is less pronounced when intercalated.
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Affiliation(s)
- Fredrik Westerlund
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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36
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Tuttle T, Kraka E, Cremer D. Docking, triggering, and biological activity of dynemicin A in DNA: a computational study. J Am Chem Soc 2005; 127:9469-84. [PMID: 15984874 DOI: 10.1021/ja046251f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The triggering and biological activity of the naturally occurring enediyne dynemicin A (1) was investigated, both inside and outside the minor groove of the duplex 10-mer B-DNA sequence d(CTACTACTGG).d(CCAGTAGTAG), using density functional theory (B3LYP with the 3-21G and 6-31G(d) basis set), BD(T)/cc-pVDZ (Brueckner doubles with a perturbative treatment of triple excitations), and the ONIOM approach. Enediyne 1 is triggered by NADPH in a strongly exothermic reaction (-88 kcal/mol), which involves a number of intermediate steps. Untriggered 1 has a high barrier for the Bergman cyclization (52 kcal/mol) that is lowered after triggering to 16.7 kcal/mol due to an epoxide opening and the accompanying strain relief. The Bergman reaction of triggered 1 is slightly exothermic by 2.8 kcal/mol. The singlet biradical formed in this reaction is kinetically stable (activation enthalpies of 19.5 and 21.8 kcal/mol for retro-Bergman reactions) and is as reactive as para-benzyne. The activity-relevant docking mode is an edge-on insertion into the minor groove, whereas the intercalation between base pairs, although leading to larger binding energies, excludes a triggering of 1 and the development of its biological activity. Therefore, an insertion-intercalation model is developed, which can explain all known experimental observations made for 1. On the basis of the insertion-intercalation model it is explained why large intercalation energies suppress the biological activity of dynemicin and why double-strand scission can be achieved only in a two-step mechanism that involves two enediyne molecules, explaining thus the high ratio of single-strand to double-strand scission observed for 1.
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Affiliation(s)
- Tell Tuttle
- Department of Chemistry and Department of Physics, University of the Pacific, 3601 Pacific Avenue, Stockton, California 95211-0110, USA
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37
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Westerlund F, Wilhelmsson LM, Nordén B, Lincoln P. Monitoring the DNA Binding Kinetics of a Binuclear Ruthenium Complex by Energy Transfer: Evidence for Slow Shuffling. J Phys Chem B 2005; 109:21140-4. [PMID: 16853738 DOI: 10.1021/jp0534838] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The semirigid binuclear ruthenium complex Delta,Delta-[mu-(11,11'-bidppz)(phen)(4)Ru(2)](4+) has been shown to rearrange slowly from an initial groove-bound nonluminescent state to a final intercalated emissive state by threading one of its bulky Ru(phen)(2) moieties through the DNA base stack. When this complex binds to poly[d(A-T)(2)], a further increase in emission from the complex is observed after completion of the intercalation, assigned to reorganization of the intercalated complex. We here report a study of the threading process in poly[d(A-T)(2)], in which the minor groove binding dye DAPI is used as an energy transfer probe molecule to assess the distribution of ruthenium complex during and also after the actual threading phase. The emission from DAPI is found to change with the same rate as the emission from the ruthenium complex, and furthermore, DAPI does not disturb the binding kinetics of the latter, justifying it as a good probe of both the threading and the reorganization processes. We conclude from the change in the emission from both DAPI and the ruthenium complex with time that DAPI-ruthenium interactions are most pronounced during the process of threading of the complex, suggesting that the complexes are initially threaded slightly anticooperatively and thereafter redistribute along the DNA to reach their thermodynamically most favorable distribution. The final distribution is characterized by a small but significant binding cooperativity, probably as a result of hydrophobic interactions between the complex ions despite their tetravalent positive charges. The mechanism of "shuffling" the complex along the DNA chain is discussed, i.e., whether the ruthenium complex remains threaded (requiring sequential base-pair openings) or if unthreading followed by lateral diffusion within the ionic atmosphere of the DNA and rethreading occurs.
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Affiliation(s)
- Fredrik Westerlund
- Department of Chemistry and Bioscience, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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38
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Lundin NJ, Walsh PJ, Howell SL, McGarvey JJ, Blackman AG, Gordon KC. Complexes of Functionalized Dipyrido[3,2-a:2‘,3‘-c]-phenazine: A Synthetic, Spectroscopic, Structural, and Density Functional Theory Study. Inorg Chem 2005; 44:3551-60. [PMID: 15877438 DOI: 10.1021/ic050179k] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ligands 11-bromodipyrido[3,2-a:2',3'-c]phenazine and ethyl dipyrido[3,2-a:2',3'-c]phenazine-11-carboxylate have been prepared and coordinated to ruthenium(II), rhenium(I), and copper(I) metal centers. The electronic effects of substitution of dipyrido[2,3-a:3',2'-c]phenazine (dppz) have been investigated by spectroscopy and electrochemistry, and some photophysical properties have been studied. The crystal structures of [Re(L)(CO)(3)Cl] (L = ethyl dipyrido[3,2-a:2',3'-c]phenazine-11-carboxylate or 11-bromodipyrido[3,2-a:2',3'-c]phenazine) are presented. Density functional theory calculations on the complexes show only small deviations in bond lengths and angles (most bonds within 0.02 Angstroms, most angles within 2 degrees) from the crystallographic data. Furthermore, the vibrational spectra of the strongest Raman and IR bands are predicted to within an average 6 cm(-1) for the complexes [Re(L)(CO)(3)Cl] and [Cu(L)(triphenylphosphine)(2)]BF(4) (in the 1000-1700 cm(-1) region). Spectroscopic and electrochemical evidence suggest that reduction of the complex causes structural changes across the entire dppz ligand. This is unusual as dppz-based ligands typically have electrochemical properties that suggest charge localization with reduction on the phenazine portion of the ligand. The excited-state lifetimes of the complexes have been measured, and they range from ca. 200 ns for the [Ru(L)(2,2'-bipyridine)(2)](PF(6))(2) complexes to over 2 mus for [Cu(11-bromodipyrido[3,2-a:2',3'-c]phenazine)(PPh(3))(2)](BF(4)) at room temperature. The emission spectra suggest that the unusually long-lived excited states of the copper complexes result from metal-to-ligand charge transfer (MLCT) transitions as they are completely quenched in methanol. Electroluminescent films may be fabricated from these compounds; they show MLCT state emission even at low doping levels [<0.1% by weight in poly(vinylcarbazole) polymer matrix].
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Affiliation(s)
- Natasha J Lundin
- Department of Chemistry, MacDiarmid Institute for Advanced Materials and Nanotechnology, University of Otago, Dunedin, New Zealand
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Eriksson M, Mehmedovic M, Westman G, Akerman B. Time-resolved electrophoretic analysis of mobility shifts for dissociating DNA ligands. Electrophoresis 2005; 26:524-32. [PMID: 15690453 DOI: 10.1002/elps.200410057] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Intercalative binding of ligands to DNA can be demonstrated by helix unwinding, monitored by gel electrophoresis of supercoiled DNA, as electrophoretic mobility is sensitive to the topological DNA state. However, we show that an apparent lack of unwinding in an electrophoretic assay could be due to dissociation of the (intercalated) ligand during the analysis, rather than evidence for a nonintercalative mode of binding to DNA. Repetitive scanning during the electrophoresis ensures that release of the ligand during electrophoresis does not affect the measured degree of unwinding, based on the electrophoretic velocity being determined as a function of time. We use this assay to establish intercalation as a mode of binding to DNA for the cyanine dyes YO, YO-PRO as well as two enantiomeric forms of the ruthenium complexes [(phen)2 Ru(tatpp)Ru(phen)2]4+, and to support groove-binding for the new unsymmetrical cyanine dyes BOXTO and BOXTO-PRO. Groove-binding could be concluded from a lack of unwinding, because we could rule out that it is caused by release of the dye during the electrophoresis. The gel electrophoresis has the advantage over hydrodynamic techniques that much smaller sample amounts are required, and our time-resolved approach can be employed in all mobility-shift assays when applied to dissociating complexes.
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Affiliation(s)
- Maja Eriksson
- Department of Chemistry and Bioscience, Chalmers University of Technology, Göteborg, Sweden
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Molecular modeling study on the binding mode of polypyridyl transition Ru metal complexes with B-DNA. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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