1
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Takahashi M, Ito K, Iwasaki H, Norden B. Linear dichroism reveals the perpendicular orientation of DNA bases in the RecA and Rad51 recombinase filaments: A possible mechanism for the strand exchange reaction. Chirality 2024; 36:e23664. [PMID: 38561319 DOI: 10.1002/chir.23664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
Linear dichroism spectroscopy is used to investigate the structure of RecA family recombinase filaments (RecA and Rad51 proteins) with DNA for clarifying the molecular mechanism of DNA strand exchange promoted by these proteins and its activation. The measurements show that the recombinases promote the perpendicular base orientation of single-stranded DNA only in the presence of activators, indicating the importance of base orientation in the reaction. We summarize the results and discuss the role of DNA base orientation.
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Affiliation(s)
- Masayuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Kentaro Ito
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Hiroshi Iwasaki
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Innovative Science Institute, Tokyo Institute of Technology, Yokohama, Japan
| | - Bengt Norden
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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2
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Kasparkova J, Novohradsky V, Ruiz J, Brabec V. Photoactivatable, mitochondria targeting dppz iridium(III) complex selectively interacts and damages mitochondrial DNA in cancer cells. Chem Biol Interact 2024; 392:110921. [PMID: 38382705 DOI: 10.1016/j.cbi.2024.110921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/05/2024] [Accepted: 02/18/2024] [Indexed: 02/23/2024]
Abstract
Cyclometalated Ir(III) complex [Ir(L)2(dppz)]PF6 (where L = 1-methyl-2-(thiophen-2-yl)-1H-benzo[d]imidazole and dppz = dipyrido [3,2-a:2',3'-c]phenazine) (Ir1) is potent anticancer agent whose potency can be significantly increased by irradiation with blue light. Structural features of the cyclometalated Ir(III) complex Ir1 investigated in this work, particularly the presence of dppz ligand possessing an extended planar area, suggest that this complex could interact with DNA. Here, we have shown that Ir1 accumulates predominantly in mitochondria of cancer cells where effectively and selectively binds mitochondrial (mt)DNA. Additionally, the results demonstrated that Ir1 effectively suppresses transcription of mitochondria-encoded genes, especially after irradiation, which may further affect mitochondrial (and thus also cellular) functions. The observation that Ir1 binds selectively to mtDNA implies that the mechanism of its biological activity in cancer cells may also be connected with its interaction and damage to mtDNA. Further investigations revealed that Ir1 tightly binds DNA in a cell-free environment, with sequence preference for GC over AT base pairs. Although the dppz ligand itself or as a ligand in structurally similar DNA-intercalating Ru polypyridine complexes based on dppz ligand intercalates into DNA, the DNA binding mode of Ir1 comprises surprisingly a groove binding rather than an intercalation. Also interestingly, after irradiation with visible (blue) light, Ir1 was capable of cleaving DNA, likely due to the production of superoxide anion radical. The results of this study show that mtDNA damage by Ir1 plays a significant role in its mechanism of antitumor efficacy. In addition, the results of this work are consistent with the hypothesis and support the view that targeting the mitochondrial genome is an effective strategy for anticancer (photo)therapy and that the class of photoactivatable dipyridophenazine Ir(III) compounds may represent prospective substances suitable for further testing.
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Affiliation(s)
- Jana Kasparkova
- Department of Biophysics, Faculty of Science, Palacky University, CZ-783 71, Olomouc, Czech Republic
| | - Vojtech Novohradsky
- Czech Academy of Sciences, Institute of Biophysics, CZ-61200, Brno, Czech Republic
| | - José Ruiz
- Departamento de Química Inorgánica, Universidad de Murcia, And Murcia BioHealth Research Institute (IMIB-Arrixaca), E-30100, Murcia, Spain
| | - Viktor Brabec
- Department of Biophysics, Faculty of Science, Palacky University, CZ-783 71, Olomouc, Czech Republic.
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3
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Takahashi M, Norden B. Linear Dichroism Measurements for the Study of Protein-DNA Interactions. Int J Mol Sci 2023; 24:16092. [PMID: 38003280 PMCID: PMC10671323 DOI: 10.3390/ijms242216092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Linear dichroism (LD) is a differential polarized light absorption spectroscopy used for studying filamentous molecules such as DNA and protein filaments. In this study, we review the applications of LD for the analysis of DNA-protein interactions. LD signals can be measured in a solution by aligning the sample using flow-induced shear force or a strong electric field. The signal generated is related to the local orientation of chromophores, such as DNA bases, relative to the filament axis. LD can thus assess the tilt and roll of DNA bases and distinguish intercalating from groove-binding ligands. The intensity of the LD signal depends upon the degree of macroscopic orientation. Therefore, DNA shortening and bending can be detected by a decrease in LD signal intensity. As examples of LD applications, we present a kinetic study of DNA digestion by restriction enzymes and structural analyses of homologous recombination intermediates, i.e., RecA and Rad51 recombinase complexes with single-stranded DNA. LD shows that the DNA bases in these complexes are preferentially oriented perpendicular to the filament axis only in the presence of activators, suggesting the importance of organized base orientation for the reaction. LD measurements detect DNA bending by the CRP transcription activator protein, as well as by the UvrB DNA repair protein. LD can thus provide information about the structures of protein-DNA complexes under various conditions and in real time.
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Affiliation(s)
- Masayuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Oookayama, Meguro, Tokyo 152-8550, Japan
| | - Bengt Norden
- Department of Chemical and Biological Engineering, Chemistry, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
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4
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Zubova EA, Strelnikov IA. Experimental detection of conformational transitions between forms of DNA: problems and prospects. Biophys Rev 2023; 15:1053-1078. [PMID: 37974981 PMCID: PMC10643659 DOI: 10.1007/s12551-023-01143-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/06/2023] [Indexed: 11/19/2023] Open
Abstract
Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.
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Affiliation(s)
- Elena A. Zubova
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
| | - Ivan A. Strelnikov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
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5
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Workman KT, Usher AJ, Henson DW, White NJ, Gichuhi WK. Predicted Negative Ion Photoelectron Spectra of 1-, 2-, and 9-Cyanoanthracene Radical Anions and Computed Thermochemical Values of the Three Cyanoanthracene Isomers. J Phys Chem A 2023; 127:4063-4076. [PMID: 37116201 DOI: 10.1021/acs.jpca.3c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
In this work, the negative ion photoelectron spectra of 1-, 2-, and 9-cyanoanthracene (anthracenecarbonitrile, ACN) radical anions, obtained via the calculation of Franck-Condon (FC) factors based on a harmonic oscillator model, are reported. The FC calculations utilize harmonic vibrational frequencies and normal mode vectors derived from density functional theory using the B3LYP/6-311++G (2d,2p) basis set. The removal of an electron from the doublet anion allows for the computation of the negative ion photoelectron spectra that represents the neutral ground singlet state (So) and the lowest triplet state (T1) in each of the three ACN molecules. The respective adiabatic electron affinity (EA) values for the So state in 1-, 2-, and 9-ACN isomers are calculated to be 1.353, 1.360, and 1.423 eV. The calculated EA of the 9-cyanoanthracene singlet isomer is in close agreement with the previously reported experimental value of 1.27 ± 0.1 eV. Calculations show that the T1 states in 1-, 2-, and 9-ACN are located 1.656, 1.663, and 1.599 eV above the So state. The calculated T1 negative ion spectra exhibit intense vibrational origins and weak FC activity beyond the origins, indicating little change in geometry following electron detachment from the doublet anionic state. Upon deprotonation, the EA values of the radical isomers increase by ∼400-700 meV, resulting in neutral deprotonated radicals with EAs between 1.740 and 2.220 eV. The calculated site-specific gas-phase acidity values of ACN isomers indicate that ACN molecules are more acidic than benzonitrile.
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6
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Carter JG, Pfukwa R, Riley L, Tucker JHR, Rodger A, Dafforn TR, Klumperman B. Linear Dichroism Activity of Chiral Poly( p-Aryltriazole) Foldamers. ACS OMEGA 2021; 6:33231-33237. [PMID: 34901675 PMCID: PMC8656205 DOI: 10.1021/acsomega.1c06139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 05/04/2023]
Abstract
Controllable higher-order assembly is a central aim of macromolecular chemistry. An essential challenge to developing these molecules is improving our understanding of the structures they adopt under different conditions. Here, we demonstrate how flow linear dichroism (LD) spectroscopy is used to provide insights into the solution structure of a chiral, self-assembled fibrillar foldamer. Poly(para-aryltriazole)s fold into different structures depending on the monomer geometry and variables such as solvent and ionic strength. LD spectroscopy provides a simple route to determine chromophore alignment in solution and is generally used on natural molecules or molecular assemblies such as DNA and M13 bacteriophage. In this contribution, we show that LD spectroscopy is a powerful tool in the observation of self-assembly processes of synthetic foldamers when complemented by circular dichroism, absorbance spectroscopy, and microscopy. To that end, poly(para-aryltriazole)s were aligned in a flow field under different solvent conditions. The extended aromatic structures in the foldamer give rise to a strong LD signal that changes in sign and in intensity with varying solvent conditions. A key advantage of LD is that it only detects the large assemblies, thus removing background due to monomers and small oligomers.
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Affiliation(s)
- Jake G. Carter
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Rueben Pfukwa
- Department
of Chemistry and Polymer Sciences, Stellenbosch
University, Private Bag X1, Matieland 7602, South Africa
| | - Liam Riley
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- School
of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Alison Rodger
- Department
of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Timothy R. Dafforn
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Bert Klumperman
- Department
of Chemistry and Polymer Sciences, Stellenbosch
University, Private Bag X1, Matieland 7602, South Africa
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7
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Fudickar W, Bauch M, Ihmels H, Linker T. DNA-Triggered Enhancement of Singlet Oxygen Production by Pyridinium Alkynylanthracenes. Chemistry 2021; 27:13591-13604. [PMID: 34263955 DOI: 10.1002/chem.202101918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 12/23/2022]
Abstract
There is an ongoing interest in 1 O2 sensitizers, whose activity is selectively controlled by their interaction with DNA. To this end, we synthesized three isomeric pyridinium alkynylanthracenes 2 o-p and a water-soluble trapping reagent for 1 O2 . In water and in the absence of DNA, these dyes show a poor efficiency to sensitize the photooxygenation of the trapping reagent as they decompose due to electron transfer processes. In contrast, in the presence of DNA 1 O2 is generated from the excited DNA-bound ligand. The interactions of 2 o-p with DNA were investigated by thermal DNA melting studies, UV/vis and fluorescence spectroscopy, and linear and circular dichroism spectroscopy. Our studies revealed an intercalative binding with an orientation of the long pyridyl-alkynyl axis parallel to the main axis of the DNA base pairs. In the presence of poly(dA : dT), all three isomers show an enhanced formation of singlet oxygen, as indicated by the reaction of the latter with the trapping reagent. With green light irradiation of isomer 2 o in poly(dA : dT), the conversion rate of the trapping reagent is enhanced by a factor >10. The formation of 1 O2 was confirmed by control experiments under anaerobic conditions, in deuterated solvents, or by addition of 1 O2 quenchers. When bound to poly(dG : dC), the opposite effect was observed only for isomers 2 o and 2 m, namely the trapping reagent reacted significantly slower. Overall, we showed that pyridinium alkynylanthracenes are very useful intercalators, that exhibit an enhanced photochemical 1 O2 generation in the DNA-bound state.
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Affiliation(s)
- Werner Fudickar
- Department of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Marcel Bauch
- Department of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany
| | - Torsten Linker
- Department of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
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8
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Arafa RK, Ismail MA, Wenzler T, Brun R, Paul A, Wilson WD, Alakhdar AA, Boykin DW. New antiparasitic flexible triaryl diamidines, their prodrugs and aza analogues: Synthesis, in vitro and in vivo biological evaluation, and molecular modelling studies. Eur J Med Chem 2021; 222:113625. [PMID: 34146914 DOI: 10.1016/j.ejmech.2021.113625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 11/28/2022]
Abstract
Dicationic diamidines have been well established as potent antiparasitic agents with proven activity against tropical diseases like trypanosomiasis and malaria. This work presents the synthesis of new mono and diflexible triaryl amidines (6a-c, 13a,b and 17), their aza analogues (23 and 27) and respective methoxyamidine prodrugs (5, 7, 12a,b, 22 and 26). All diamidines were assessed in vitro against Trypanosoma brucei rhodesiense (T. b. r.) and Plasmodium falciparum (P. f.) where they displayed potent to moderate activities at the nanomolar level with IC50s = 11-378 nM for T. b. r. and 4-323 nM against P. f.. In vivo efficacy testing against T. b. r. STIB900 has shown the monoflexible diamidine 6c as the most potent derivative in this study eliciting 4/4 cures of infected mice for a treatment period of >60 days upon a 4 × 5 mg/kg dose i. p. treatment. Moreover, thermal melting analysis measurement ΔTm for this series of diamidines/poly (dA-dT) complexes fell between 0.5 and 19 °C with 6c showing the highest binding to the DNA minor groove. Finally, a 50 ns molecular dynamics study of an AT-rich DNA dodecamer with compound 6c revealed a strong binding complex supported by vdW and electrostatic interactions.
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Affiliation(s)
- Reem K Arafa
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Cairo, 12578, Egypt; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, 12578, Egypt.
| | - Mohamed A Ismail
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
| | - Tanja Wenzler
- Swiss Tropical and Public Health Institute, 4002, Basel, Switzerland; University of Basel, 4003, Basel, Switzerland
| | - Reto Brun
- Swiss Tropical and Public Health Institute, 4002, Basel, Switzerland; University of Basel, 4003, Basel, Switzerland
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, Georgia
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, Georgia
| | - Amira A Alakhdar
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Cairo, 12578, Egypt; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, 12578, Egypt
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, Georgia
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9
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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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10
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Abeywickrama CS, Wijesinghe KJ, Plescia CB, Fisher LS, Goodson T, Stahelin RV, Pang Y. A pyrene-based two-photon excitable fluorescent probe to visualize nuclei in live cells. Photochem Photobiol Sci 2020; 19:1152-1159. [PMID: 32639494 DOI: 10.1039/d0pp00107d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The two-photon absorption properties of a pyrene-pyridinium dye (1) were studied for potential application in two-photon spectroscopy. When probe 1 was used in cellular two-photon fluorescence microscopy imaging, it allowed the visualization of nuclei in live cells with a relatively low probe concentration (such as 1 μM). Spectroscopic evidence further revealed that probe 1 interacted with DNA as an intercalator. The proposed DNA intercalation properties of probe 1 were consistent with the experimental findings that suggested that the observed nucleus staining ability is dependent on the substituents on the pyridinium fragment of the probe.
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Affiliation(s)
| | - Kaveesha J Wijesinghe
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Caroline B Plescia
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 47907, West Lafayette, Indiana, USA
| | - Lloyd S Fisher
- Department of Chemistry, University of Michigan, 48109, Ann Arbor, MI, USA
| | - Theodore Goodson
- Department of Chemistry, University of Michigan, 48109, Ann Arbor, MI, USA
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 47907, West Lafayette, Indiana, USA
| | - Yi Pang
- Department of Chemistry, University of Akron, 44325, Akron, Ohio, USA. .,Maurice Morton Institute of Polymer Science, University of Akron, 44325, Akron, Ohio, USA.
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11
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Cho SY, Han JH, Jang YJ, Kim SK, Lee YA. Binding Properties of Various Cationic Porphyrins to DNA in the Molecular Crowding Condition Induced by Poly(ethylene glycol). ACS OMEGA 2020; 5:10459-10465. [PMID: 32426603 PMCID: PMC7226857 DOI: 10.1021/acsomega.0c00471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/23/2020] [Indexed: 05/08/2023]
Abstract
The binding modes of various cationic porphyrins to DNA in an aqueous solution and under the molecular crowding condition induced by poly(ethylene glycol) (PEG) were compared by normal absorption, circular dichroism (CD), and linear dichroism (LD) spectroscopy techniques. Large negative CD and LD signals in the Soret absorption regions of the meta- and para-TMPyP [meso-tetrakis (n-N-methylpyridiniumyl) porphyrin (meta, n = 3) and (para, n = 4)] were apparent in the aqueous solution, indicating an intercalative-binding mode, while a positive CD spectrum and a less intense negative LD spectrum for the ortho-TMPyP (n = 2)-complexed DNA suggested a major-groove-binding mode. These binding modes are retained under a molecular crowding condition, suggesting that the PEG cluster cannot access the TMPyPs that are intercalated between the DNA base pairs or that bind at the major groove. The spectral properties of the ortho-, meta-, and para-trans-BMPyP [trans-bis(N-methylpyrodinium-n-yl)diphenyl porphyrin, n = 2,3,4]-bound DNA in an aqueous solution correspond to neither the intercalative-binding nor the groove-binding mode, which is in contrast with the TMPyP cases. The spectral properties under the molecular crowding condition are altered considerably for all of the three trans-BMPyPs compared to those in an aqueous solution, suggesting that the matted PEG cluster is in contact with the cationic trans-BMPyPs, causing a change in the polarity of the porphyrin environment. Consequently, trans-BMPyPs bind to the external side of the DNA.
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Affiliation(s)
- Su Yeon Cho
- Department
of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Ji Hoon Han
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Yoon Jung Jang
- College
of Basis Education, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Seog K. Kim
- Department
of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
- ,
| | - Young-Ae Lee
- Department
of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
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12
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Antiproliferative, DNA binding, and cleavage properties of dinuclear Co(III) complexes containing the bioactive quinizarin ligand. J Biol Inorg Chem 2020; 25:339-350. [DOI: 10.1007/s00775-020-01765-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/12/2020] [Indexed: 01/23/2023]
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13
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Walinda E, Morimoto D, Shirakawa M, Scheler U, Sugase K. Visualizing protein motion in Couette flow by all-atom molecular dynamics. Biochim Biophys Acta Gen Subj 2020; 1864:129383. [DOI: 10.1016/j.bbagen.2019.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 12/29/2022]
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14
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Jeon BR, Chitrapriya N, Kwak MI, Jung MJ, Kim SK, Jang YJ. Effect of the bridge structure on the binding mode of the binuclear ruthenium complex to native DNA. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.126954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Zhou Y, Chen J, Liu C, Liu C, Lai P, Wang L. Single-shot linear dichroism optical-resolution photoacoustic microscopy. PHOTOACOUSTICS 2019; 16:100148. [PMID: 31871890 PMCID: PMC6909087 DOI: 10.1016/j.pacs.2019.100148] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 05/06/2023]
Abstract
Dichroism is a material property that causes anisotropic light-matter interactions for different optical polarizations. Dichroism relates to molecular types and material morphology and thus can be used to distinguish different dichroic tissues. In this paper, we present single-shot dichroism photoacoustic microscopy that can image tissue structure, linear dichroism, and polarization angle with a single raster scanning. We develop a fiber-based laser system to split one laser pulse into three with different polarization angles, sub-microseconds time delay, and identical pulse energy. A dual-fiber optical-resolution photoacoustic microscopy system is developed to acquire three A-lines per scanning step. In such a way, dichroism imaging can achieve the same speed as single-wavelength photoacoustic microscopy. Moreover, the three polarized pulses originate from one laser pulse, which decreases pulse energy fluctuations and reduces dichroism measurement noise by ∼35 %. The new dichroism photoacoustic imaging technique can be used to image endogenous or exogenous polarization-dependent absorption contrasts, such as dichroic tumor or molecule-labeled tissue.
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Affiliation(s)
- Yingying Zhou
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China
| | - Jiangbo Chen
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Chao Liu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Chengbo Liu
- Research Laboratory for Biomedical Optics and Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Puxiang Lai
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China
| | - Lidai Wang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
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16
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Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects. Proc Natl Acad Sci U S A 2019; 116:17169-17174. [PMID: 31413203 PMCID: PMC6717297 DOI: 10.1073/pnas.1909122116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The main stabilizer of the DNA double helix is not the base-pair hydrogen bonds but coin-pile stacking of base pairs, whose hydrophobic cohesion, requiring abundant water, indirectly makes the DNA interior dry so that hydrogen bonds can exert full recognition power. We report that certain semihydrophobic agents depress the stacking energy (measurable in single-molecule experiments), leading to transiently occurring holes in the base-pair stack (monitorable via binding of threading intercalators). Similar structures observed in DNA complexes with RecA and Rad51, and previous observations of spontaneous strand exchange catalyzed in semihydrophobic model systems, make us propose that some hydrophobic protein residues may have roles in catalyzing homologous recombination. We speculate that hydrophobic catalysis is a general phenomenon in DNA enzymes. Hydrophobic base stacking is a major contributor to DNA double-helix stability. We report the discovery of specific unstacking effects in certain semihydrophobic environments. Water-miscible ethylene glycol ethers are found to modify structure, dynamics, and reactivity of DNA by mechanisms possibly related to a biologically relevant hydrophobic catalysis. Spectroscopic data and optical tweezers experiments show that base-stacking energies are reduced while base-pair hydrogen bonds are strengthened. We propose that a modulated chemical potential of water can promote “longitudinal breathing” and the formation of unstacked holes while base unpairing is suppressed. Flow linear dichroism in 20% diglyme indicates a 20 to 30% decrease in persistence length of DNA, supported by an increased flexibility in single-molecule nanochannel experiments in poly(ethylene glycol). A limited (3 to 6%) hyperchromicity but unaffected circular dichroism is consistent with transient unstacking events while maintaining an overall average B-DNA conformation. Further information about unstacking dynamics is obtained from the binding kinetics of large thread-intercalating ruthenium complexes, indicating that the hydrophobic effect provides a 10 to 100 times increased DNA unstacking frequency and an “open hole” population on the order of 10−2 compared to 10−4 in normal aqueous solution. Spontaneous DNA strand exchange catalyzed by poly(ethylene glycol) makes us propose that hydrophobic residues in the L2 loop of recombination enzymes RecA and Rad51 may assist gene recombination via modulation of water activity near the DNA helix by hydrophobic interactions, in the manner described here. We speculate that such hydrophobic interactions may have catalytic roles also in other biological contexts, such as in polymerases.
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17
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van Mameren J, Vermeulen K, Wuite GJL, Peterman EJG. A polarized view on DNA under tension. J Chem Phys 2018; 148:123306. [PMID: 29604805 DOI: 10.1063/1.5004019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the past decades, sensitive fluorescence microscopy techniques have contributed significantly to our understanding of the dynamics of DNA. The specific labeling of DNA using intercalating dyes has allowed for quantitative measurement of the thermal fluctuations the polymers undergo. On the other hand, recent advances in single-molecule manipulation techniques have unraveled the mechanical and elastic properties of this intricate polymer. Here, we have combined these two approaches to study the conformational dynamics of DNA under a wide range of tensions. Using polarized fluorescence microscopy in conjunction with optical-tweezers-based manipulation of YOYO-intercalated DNA, we controllably align the YOYO dyes using DNA tension, enabling us to disentangle the rapid dynamics of the dyes from that of the DNA itself. With unprecedented control of the DNA alignment, we resolve an inconsistency in reports about the tilted orientation of intercalated dyes. We find that intercalated dyes are on average oriented perpendicular to the long axis of the DNA, yet undergo fast dynamics on the time scale of absorption and fluorescence emission. In the overstretching transition of double-stranded DNA, we do not observe changes in orientation or orientational dynamics of the dyes. Only beyond the overstretching transition, a considerable depolarization is observed, presumably caused by an average tilting of the DNA base pairs. Our combined approach thus contributes to the elucidation of unique features of the molecular dynamics of DNA.
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Affiliation(s)
- Joost van Mameren
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
| | - Karen Vermeulen
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
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18
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Jin B, Sung GW, Jang YJ. Binding mode of proflavine to DNA probed by polarized light spectroscopy. J CHIN CHEM SOC-TAIP 2018. [DOI: 10.1002/jccs.201800246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Biao Jin
- Instrumental Analysis CenterYanbian University Yanji City Jilin Province China
| | - Gi Woong Sung
- Department of ChemistryYeungnam University Dae‐dong Gyeongsan City Gyeong‐buk Republic of Korea
| | - Yoon Jung Jang
- College of Basic Education, Yeungnam University Dae‐dong Gyeongsan City Gyeong‐buk Republic of Korea
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19
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Dorrington G, Chmel NP, Norton SR, Wemyss AM, Lloyd K, Praveen Amarasinghe D, Rodger A. Light scattering corrections to linear dichroism spectroscopy for liposomes in shear flow using calcein fluorescence and modified Rayleigh-Gans-Debye-Mie scattering. Biophys Rev 2018; 10:1385-1399. [PMID: 30255222 PMCID: PMC6233352 DOI: 10.1007/s12551-018-0458-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/13/2018] [Indexed: 12/02/2022] Open
Abstract
The interpretation of data from absorbance spectroscopy experiments of liposomes in flow systems is often complicated by the fact that there is currently no easy way to account for scattering artefacts. This has proved particularly problematic for linear dichroism (LD) spectroscopy, which may be used to determine binding modes of small molecules, peptides and proteins to liposomes if we can extract the absorbance signal from the combined absorbance/scattering experiment. Equations for a modified Rayleigh-Gans-Debye (RGD) approximation to the turbidity (scattering) LD spectrum are available in the literature though have not been implemented. This review summarises the literature and shows how it can be implemented. The implementation proceeds by first determining volume loss that occurs when a spherical liposome is subjected to flow. Calcein fluorescence can be used for this purpose since at high concentrations (> 60 mM) it has low intensity fluorescence with maxima at 525 and 563 nm whereas at low concentrations (<1 mM) the fluorescence intensity is enhanced and the band shifts to 536 nm. The scattering calculation process yields the average axis ratios of the distorted liposome ellipsoids and extent of orientation of the liposomes in flow. The scattering calculations require methods to estimate liposome integrity, volume loss, and orientation when subjected to shear stresses under flow.
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Affiliation(s)
- Glen Dorrington
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - Nikola P Chmel
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - Stephen R Norton
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - Alan M Wemyss
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - Katherine Lloyd
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - D Praveen Amarasinghe
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- MOAC Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - Alison Rodger
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
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20
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Rodger A, Dorrington G, Ang DL. Linear dichroism as a probe of molecular structure and interactions. Analyst 2018; 141:6490-6498. [PMID: 27840872 DOI: 10.1039/c6an01771a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Linear dichroism (LD) spectroscopy involves measuring the wavelength (or energy) dependence of the difference in absorption of light parallel and perpendicular to an orientation direction. It requires samples to have a net orientation. The aim of this review is to summarise some UV-visible linear dichroism (LD) methods that can be usefully applied to increase our understanding of biomacromolecules and their complexes that have a high aspect ratio. LD shares the advantages of most spectroscopic techniques including the fact that data collection is fairly straightforward and many sample types can be investigated. Conversely, LD shares the disadvantage that the measured signal is an average over all species in the sample on which the light beam is incident. LD mitigates this disadvantage somewhat in that only species which are oriented give a net signal. How the data can be analysed to give structural information about small molecules in stretched films and membrane systems or bound to biomacromolecules and directly about biomacromolecules such as DNA and protein fibres forms part of this review. In the UV-visible region LD often suffers noticeably from light scattering since the samples tend to be large relative to the wavelength of the incident light, so consideration is also given to data analysis challenges including removal of scattering contributions to an observed signal. Brief mention is made of fluorescence detected LD.
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Affiliation(s)
- Alison Rodger
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Glen Dorrington
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Dale L Ang
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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21
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Lee HS, Han JH, Park JH, Heo ME, Hirakawa K, Kim SK, Cho DW. Relationship between the photoinduced electron transfer and binding modes of a pyrene-porphyrin dyad to DNA. Phys Chem Chem Phys 2018; 19:27123-27131. [PMID: 28967018 DOI: 10.1039/c7cp05211a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding modes of a pyrene-porphyrin dyad, (1-pyrenyl)-tris(N-methyl-p-pyridino)porphyrin (PyTMpyP), to DNA and its photophysical properties have been investigated using various spectroscopic techniques. The circular dichroism (CD) spectrum of PyTMpyP bound to DNA (PyTMpyP-DNA) showed one negative and two positive bands in the Soret region. The CD signal in the pyrene absorption region was positive. The shape of the CD spectrum does not support an intercalative binding mode of TMpyP, which would typically afford a negative CD band in the absence of the pyrene moiety. Linear dichroism (LD) experiments revealed a very small signal in the Soret region, which also challenges the intercalation of TMpyP into DNA. Upon excitation of the pyrene moiety, the emission intensity of porphyrin in aqueous solution was quenched due to a photoinduced electron transfer (PET) process between the pyrenyl and porphyrin moieties. On the other hand, the emission of porphyrin was markedly enhanced upon binding to DNA, as the PET process from the excited pyrene moiety to TMpyP was suppressed when bound to DNA. The PET process occurs in the timescale of 65 ps, and could be detected by femtosecond transient absorption spectroscopic methods. Two fluorescence decay times were observed for PyTMpyP in aqueous solution (0.78 and 4.8 ns). Both decay times increased upon binding to DNA owing to environment and/or conformational changes in PyTMpyP. The driving force (ΔG) of the PET process was evaluated under conditions of minor and major groove binding. The PET process and photophysical properties of the PyTMpyP dyad were concluded to be influenced by the binding mode.
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Affiliation(s)
- Hyun Suk Lee
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea.
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22
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Nejat Dehkordi M, Akerman B. Interaction of DNA with water soluble complex of Nickle and formation of DNA cross-links. Chem Biol Interact 2018; 282:55-62. [DOI: 10.1016/j.cbi.2018.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 07/16/2017] [Accepted: 01/05/2018] [Indexed: 11/24/2022]
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23
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Kwak MI, Jeon BR, Kim SK, Jang YJ. Binding Mode of Cationic Porphyrin with CT-DNA: Importance of the Location and the Number of Positively Charged of Periphery Cationic Ions of Porphyrin. ACS OMEGA 2018; 3:946-953. [PMID: 31457940 PMCID: PMC6641333 DOI: 10.1021/acsomega.7b01627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/25/2017] [Indexed: 05/24/2023]
Abstract
The binding modes of o-, m-, and p-trans-BMPyP with DNA were studied using their spectroscopic properties. Also, the binding modes were compared based on the location and number of periphery cationic methylpyridine ions of the cationic porphyrins. The optical absorption spectra of the o-, m-, and p-trans-BMPyP when bound to DNA presented red shifts and hypochromicity compared to the optical absorption spectrum of DNA-free cationic porphyrins. m-trans-BMPyP-DNA presented the largest red shifts and hypochromicity. The results of the circular dichroism spectral analysis indicated positive and negative bisignate absorption bands in the Soret band of the porphyrins in the case of all concentration ratios of o- and p-trans-BMPyP-DNA, and two negative absorption bands were observed in m-trans-BMPyP-DNA. Compared to the size of the absorption band of the DNA optical absorption spectrum, the results of the reduced linear (LDr) spectral analysis indicated mainly small sizes of Soret absorption bands (the absorption spectrum of porphyrins) and positive LDr values for o- and p-trans-BMPyP-DNA. In consideration of several of such spectroscopic properties, the binding of o- and p-trans-BMPyP with DNA can be said to be distant to insertion modes. Although the case of m-trans-BMPyP to DNA is an insertion mode, the m-trans-BMPyP molecular surface presented much tilt within the intercalation pocket. The results of comparing the binding modes of TMPyP having four periphery cationic methylpyridine ions of cationic porphyrin indicated that regardless of the number of periphery cationic methylpyridine ions of cationic porphyrin, in the case of the ortho-position, nonplanarity due to steric hindrance of the periphery cationic methylpyridine ions presented outside or groove-binding modes indicative of interaction with DNA phosphates. Unlike the ortho-position, the para-position presented different binding modes based on the number of periphery cationic methylpyridine ions. Only cationic porphyrins having four periphery cationic methylpyridine ions were inserted into the DNA. Lastly, regardless of the number of periphery cationic methylpyridine ions, all meta-positions were inserted into the DNA. This indicated that at the least the location and the number of periphery cationic methylpyridine ions of the porphyrins used in this experiment were important elements that determine insertion into DNA base pairs.
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Affiliation(s)
- Min Ik Kwak
- Department of Chemistry and College of Basic Education, Yeungnam University, Dae-dong, Gyeongsan City, Gyeong-buk 38541, Republic of Korea
| | - Bo Ram Jeon
- Department of Chemistry and College of Basic Education, Yeungnam University, Dae-dong, Gyeongsan City, Gyeong-buk 38541, Republic of Korea
| | - Seog K Kim
- Department of Chemistry and College of Basic Education, Yeungnam University, Dae-dong, Gyeongsan City, Gyeong-buk 38541, Republic of Korea
| | - Yoon Jung Jang
- Department of Chemistry and College of Basic Education, Yeungnam University, Dae-dong, Gyeongsan City, Gyeong-buk 38541, Republic of Korea
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24
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Šmidlehner T, Piantanida I, Pescitelli G. Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids - tutorial. Beilstein J Org Chem 2018; 14:84-105. [PMID: 29441133 PMCID: PMC5789433 DOI: 10.3762/bjoc.14.5] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/13/2017] [Indexed: 01/19/2023] Open
Abstract
The structural characterization of non-covalent complexes between nucleic acids and small molecules (ligands) is of a paramount significance to bioorganic research. Highly informative methods about nucleic acid/ligand complexes such as single crystal X-ray diffraction or NMR spectroscopy cannot be performed under biologically compatible conditions and are extensively time consuming. Therefore, in search for faster methods which can be applied to conditions that are at least similar to the naturally occurring ones, a set of polarization spectroscopy methods has shown highly promising results. Electronic circular dichroism (ECD) is the most commonly used method for the characterization of the helical structure of DNA and RNA and their complexes with ligands. Less common but complementary to ECD, is flow-oriented linear dichroism (LD). Other methods such as vibrational CD (VCD) and emission-based methods (FDCD, CPL), can also be used for suitable samples. Despite the popularity of polarization spectroscopy in biophysics, aside several highly focused reviews on the application of these methods to DNA/RNA research, there is no systematic tutorial covering all mentioned methods as a tool for the characterization of adducts between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably.
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Affiliation(s)
- Tamara Šmidlehner
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute; P. O. Box 180, 10002 Zagreb, Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute; P. O. Box 180, 10002 Zagreb, Croatia
| | - Gennaro Pescitelli
- Department of Chemistry, University of Pisa, via Moruzzi 13, Pisa, Italy
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25
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Berdnikova DV, Sosnin NI, Fedorova OA, Ihmels H. Governing the DNA-binding mode of styryl dyes by the length of their alkyl substituents – from intercalation to major groove binding. Org Biomol Chem 2018; 16:545-554. [DOI: 10.1039/c7ob02736b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The length of alkyl substituents governs the DNA binding mode of mono- and bis-chromophoric styryl dyes.
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Affiliation(s)
- Daria V. Berdnikova
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- 119991 Moscow
- Russia
- Department of Chemistry–Biology and Center of Micro and Nanochemistry and Engineering
| | - Nikolai I. Sosnin
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- 119991 Moscow
- Russia
| | - Olga A. Fedorova
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- 119991 Moscow
- Russia
| | - Heiko Ihmels
- Department of Chemistry–Biology and Center of Micro and Nanochemistry and Engineering
- University of Siegen
- 57068 Siegen
- Germany
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26
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Oh YS, Park JH, Han SW, Kim SK, Lee YA. Retained binding mode of various DNA-binding molecules under molecular crowding condition. J Biomol Struct Dyn 2017; 36:3035-3046. [DOI: 10.1080/07391102.2017.1375992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ye Sol Oh
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Jin Ha Park
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Sung Wook Han
- Department of Health & Biotechnology, Kyungwoon University, Kumi City, Gyeong-buk 39253, Republic of Korea
| | - Seog K. Kim
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Young-Ae Lee
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
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27
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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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28
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Ranjan N, Arya DP. Linker dependent intercalation of bisbenzimidazole-aminosugars in an RNA duplex; selectivity in RNA vs. DNA binding. Bioorg Med Chem Lett 2016; 26:5989-5994. [PMID: 27884695 PMCID: PMC6201841 DOI: 10.1016/j.bmcl.2016.10.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 01/08/2023]
Abstract
Neomycin and Hoechst 33258 are two well-known nucleic acid binders that interact with RNA and DNA duplexes with high affinities respectively. In this manuscript, we report that covalent attachment of bisbenzimidazole unit derived from Hoechst 33258 to neomycin leads to intercalative binding of the bisbenzimidazole unit (oriented at 64-74° with respected to the RNA helical axis) in a linker length dependent manner. The dual binding and intercalation of conjugates were supported by thermal denaturation, CD, LD and UV-Vis absorption experiments. These studies highlight the importance of linker length in dual recognition by conjugates, for effective RNA recognition, which can lead to novel ways of recognizing RNA structures. Additionally, the ligand library screens also identify DNA and RNA selective compounds, with compound 9, containing a long linker, showing a 20.3°C change in RNA duplex Tm with only a 13.0°C change in Tm for the corresponding DNA duplex. Significantly, the shorter linker in compound 3 shows almost the reverse trend, a 23.8°C change in DNA Tm, with only a 9.1°C change in Tm for the corresponding RNA duplex.
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Affiliation(s)
- Nihar Ranjan
- Laboratory of Bioorganic and Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States
| | - Dev P Arya
- Laboratory of Bioorganic and Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States.
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29
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Németh E, Balogh RK, Borsos K, Czene A, Thulstrup PW, Gyurcsik B. Intrinsic protein disorder could be overlooked in cocrystallization conditions: An SRCD case study. Protein Sci 2016; 25:1977-1988. [PMID: 27508941 DOI: 10.1002/pro.3010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/08/2016] [Indexed: 12/21/2022]
Abstract
X-ray diffractometry dominates protein studies, as it can provide 3D structures of these diverse macromolecules or their molecular complexes with interacting partners: substrates, inhibitors, and/or cofactors. Here, we show that under cocrystallization conditions the results could reflect induced protein folds instead of the (partially) disordered original structures. The analysis of synchrotron radiation circular dichroism spectra revealed that the Im7 immunity protein stabilizes the native-like solution structure of unfolded NColE7 nuclease mutants via complex formation. This is consistent with the fact that among the several available crystal structures with its inhibitor or substrate, all NColE7 structures are virtually the same. Our results draw attention to the possible structural consequence of protein modifications, which is often hidden by compensational effects of intermolecular interactions. The growing evidence on the importance of protein intrinsic disorder thus, demands more extensive complementary experiments in solution phase with the unligated form of the protein of interest.
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Affiliation(s)
- Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary.,MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary
| | - Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary
| | - Katalin Borsos
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary
| | - Anikó Czene
- MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary. .,MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary.
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30
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Amirbekyan K, Duchemin N, Benedetti E, Joseph R, Colon A, Markarian SA, Bethge L, Vonhoff S, Klussmann S, Cossy J, Vasseur JJ, Arseniyadis S, Smietana M. Design, Synthesis, and Binding Affinity Evaluation of Hoechst 33258 Derivatives for the Development of Sequence-Specific DNA-Based Asymmetric Catalysts. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00495] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karen Amirbekyan
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
- Department
of Physical Chemistry, Yerevan State University, 1 Alex Manoogian, Yerevan 0025, Armenia
| | - Nicolas Duchemin
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Erica Benedetti
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Rinah Joseph
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Aude Colon
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Shiraz A. Markarian
- Department
of Physical Chemistry, Yerevan State University, 1 Alex Manoogian, Yerevan 0025, Armenia
| | - Lucas Bethge
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Stephan Vonhoff
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Sven Klussmann
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Janine Cossy
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Jean-Jacques Vasseur
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
| | - Stellios Arseniyadis
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
- School
of Biological and Chemical Sciences, Queen Mary University of London, Joseph Priestley Building, Mile End Road, London E1 4NS, United Kingdom
| | - Michael Smietana
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
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31
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Bergen A, Rudiuk S, Morel M, Le Saux T, Ihmels H, Baigl D. Photodependent Melting of Unmodified DNA Using a Photosensitive Intercalator: A New and Generic Tool for Photoreversible Assembly of DNA Nanostructures at Constant Temperature. NANO LETTERS 2016; 16:773-80. [PMID: 26652690 DOI: 10.1021/acs.nanolett.5b04762] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
External control of DNA melting and hybridization, a key step in bio- and DNA nanotechnology, is commonly achieved with temperature. The use of light to direct this process is a challenging alternative, which has been only possible with a DNA modification, such as covalent grafting or mismatch introduction, so far. Here we describe the first photocontrol of DNA melting that relies on the addition of a molecule that noncovalently interacts with unmodified DNA and affects its melting properties in a photoreversible and highly robust manner, without any prerequisite in the length or sequence of the target DNA molecule. We synthesize azobenzene-containing guanidinium derivatives and show that a bivalent molecule with a conformation-dependent binding mode, AzoDiGua, strongly increases the melting temperature (Tm) of DNA under dark conditions because its trans isomer intercalates in the DNA double helix. Upon UV irradiation at 365 nm, the trans-cis isomerization induced the ejection of AzoDiGua from the intercalation binding sites, resulting in a decrease in Tm up to 18 °C. This illumination-dependent Tm shift is observed on many types of DNA, from self-complementary single-stranded or double-stranded oligonucleotides to long genomic duplex DNA molecules. Finally, we show that simply adding AzoDiGua allows us to photoreversibly control the assembly/disassembly of a DNA nanostructure at constant temperature, as demonstrated here with a self-hybridized DNA hairpin. We anticipate that this strategy will be the key ingredient in a new and generic way of placing DNA-based bio- and nanotechnologies under dynamic control by light.
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Affiliation(s)
- Anna Bergen
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Sergii Rudiuk
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Mathieu Morel
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Thomas Le Saux
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Heiko Ihmels
- Department of Chemistry-Biology, University of Siegen , Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Damien Baigl
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
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32
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Paul A, Nanjunda R, Kumar A, Laughlin S, Nhili R, Depauw S, Deuser SS, Chai Y, Chaudhary AS, David-Cordonnier MH, Boykin DW, Wilson WD. Mixed up minor groove binders: Convincing A·T specific compounds to recognize a G·C base pair. Bioorg Med Chem Lett 2015; 25:4927-4932. [PMID: 26051649 DOI: 10.1016/j.bmcl.2015.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 05/06/2015] [Indexed: 01/08/2023]
Abstract
DNA minor-groove-binding compounds have limited biological applications, in part due to problems with sequence specificity that cause off-target effects. A model to enhance specificity has been developed with the goal of preparing compounds that bind to two AT sites separated by G·C base pairs. Compounds of interest were probed using thermal melting, circular dichroism, mass spectrometry, biosensor-SPR, and molecular modeling methods. A new minor groove binder that can strongly and specifically recognize a single G·C base pair with flanking AT sequences has been prepared. This multi-site DNA recognition mode offers novel design principles to recognize entirely new DNA motifs.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Rupesh Nanjunda
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Sarah Laughlin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Raja Nhili
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM-University of Lille and Centre Hospitalier of Lille, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | - Sabine Depauw
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM-University of Lille and Centre Hospitalier of Lille, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | - Shelby Sheldon Deuser
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Yun Chai
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Arpana S Chaudhary
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Marie-Hélène David-Cordonnier
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM-University of Lille and Centre Hospitalier of Lille, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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33
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Tacrine derivatives as dual topoisomerase I and II catalytic inhibitors. Bioorg Chem 2015; 59:168-76. [DOI: 10.1016/j.bioorg.2015.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 11/17/2022]
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34
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Berdnikova DV, Fedorova OA, Tulyakova EV, Li H, Kölsch S, Ihmels H. Interaction of Crown Ether-Annelated Styryl Dyes with Double-Stranded DNA. Photochem Photobiol 2015; 91:723-31. [DOI: 10.1111/php.12405] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/04/2014] [Indexed: 02/02/2023]
Affiliation(s)
- Daria V. Berdnikova
- A. N. Nesmeyanov Institute of Organoelement Compounds; Russian Academy of Sciences; Moscow Russia
- Department Chemie-Biologie; Universität Siegen; Organische Chemie II; Siegen Germany
| | - Olga A. Fedorova
- A. N. Nesmeyanov Institute of Organoelement Compounds; Russian Academy of Sciences; Moscow Russia
| | - Elena V. Tulyakova
- A. N. Nesmeyanov Institute of Organoelement Compounds; Russian Academy of Sciences; Moscow Russia
| | - Haixing Li
- Department Chemie-Biologie; Universität Siegen; Organische Chemie II; Siegen Germany
| | - Sarah Kölsch
- Department Chemie-Biologie; Universität Siegen; Organische Chemie II; Siegen Germany
| | - Heiko Ihmels
- Department Chemie-Biologie; Universität Siegen; Organische Chemie II; Siegen Germany
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35
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Chitrapriya N, Shin JH, Hwang IH, Kim Y, Kim C, Kim SK. Synthesis, DNA binding profile and DNA cleavage pathway of divalent metal complexes. RSC Adv 2015. [DOI: 10.1039/c5ra10695h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Divalent metal complexes of dipyridylamine ligand with an anthracene moiety induced considerable oxidative DNA cleavage in the presence hydrogen peroxide and dioxygen.
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Affiliation(s)
| | - Jong Heon Shin
- Department of Chemistry
- Yeungnam University
- Gyeongsan
- Republic of Korea
| | - In Hong Hwang
- Department of Fine Chemistry and Department of Interdisciplinary Bio IT Materials
- Seoul National University of Science and Technology
- Seoul 139-743
- Republic of Korea
| | - Youngmee Kim
- Department of Chemistry and Nano Science
- Ewha Womans University
- Seoul 120-750
- Republic of Korea
| | - Cheal Kim
- Department of Fine Chemistry and Department of Interdisciplinary Bio IT Materials
- Seoul National University of Science and Technology
- Seoul 139-743
- Republic of Korea
| | - Seog K. Kim
- Department of Chemistry
- Yeungnam University
- Gyeongsan
- Republic of Korea
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36
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Jin B, Han SW, Lee DJ. Behavior in Solution and Mixing Ratio-Dependent Binding Modes of Carcinogenic Benzo[a]pyrene-7,8-dione to Calf Thymus DNA. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.10.3015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Hammarson M, Nilsson JR, Li S, Lincoln P, Andréasson J. DNA-Binding Properties of Amidine-Substituted Spiropyran Photoswitches. Chemistry 2014; 20:15855-62. [DOI: 10.1002/chem.201405113] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Indexed: 12/25/2022]
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38
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Fornander LH, Feng B, Beke-Somfai T, Nordén B. UV Transition Moments of Tyrosine. J Phys Chem B 2014; 118:9247-57. [DOI: 10.1021/jp5065352] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Louise H. Fornander
- Department of Chemical and
Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Bobo Feng
- Department of Chemical and
Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Tamás Beke-Somfai
- Department of Chemical and
Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Bengt Nordén
- Department of Chemical and
Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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39
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Németh E, Körtvélyesi T, Thulstrup PW, Christensen HEM, Kožíšek M, Nagata K, Czene A, Gyurcsik B. Fine tuning of the catalytic activity of colicin E7 nuclease domain by systematic N-terminal mutations. Protein Sci 2014; 23:1113-22. [PMID: 24895333 DOI: 10.1002/pro.2497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/20/2014] [Accepted: 05/29/2014] [Indexed: 11/11/2022]
Abstract
The nuclease domain of colicin E7 (NColE7) promotes the nonspecific cleavage of nucleic acids at its C-terminal HNH motif. Interestingly, the deletion of four N-terminal residues (446-449 NColE7 = KRNK) resulted in complete loss of the enzyme activity. R447A mutation was reported to decrease the nuclease activity, but a detailed analysis of the role of the highly positive and flexible N-terminus is still missing. Here, we present the study of four mutants, with a decreased activity in the following order: NColE7 >> KGNK > KGNG ∼ GGNK > GGNG. At the same time, the folding, the metal-ion, and the DNA-binding affinity were unaffected by the mutations as revealed by linear and circular dichroism spectroscopy, isothermal calorimetric titrations, and gel mobility shift experiments. Semiempirical quantum chemical calculations and molecular dynamics simulations revealed that K446, K449, and/or the N-terminal amino group are able to approach the active centre in the absence of the other positively charged residues. The results suggested a complex role of the N-terminus in the catalytic process that could be exploited in the design of a controlled nuclease.
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Affiliation(s)
- Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, 6720, Szeged, Hungary; Department of Physical Chemistry and Material Sciences, University of Szeged, 6720, Szeged, Hungary
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40
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Kim HJ, Sung G, Kim G, Park J, Jin B, Kim SK. Effect of various intercalators on the fenton-type oxidative cleavage of double-stranded DNA. Chem Asian J 2014; 9:1341-8. [PMID: 24665066 DOI: 10.1002/asia.201400099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Indexed: 11/10/2022]
Abstract
The intensity of the linear dichroism (LD) in the absorption region of DNA (about 260 nm) decreased with time in the presence of [Fe(EDTA)](2+) (EDTA = ethylenediaminetetraacetic acid), H2O2, and ascorbate. The decrease in the LD signal indicated either an increase in flexibility, a shortening of the DNA stem, or both, owing to oxidative cleavage, and was best described by the difference between the two single-exponential-decay curves, thereby suggesting the involvement of two sequential first-order reactions. The fast reaction was assigned to cleavage of one of two DNA strands, which increased the flexibility of the DNA. The slow reaction corresponded to cleavage at or near the first cleavage site, thereby shortening the DNA stem. The presence of an intercalator, including ethidium, propidium, 9-aminoacridine, and proflavine, inhibited the first step of the cleavage reaction. One of the possible reasons for the observed inhibition might be a change in the DNA conformation near the intercalation site. Intercalation caused an unwinding and elongation of the DNA and resulted in changes in the location of the H atoms of the sugar moiety, which is known to be the main site at which hydroxyl radicals react.
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Affiliation(s)
- Hyeon Jeong Kim
- Department of Chemistry, Yeungnam University, Dae-dong, Gyeongsan City, Gyeong-buk, 712-749 (Republic of Korea), Fax: (+82) 53-815-5412
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41
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Chai Y, Paul A, Rettig M, Wilson WD, Boykin DW. Design and synthesis of heterocyclic cations for specific DNA recognition: from AT-rich to mixed-base-pair DNA sequences. J Org Chem 2014; 79:852-66. [PMID: 24422528 PMCID: PMC3985508 DOI: 10.1021/jo402599s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 01/18/2023]
Abstract
The compounds synthesized in this research were designed with the goal of establishing a new paradigm for mixed-base-pair DNA sequence-specific recognition. The design scheme starts with a cell-permeable heterocyclic cation that binds to AT base pair sites in the DNA minor groove. Modifications were introduced in the original compound to include an H-bond accepting group to specifically recognize the G-NH that projects into the minor groove. Therefore, a series of heterocyclic cations substituted with an azabenzimidazole ring has been designed and synthesized for mixed-base-pair DNA recognition. The most successful compound, 12a, had an azabenzimidazole to recognize G and additional modifications for general minor groove interactions. It binds to the DNA site -AAAGTTT- more strongly than the -AAATTT- site without GC and indicates the design success. Structural modifications of 12a generally weakened binding. The interactions of the new compound with a variety of DNA sequences with and without GC base pairs were evaluated by thermal melting analysis, circular dichroism, fluorescence emission spectroscopy, surface plasmon resonance, and molecular modeling.
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Affiliation(s)
- Yun Chai
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Ananya Paul
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Michael Rettig
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - W. David Wilson
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - David W. Boykin
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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42
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DNA-binding of nickel(II), copper(II) and zinc(II) complexes: Structure–affinity relationships. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.023] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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43
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Chitrapriya N, Kim R, Jang YJ, Cho DW, Han SW, Kim SK. Sequence Dependent Binding Modes of the ΔΔ- and ΛΛ-binuclear Ru(II) Complexes to poly[d(G-C) 2] and poly[d(A-T) 2]. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.7.2117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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44
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Park HJ, Kwon JH, Cho TS, Kim JM, Hwang IH, Kim C, Kim S, Kim J, Kim SK. Real-time detection of DNA cleavage induced by [M(2,2'-bipyridine)2(NO3)](NO3) (M=Cu(II), Zn(II) and Cd(II)) complexes using linear dichroism technique. J Inorg Biochem 2013; 127:46-52. [PMID: 23850668 DOI: 10.1016/j.jinorgbio.2013.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/28/2013] [Accepted: 06/15/2013] [Indexed: 10/26/2022]
Abstract
The catalytic effect of [M(2,2'-bipyridine)2(NO3)](NO3) (M(bpy)2, M=Cu(II), Zn(II) and Cd(II)) on the super-coiled and double stranded DNA (scDNA and dsDNA) was examined by electrophoresis and a real-time detection linear dichroism (LD) technique. Although the Cu(bpy)2 complex effectively cleaved both types of DNA, the other two complexes were inactive. This was explained by the electrochemical properties of the metal complexes. The Cu(bpy)2 complex exhibited a redox potential at -0.222V with a peak to peak separation of 0.201V, whereas the other two metal complexes did not undergo any redox reaction. Both electrophoresis and LD measurements revealed the superoxide radical, ·O2(-), to be responsible for DNA cleavage. A kinetic study using the LD technique showed that the cleavage of dsDNA consisted of two first order reactions. The fast reaction is believed to reflect the cleavage of one strand, whereas the slow reaction involves the cleavage of the complementary strand at or near the first cleaved site.
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Affiliation(s)
- Hee-Jin Park
- Department of Chemistry, Yeungnam University, Gyeongsan City, Gyeong-buk 712-749, Republic of Korea
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45
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Fornander LH, Wu L, Billeter M, Lincoln P, Nordén B. Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule? J Phys Chem B 2013; 117:5820-30. [DOI: 10.1021/jp400418w] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Louise H. Fornander
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Lisha Wu
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Martin Billeter
- Department of Chemistry and
Molecular Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Bengt Nordén
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
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46
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Kel O, Fürstenberg A, Mehanna N, Nicolas C, Laleu B, Hammarson M, Albinsson B, Lacour J, Vauthey E. Chiral Selectivity in the Binding of [4]Helicene Derivatives to Double-Stranded DNA. Chemistry 2013; 19:7173-80. [DOI: 10.1002/chem.201203915] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Indexed: 11/11/2022]
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47
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Comprehensive Study on the Binding of Iron Schiff Base Complex with DNA and Determining the Binding Mode. J Fluoresc 2013; 23:813-21. [DOI: 10.1007/s10895-013-1181-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 02/24/2013] [Indexed: 10/27/2022]
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48
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49
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Pace TCS, Müller V, Li S, Lincoln P, Andréasson J. Enantioselective Cyclization of Photochromic Dithienylethenes Bound to DNA. Angew Chem Int Ed Engl 2013; 52:4393-6. [DOI: 10.1002/anie.201209773] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 02/01/2013] [Indexed: 11/09/2022]
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50
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Pitter DRG, Wigenius J, Brown AS, Baker JD, Westerlund F, Wilson JN. Turn-on, fluorescent nuclear stains with live cell compatibility. Org Lett 2013; 15:1330-3. [PMID: 23461418 DOI: 10.1021/ol400268t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA-binding, green and yellow fluorescent probes with excellent brightness and high on/off ratios are reported. The probes are membrane permeable, live-cell compatible, and optimally matched to 405 nm and 514 nm laser lines, making them attractive alternatives to UV-excited and blue emissive Hoechst 33342 and DAPI nuclear stains. Their electronic structure was investigated by optical spectroscopy supported by TD-DFT calculations. DNA binding is accompanied by 27- to 75-fold emission enhancements, and linear dichroism demonstrates that one dye is a groove binder while the other intercalates into DNA.
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Affiliation(s)
- Demar R G Pitter
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, USA
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