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Pronkin PG, Tatikolov AS. Spectral-fluorescent and photochemical study of 6,6'-di(benzoylamino)trimethine cyanine dyes in solutions as possible probes for DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 292:122416. [PMID: 36746042 DOI: 10.1016/j.saa.2023.122416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Spectral-fluorescent and photochemical properties of trimethine cyanine dyes T-304, T-306, and T-307, having substituents in 6,6'-positions, in various organic solvents, in aqueous buffer solutions, in the presence of surfactants and ethanol additives, and the effect on these properties of addition of DNA have been studied. Strong aggregation of the dyes in aqueous and aqueous buffer solutions has been shown. This is due to increased hydrophobicity of the dyes, which makes it difficult to use them as spectral-fluorescent probes for DNA. In the presence of DNA, trimethine cyanines partially form highly fluorescent complexes of dye monomers with the biomolecule, with slight decomposition of the initial aggregates and the formation of aggregates on DNA molecules. The formation of different types of dye-DNA complexes, i.e., intercalation and binding in the DNA grooves, was modeled by molecular docking. Dye-DNA complexes were also studied by circular dichroism spectroscopy and by thermal dissociation of DNA. To reveal selectivity of the dyes, their interaction with human serum albumin was briefly studied. The presence of moderate concentrations of nonionic surfactants does not lead to a significant decomposition of aggregates, but leads to a biphasic dependence of the fluorescence intensity on the DNA concentration. At the same time, ethanol additives (15%) lead to a more or less linear concentration dependence of the fluorescence intensity, which makes it possible to use these dyes as fluorescent probes for DNA. The effective binding constants of the dyes to DNA and the limits of DNA detection using the dyes in the presence of 15% ethanol were estimated. Photoisomerization and generation of the triplet states of T-304, T-306, and T-307 have been also studied. Along with the fluorescence growth, complexation with DNA leads to an increase in the yield of the triplet states of the dyes. This creates a prerequisite for using the dyes in targeted PDT. In the presence of DNA, the decay kinetics of the triplet states are biexponential, which indicates different types of dye complexes with DNA. The rate constants of oxygen quenching of the triplet states of the dyes bound to DNA are significantly lower than the diffusion-controlled values (taking into account the spin-statistical factor), which is explained by the shielding effect on the triplet molecules in complexes with DNA. The data obtained show that dyes T-304, T-306 and T-307, with addition of 15% ethanol, can be used as possible fluorescent probes for DNA.
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Affiliation(s)
- P G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Str., 119334 Moscow, Russia.
| | - A S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Str., 119334 Moscow, Russia
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Photonics of Trimethine Cyanine Dyes as Probes for Biomolecules. Molecules 2022; 27:molecules27196367. [PMID: 36234904 PMCID: PMC9573451 DOI: 10.3390/molecules27196367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Cyanine dyes are widely used as fluorescent probes in biophysics and medical biochemistry due to their unique photophysical and photochemical properties (their photonics). This review is focused on a subclass of the most widespread and studied cyanine dyes—trimethine cyanines, which can serve as potential probes for biomolecules. The works devoted to the study of the noncovalent interaction of trimethine cyanine dyes with biomolecules and changing the properties of these dyes upon the interaction are reviewed. In addition to the spectral-fluorescent properties, elementary photochemical properties of trimethine cyanines are considered, including: photoisomerization and back isomerization of the photoisomer, generation and decay of the triplet state, and its quenching by oxygen and other quenchers. The influence of DNA and other nucleic acids, proteins, and other biomolecules on these properties is covered. The interaction of a monomer dye molecule with a biomolecule usually leads to a fluorescence growth, damping of photoisomerization (if any), and an increase in intersystem crossing to the triplet state. Sometimes aggregation of dye molecules on biomolecules is observed. Quenching of the dye triplet state in a complex with biomolecules by molecular oxygen usually occurs with a rate constant much lower than the diffusion limit with allowance for the spin-statistical factor 1/9. The practical application of trimethine cyanines in biophysics and (medical) biochemistry is also considered. In conclusion, the prospects for further studies on the cyanine dye–biomolecule system and the development of new effective dye probes (including probes of a new type) for biomolecules are discussed.
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Ustimova MA, Fedorov YV, Tsvetkov VB, Tokarev SD, Shepel NA, Fedorova OA. Helical aggregates of bis(styryl) dyes formed by DNA templating. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2021.113378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Sidstedt M, Rådström P, Hedman J. PCR inhibition in qPCR, dPCR and MPS-mechanisms and solutions. Anal Bioanal Chem 2020; 412:2009-2023. [PMID: 32052066 PMCID: PMC7072044 DOI: 10.1007/s00216-020-02490-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 12/24/2022]
Abstract
DNA analysis has seen an incredible development in terms of instrumentation, assays and applications over the last years. Massively parallel sequencing (MPS) and digital PCR are now broadly applied in research and diagnostics, and quantitative PCR is used for more and more practises. All these techniques are based on in vitro DNA polymerization and fluorescence measurements. A major limitation for successful analysis is the various sample-related substances that interfere with the analysis, i.e. PCR inhibitors. PCR inhibition affects library preparation in MPS analysis and skews quantification in qPCR, and some inhibitors have been found to quench the fluorescence of the applied fluorophores. Here, we provide a deeper understanding of mechanisms of specific PCR inhibitors and how these impact specific analytical techniques. This background knowledge is necessary in order to take full advantage of modern DNA analysis techniques, specifically for analysis of samples with low amounts of template and high amounts of background material. The classical solution to handle PCR inhibition is to purify or dilute DNA extracts, which leads to DNA loss. Applying inhibitor-tolerant DNA polymerases, either single enzymes or blends, provides a more straightforward and powerful solution. This review includes mechanisms of specific PCR inhibitors as well as solutions to the inhibition problem in relation to cutting-edge DNA analysis.
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Affiliation(s)
- Maja Sidstedt
- Swedish National Forensic Centre, Swedish Police Authority, 581 94, Linköping, Sweden
| | - Peter Rådström
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Johannes Hedman
- Swedish National Forensic Centre, Swedish Police Authority, 581 94, Linköping, Sweden.
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden.
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Kurutos A, Ryzhova O, Tarabara U, Trusova V, Gorbenko G, Gadjev N, Deligeorgiev T. Novel synthetic approach to near-infrared heptamethine cyanine dyes and spectroscopic characterization in presence of biological molecules. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2016.05.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Fluorescence probing of the local environment in a hydrogel: TICT and photoisomerization in chitosan hydrogel beads. Colloids Surf A Physicochem Eng Asp 2014. [DOI: 10.1016/j.colsurfa.2014.05.067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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Photoisomerization and reorientational mobility of symmetric carbocyanines in AOT/alkane/polar solvent microemulsions. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Stockert JC. Predictive binding geometry of ligands to DNA minor groove: isohelicity and hydrogen-bonding pattern. Methods Mol Biol 2014; 1094:1-12. [PMID: 24162975 DOI: 10.1007/978-1-62703-706-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The interaction of drugs and dyes with nucleic acids, particularly when binding to DNA minor groove occurs, has increasing importance in biomedical sciences. This is due to the resulting biological activity and to the possibility of recognizing AT and GC base pairs. In such cases, DNA binding can be predicted if appropriate helical and hydrogen-bonding parameters are deduced from DNA models, and a simplified geometrical rule in the form of a stencil is then applied on computer-drawn molecules of interest. Relevant structure parameter values for minor groove binders are the length (4.6 < L < 5.4 Å) and angle (152 < σ < 156.5°) between three consecutive units, measured at the level of hydrogen donor or acceptor groups. Application of the stencil shows that predictive methods can aid in the design of new compounds, by checking the possible binding of isohelical sequence-specific ligands along the DNA minor groove.
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Affiliation(s)
- Juan C Stockert
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Cantoblanco, Madrid, Spain
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Oxidative cleavage of DNA by pentamethine carbocyanine dyes irradiated with long-wavelength visible light. Bioorg Med Chem Lett 2013; 24:214-9. [PMID: 24332091 DOI: 10.1016/j.bmcl.2013.11.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 12/26/2022]
Abstract
Here we report the synthesis of seven symmetrical carbocyanine dyes in which two nitrogen-substituted benz[e]indolium rings are joined by a pentamethine bridge that is meso-substituted with chlorine or bromine versus hydrogen. The heteroatom of benz[e]indolium is modified with a phenylpropyl, methyl, or cationic quaternary ammonium group. In reactions containing micro molar concentrations of halogenated dye, irradiation at 575, 588, 623, or 700nm produces good photocleavage of plasmid DNA. UV-visible spectra show that the carbocyanines are in their H-aggregated and monomeric forms. Scavenger experiments point to the involvement of singlet oxygen and hydroxyl radicals in DNA photocleavage.
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Jędrzejewska B, Bajorek A, Moraczewska J. Interaction of carbocyanine dyes with DNA: synthesis and spectroscopic studies. APPLIED SPECTROSCOPY 2013; 67:672-680. [PMID: 23735253 DOI: 10.1366/12-06887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Six carbocyanine dyes have been synthesized and their interactions with DNA have been investigated for their prospective use as fluorescent markers in molecular biology. The noncovalent binding of the compounds with DNA was explored by fluorescence spectroscopy, ultraviolet/visible spectrophotometry, and photobleaching. The electron-withdrawing ability of the substituents in N-position of free thio- and selenocarbocyanines strongly affected their photostabilities. Changes in the experimental conditions, such as the presence or absence of oxygen, had an impact on the rate of photobleaching. In the presence of DNA, absorbance photofading and fluorescence photobleaching occurred. It appears that the reduction of fluorescence intensity was due to quenching of the dye fluorescence by interaction with DNA.
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Affiliation(s)
- Beata Jędrzejewska
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna 3, 85-326 Bydgoszcz, Poland.
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Polymethine dyes as spectral-fluorescent probes for biomacromolecules. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2011.11.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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12
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Alvarez M, Villanueva A, Acedo P, Cañete M, Stockert JC. Cell death causes relocalization of photosensitizing fluorescent probes. Acta Histochem 2011; 113:363-8. [PMID: 20138336 DOI: 10.1016/j.acthis.2010.01.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 01/17/2010] [Accepted: 01/18/2010] [Indexed: 12/12/2022]
Abstract
When cultured cells are treated with fluorescent organelle probes or photosensitizer agents, a characteristic redistribution of fluorescence in cell structures occurs frequently after light irradiation. It is currently assumed that such changes, referred to as relocalizations of the fluorescent compounds, represent an important aspect of the photodynamic process, which is based on the excitation of photosensitizers by light in the presence of oxygen. As cell damage and death result from the oxidative stress induced by photodynamic treatments, we have studied here the redistribution of acridine orange (AO) and 3,3'-dimethyl-oxacarbocyanine (DiOC(1)(3)) fluorescence after incubation of HeLa cell cultures with these compounds followed by blue light irradiation to achieve lethal effects. The relocalization of dyes from their original labeling sites (AO: lysosomes, DiOC(1)(3): mitochondria) to nucleic acid-containing structures (cytoplasm, nuclei and nucleoli) appeared clearly associated with cell death. Therefore, the relocalization phenomenon simply reflects fluorescence changes due to the different affinity of these dyes for living and damaged or dead cells. As fluorescent probes are often photosensitizers, prolonged light exposures using fluorescence microscopy will produce lethal photodynamic effects with relocalization of the fluorescent signal and changes in the cell morphology.
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Affiliation(s)
- Marco Alvarez
- Anatomical Institute José Izquierdo, Faculty of Medicine, Central University of Venezuela, 1050 Caracas, Venezuela
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Yarmoluk SM, Kovalska VB, Volkova KD. Optimized Dyes for Protein and Nucleic Acid Detection. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments. Q Rev Biophys 2010; 44:123-51. [DOI: 10.1017/s0033583510000247] [Citation(s) in RCA: 294] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThe breakthroughs in single molecule spectroscopy of the last decade and the recent advances in super resolution microscopy have boosted the popularity of cyanine dyes in biophysical research. These applications have motivated the investigation of the reactions and relaxation processes that cyanines undergo in their electronically excited states. Studies show that the triplet state is a key intermediate in the photochemical reactions that limit the photostability of cyanine dyes. The removal of oxygen greatly reduces photobleaching, but induces rapid intensity fluctuations (blinking). The existence of non-fluorescent states lasting from milliseconds to seconds was early identified as a limitation in single-molecule spectroscopy and a potential source of artifacts. Recent studies demonstrate that a combination of oxidizing and reducing agents is the most efficient way of guaranteeing that the ground state is recovered rapidly and efficiently. Thiol-containing reducing agents have been identified as the source of long-lived dark states in some cyanines that can be photochemically switched back to the emissive state. The mechanism of this process is the reversible addition of the thiol-containing compound to a double bond in the polymethine chain resulting in a non-fluorescent molecule. This process can be reverted by irradiation at shorter wavelengths. Another mechanism that leads to non-fluorescent states in cyanine dyes is cis–trans isomerization from the singlet-excited state. This process, which competes with fluorescence, involves the rotation of one-half of the molecule with respect to the other with an efficiency that depends strongly on steric effects. The efficiency of fluorescence of most cyanine dyes has been shown to depend dramatically on their molecular environment within the biomolecule. For example, the fluorescence quantum yield of Cy3 linked covalently to DNA depends on the type of linkage used for attachment, DNA sequence and secondary structure. Cyanines linked to the DNA termini have been shown to be mostly stacked at the end of the helix, while cyanines linked to the DNA internally are believed to partially bind to the minor or major grooves. These interactions not only affect the photophysical properties of the probes but also create a large uncertainty in their orientation.
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Richardson JA, Gerowska M, Shelbourne M, French D, Brown T. Six-Colour HyBeacon Probes for Multiplex Genetic Analysis. Chembiochem 2010; 11:2530-3. [DOI: 10.1002/cbic.201000623] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Wang M, Holmes-Davis R, Rafinski Z, Jedrzejewska B, Choi KY, Zwick M, Bupp C, Izmailov A, Paczkowski J, Warner B, Koshinsky H. Accelerated photobleaching of a cyanine dye in the presence of a ternary target DNA, PNA probe, dye catalytic complex: a molecular diagnostic. Anal Chem 2010; 81:2043-52. [PMID: 19231844 DOI: 10.1021/ac702519k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In many settings, molecular testing is needed but unavailable due to complexity and cost. Simple, rapid, and specific DNA detection technologies would provide important alternatives to existing detection methods. Here we report a novel, rapid nucleic acid detection method based on the accelerated photobleaching of the light-sensitive cyanine dye, 3,3'-diethylthiacarbocyanine iodide (DiSC(2)(3) I(-)), in the presence of a target genomic DNA and a complementary peptide nucleic acid (PNA) probe. On the basis of the UV-vis, circular dichroism, and fluorescence spectra of DiSC(2)(3) with PNA-DNA oligomer duplexes and on characterization of a product of photolysis of DiSC(2)(3) I(-), a possible reaction mechanism is proposed. We propose that (1) a novel complex forms between dye, PNA, and DNA, (2) this complex functions as a photosensitizer producing (1)O(2), and (3) the (1)O(2) produced promotes photobleaching of dye molecules in the mixture. Similar cyanine dyes (DiSC(3)(3), DiSC(4)(3), DiSC(5)(3), and DiSC(py)(3)) interact with preformed PNA-DNA oligomer duplexes but do not demonstrate an equivalent accelerated photobleaching effect in the presence of PNA and target genomic DNA. The feasibility of developing molecular diagnostic assays based on the accelerated photobleaching (the smartDNA assay) that results from the novel complex formed between DiSC(2)(3) and PNA-DNA is under way.
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Affiliation(s)
- M Wang
- Investigen Inc., Hercules, California, USA
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Stockert JC, Abasolo MI. Inaccurate chemical structures of dyes and fluorochromes found in the literature can be problematic for teaching and research. Biotech Histochem 2010; 86:52-60. [DOI: 10.3109/10520295.2010.489428] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Yarmoluk SM, Kovalska VB, Losytskyy MY. Symmetric cyanine dyes for detecting nucleic acids. Biotech Histochem 2009; 83:131-45. [DOI: 10.1080/10520290802383684] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- SM Yarmoluk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - VB Kovalska
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - MY Losytskyy
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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Mao F, Leung WY, Xin X. Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications. BMC Biotechnol 2007; 7:76. [PMID: 17996102 PMCID: PMC2213645 DOI: 10.1186/1472-6750-7-76] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 11/09/2007] [Indexed: 11/19/2022] Open
Abstract
Background EvaGreen (EG) is a newly developed DNA-binding dye that has recently been used in quantitative real-time PCR (qPCR), post-PCR DNA melt curve analysis and several other applications. However, very little is known about the physicochemical properties of the dye and their relevance to the applications, particularly to qPCR and post PCR DNA melt curve analysis. In this paper, we characterized EG along with a widely used qPCR dye, SYBR Green I (SG), for their DNA-binding properties and stability, and compared their performance in qPCR under a variety of conditions. Results This study systematically compared the DNA binding profiles of the two dyes under different conditions and had these findings: a) EG had a lower binding affinity for both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) than SG; b) EG showed no apparent preference for either GC- or AT-rich sequence while SG had a slight preference for AT-rich sequence; c) both dyes showed substantially lower affinity toward ssDNA than toward dsDNA and even lower affinity toward shorter ssDNA fragments except that this trend was more pronounced for EG. Our results also demonstrated that EG was stable both under PCR condition and during routine storage and handling. In the comparative qPCR study, both EG and SG exhibited PCR interference when used at high dye concentration, as evident from delayed Ct and/or nonspecific product formation. The problem worsened when the chain extension time was shortened or when the amplicon size was relatively long (>500 bp). However, qPCR using EG tolerated a significantly higher dye concentration, thus permitting a more robust PCR signal as well as a sharper and stronger DNA melt peak. These differences in qPCR performance between the two dyes are believed to be attributable to their differences in DNA binding profiles. Conclusion These findings suggest that an ideal qPCR dye should possess several DNA-binding characteristics, including a "just right" affinity for dsDNA and low or no affinity for ssDNA and short DNA fragments. The favorable DNA-binding profile of EG, coupled with its good stability and instrument-compatibility, should make EG a promising dye for qPCR and related applications.
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Affiliation(s)
- Fei Mao
- Biotium, Inc. Hayward, California, USA.
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Fürstenberg A, Vauthey E. Ultrafast Excited-State Dynamics of Oxazole Yellow DNA Intercalators. J Phys Chem B 2007; 111:12610-20. [DOI: 10.1021/jp073182t] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandre Fürstenberg
- Department of Physical Chemistry of the University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry of the University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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Tarasov SG, Casas-Finet JR, Cholody WM, Kosakowska-Cholody T, Gryczynski ZK, Michejda CJ. Bisimidazoacridones: 2. Steady-state and Time-resolved Fluorescence Studies of Their Diverse Interactions with DNA¶§. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0780313bsatfs2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Eriksson M, Westerlund F, Mehmedovic M, Lincoln P, Westman G, Larsson A, Akerman B. Comparing mono- and divalent DNA groove binding cyanine dyes—Binding geometries, dissociation rates, and fluorescence properties. Biophys Chem 2006; 122:195-205. [PMID: 16624475 DOI: 10.1016/j.bpc.2006.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 03/16/2006] [Accepted: 03/19/2006] [Indexed: 11/17/2022]
Abstract
The unsymmetrical cyanine dyes BOXTO-PRO and BOXTO-MEE were derived from the DNA groove binder BOXTO, by adding a positively charged or a non-ionic hydrophilic tail to BOXTO, respectively. The main objective was to obtain more efficient DNA probes, for instance in electrophoresis and microscopy, by slowing down the dissociation of BOXTO from DNA. The interactions with mixed sequence DNA was studied with fluorescence and absorbance spectroscopy, stopped-flow dissociation and gel electrophoresis. Both the derivatives are groove bound as BOXTO, and have similar fluorescence properties when bound to mixed sequence DNA in free solution. BOXTO-PRO exhibits a slower dissociation than BOXTO from DNA, whereas the dissociation rate for BOXTO-MEE is faster and, unexpectedly independent of the ionic strength. During gel electrophoresis both BOXTO-PRO and BOXTO-MEE exhibit a faster dissociation rate than BOXTO. Still, BOXTO-PRO seems to be a good alternative as DNA probe, especially for applications in free solution where the dissociation is slower than for the corresponding intercalator TOPRO-1.
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Affiliation(s)
- Maja Eriksson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, S-412 96 Göteborg, Sweden.
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Fong S, Liu Y, Heath T, Fong P, Liggitt D, Debs RJ. Membrane-permeant, DNA-binding agents alter intracellular trafficking and increase the transfection efficiency of complexed plasmid DNA. Mol Ther 2004; 10:706-18. [PMID: 15451455 DOI: 10.1016/j.ymthe.2004.06.1016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2004] [Revised: 06/11/2004] [Accepted: 06/15/2004] [Indexed: 10/26/2022] Open
Abstract
Nuclear delivery of extracellular DNA by nonviral vectors is inhibited by a series of cell membrane and compartmental barriers. Certain cationic amphiphiles that partition through cellular membranes to bind genomic DNA can enhance nuclear delivery of plasmid DNA. Specifically, delivering plasmid DNA complexed to the DNA-binding dye Hoechst 33258 produces cellular transfection levels similar to those achieved by cationic liposome:DNA complexes (CLDC), with less toxicity. Incorporating Hoechst into CLDC or polyethyleneimine:DNA complexes significantly increased reporter gene expression, as well as the percentage of cells transfected. Hoechst:CLDC significantly improved transfection of nondividing cells and efficiently transfected cells in the presence of anionic molecules that block cellular uptake of and transfection by CLDC alone. Hoechst:CLDC also increased gene expression in mouse tissues following intravenous delivery. Delivery of fluorescently labeled plasmid DNA via Hoechst altered its intracellular trafficking by both minimizing lysosomal sequestration and accelerating delivery into the nucleus. Agents such as Hoechst constitute a novel class of nonviral carriers that can confer their membrane-permeant properties on complexed DNA, thus redirecting its intracellular trafficking. In addition, binding of Hoechst 33258 to specific chromosomal DNA target sequences and its ability to modulate transcription may further enhance the expression of delivered genes.
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Affiliation(s)
- Sylvia Fong
- California Pacific Medical Center Research Institute, San Francisco, CA 94115, USA
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Karlsson HJ, Bergqvist MH, Lincoln P, Westman G. Syntheses and DNA-binding studies of a series of unsymmetrical cyanine dyes: structural influence on the degree of minor groove binding to natural DNA. Bioorg Med Chem 2004; 12:2369-84. [PMID: 15080934 DOI: 10.1016/j.bmc.2004.02.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2003] [Accepted: 02/03/2004] [Indexed: 11/28/2022]
Abstract
Twelve crescent-shaped unsymmetrical dyes have been synthesized and their interactions with DNA have been investigated by spectroscopic methods. A new facile synthetic route to this type of cyanine dyes has been developed, involving the preparation of 6-substituted 2-thiomethyl-benzothiazoles in good yields. The new dyes are analogues to the minor groove binding unsymmetrical cyanine dye, BEBO, recently reported by us. In this dye, the structure of the known intercalating cyanine dye BO was extended with a 6-methylbenzothiazole substituent. Herein we further investigate the role of the extending benzazole heterocycle, as well as of the pyridine or quinoline moiety of the cyanine chromophore, for the binding mode of these crescent-shaped dyes to calf thymus DNA. Flow LD and CD studies of the 12 dyes show that the extent of minor groove binding to mixed sequence DNA varies significantly between the dyes. We find that hydrophobicity and size are the crucial parameters for recognition of the minor groove. The relatively high fluorescence quantum yield of many of these cyanines bound to DNA, combined with their absorption at long wavelengths, may render them useful in biological applications. In particular, two of the benzoxazole containing dyes BOXTO and 2-BOXTO show a high degree of minor groove binding and quantum yields of 0.52 and 0.32, respectively, when bound to DNA.
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Affiliation(s)
- H Jonas Karlsson
- Department of Chemistry and Bioscience, Chalmers University of Technology, S-412 96 Gothenburg, Sweden.
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25
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Abstract
Covalent attachment of dsDNA molecules inside a glass capillary without the need for hybridization is described. It is shown that the glass capillary has a surface density of 2.5 x 10(13) molecules/cm(2) with specific binding capacity of 62.5%. The resulting substrate was used to develop a biosensor for determining fluorescent organic analytes and metal binding with DNA. The biosensor combines highly specific immobilization chemistry with a capillary-geometry flow cell arrangement. The results show that fluorescent dyes are retained in the dsDNA-modified surface and that exposure to concentrations of nickel and lead ions resulted in a recoverable, highly reproducible diminishment of the fluorescence intensity.
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Affiliation(s)
- Marc A Breimer
- Department of Chemistry, State University of New York at Binghamton, PO Box 6016, Binghamton, NY 13902-6016, USA
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26
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Sovenyhazy KM, Bordelon JA, Petty JT. Spectroscopic studies of the multiple binding modes of a trimethine-bridged cyanine dye with DNA. Nucleic Acids Res 2003; 31:2561-9. [PMID: 12736305 PMCID: PMC156045 DOI: 10.1093/nar/gkg363] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The interaction between DNA and a benzothiazole-quinoline cyanine dye with a trimethine bridge (TO-PRO-3) results in the formation of three noncovalent complexes. Unbound TO-PRO-3 has an absorption maximum (lambda(max)) of 632 nm, while the bound dyes (with calf thymus DNA) have electronic transitions with lambda(max) = 514 nm (complex I), 584 nm (complex II) and 642 nm (complex III). The blue shifts in the electronic transitions and the bisignate shape of the circular dichroism bands indicate that TO-PRO-3 aggregates with DNA. Complex I has a high dye:base pair stoichiometry, which does not depend on base sequence or base modifications. The bound dyes exhibit strong interdye coupling, based on studies with a short oligonucleotide and on enhanced resonance scattering. From thermal dissociation studies, the complex is weakly associated with DNA. Studies with poly(dGdC)2 and poly(dIdC)2 and competitive binding with distamycin demonstrate that complex II is bound in the minor groove. This complex stabilizes the helix against dissociation. For complex III, the slightly red-shifted electronic transition and the stoichiometry are most consistent with intercalation. Using poly(dAdT)2, the complexes have the following dye mole fractions (X(dye)): X(dye) = 0.65 (complex I), 0.425 (complex II) and 0.34 (complex III).
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27
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Karlsson HJ, Lincoln P, Westman G. Synthesis and DNA binding studies of a new asymmetric cyanine dye binding in the minor groove of [poly(dA-dT)]2. Bioorg Med Chem 2003; 11:1035-40. [PMID: 12614890 DOI: 10.1016/s0968-0896(02)00463-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A new asymmetric cyanine dye has been synthesised and its interaction with different DNA has been investigated. In this dye, BEBO, the structure of the known intercalating cyanine dye BO has been extended with a benzothiazole substituent. The resulting crescent-shape of the molecule is similar to that of the well-known minor groove binder Hoechst 33258. Indeed, comparative studies of BO illustrate a considerable change in binding mode induced by this structural modification. Linear and circular dichroism studies indicate that BEBO binds in the minor groove to [poly (dA-dT)](2), but that the binding to calf thymus DNA is heterogeneous, although still with a significant contribution of minor groove binding. Similar to other DNA binding asymmetric cyanine dyes, BEBO has a large increase in fluorescence intensity upon binding and a relatively large quantum yield when bound. The minor groove binding of BEBO to [poly (dA-dT)](2) affords roughly a 180-fold increase in intensity, which is larger than to that of the commonly used minor groove binding probes DAPI and Hoechst 33258.
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Affiliation(s)
- H Jonas Karlsson
- Department of Chemistry and Bioscience, Chalmers University of Technology, Kemivägen 10, S-41296 Göteborg, Sweden
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28
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Tsourkas A, Behlke MA, Rose SD, Bao G. Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Res 2003; 31:1319-30. [PMID: 12582252 PMCID: PMC150230 DOI: 10.1093/nar/gkg212] [Citation(s) in RCA: 263] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Molecular beacons are increasingly being used in many applications involving nucleic acid detection and quantification. The stem-loop structure of molecular beacons provides a competing reaction for probe-target hybridization that serves to increase probe specificity, which is particularly useful when single-base discrimination is desired. To fully realize the potential of molecular beacons, it is necessary to optimize their structure. Here we report a systematic study of the thermodynamic and kinetic parameters that describe the molecular beacon structure-function relationship. Both probe and stem lengths are shown to have a significant impact on the binding specificity and hybridization kinetic rates of molecular beacons. Specifically, molecular beacons with longer stem lengths have an improved ability to discriminate between targets over a broader range of temperatures. However, this is accompanied by a decrease in the rate of molecular beacon-target hybridization. Molecular beacons with longer probe lengths tend to have lower dissociation constants, increased kinetic rate constants, and decreased specificity. Molecular beacons with very short stems have a lower signal-to-background ratio than molecular beacons with longer stems. These features have significant implications for the design of molecular beacons for various applications.
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Affiliation(s)
- Andrew Tsourkas
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
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29
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Tarasov SG, Casas-Finet JR, Cholody WM, Kosakowska-Cholody T, Gryczynski ZK, Michejda CJ. Bisimidazoacridones: 2. Steady-state and Time-resolved Fluorescence Studies of Their Diverse Interactions with DNA¶§. Photochem Photobiol 2003; 78:313-22. [PMID: 14626657 DOI: 10.1562/0031-8655(2003)078<0313:bsatfs>2.0.co;2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Several bisimidazoacridones (BIA) are potent, selective antineoplastic agents, whereas others have potent anti-human immunodeficiency virus activity. BIA are bifunctional agents that consist of two imidazoacridone (IA) chromophores held together by various linkers. Interaction of BIA with DNA has been postulated to be required for their biological activity. Fluorescence data on free and bound BIA suggest that the binding of BIA and similar drugs to DNA is driven by a transfer of hydrophobic molecules from aqueous media to the more amphiphilic DNA environment. Binding to DNA was sensitive to sequence and depended on the length and rigidity of the linker. Time-resolved fluorescence measurements showed that BIA adopt an extended conformation upon binding and that all of the molecules are tightly associated with DNA. Gel-shift and melting assays indicated that one of the aromatic residues of BIA is intercalated, whereas the other, together with a linker, resides in a groove, probably the minor groove. A continuum of structures may be possible where intercalation and classical minor groove binding are limiting structures. In general, the hypothesis for the mechanism of action of BIA wherein the unintercalated residue, accessible for additional interactions, captures a critical protein involved in repair or transcription, is consistent with this model.
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Affiliation(s)
- Sergey G Tarasov
- Molecular Aspects of Drug Design Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, Frederick, MD, USA.
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30
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Yarmoluk SM, Lukashov SS, Losytskyy MY, Akerman B, Kornyushyna OS. Interaction of cyanine dyes with nucleic acids: XXVI. Intercalation of the trimethine cyanine dye cyan 2 into double-stranded DNA: study by spectral luminescence methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2002; 58:3223-3232. [PMID: 12511106 DOI: 10.1016/s1386-1425(02)00100-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The interaction between double-stranded (ds) DNA and the cyanine dye Cyan 2 has been studied with spectral luminescence methods. Binding constant values have been determined by fluorescence titration and dye distribution in the two-phase system ethyl acetate-water (3.6 x 10(4) and 1.5 x 10(4) M(-1), respectively). Cyan 2 exhibits a small specificity for guanine-cytosine (GC) sequences in total DNA and synthetic polydeoxynucleotides poly(dA/dT) and poly(dGdC/dGdC). The DNA complexes with Cyan 2 are stable at high-ionic strength solution when NaCl is added. The dye molecule complexed with DNA is apparently shielded from the anionic quencher--iodide ion. The negative linear dichroism of the visible absorption band of aligned Cyan 2-DNA complexes indicates that the bound dye lies almost perpendicularly to the DNA helix axis. The linear dichroism of the absorption band at 260 nm suggests a considerable change in the DNA B-form. The results are consistent with an intercalative binding interaction between Cyan 2 and ds DNA.
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Affiliation(s)
- S M Yarmoluk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnogo Street, 03143 Kiev, Ukraine.
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31
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Kerwin SM, Sun D, Kern JT, Rangan A, Thomas PW. G-quadruplex DNA binding by a series of carbocyanine dyes. Bioorg Med Chem Lett 2001; 11:2411-4. [PMID: 11549435 DOI: 10.1016/s0960-894x(01)00490-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We have examined a number of carbocyanine dyes for their ability to bind intramolecular G-quadruplex DNA structures (G4'-DNA) using a Taq polymerase stop assay. Of the five dyes examined, only one, N,N'-diethylthiacarbocyanine iodide (DTC), was found to bind to G4'-DNA. DTC was also the only dye found to inhibit human telomerase at 50 microM concentration.
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Affiliation(s)
- S M Kerwin
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, 78712, USA.
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32
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Cao R, Venezia CF, Armitage BA. Investigation of DNA binding modes for a symmetrical cyanine dye trication: effect of DNA sequence and structure. J Biomol Struct Dyn 2001; 18:844-56. [PMID: 11444373 DOI: 10.1080/07391102.2001.10506712] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The DNA binding behavior of a tricationic cyanine dye (DiSC3+(5)) was studied using the [Poly(dA-dT)]2, [Poly(dI-dC)]2 and Poly(dA) x Poly(dT) duplex sequences and the Poly(dA) x 2Poly(dT) triplex. Optical spectroscopy and viscometry results indicate that the dye binds to the triplex structure by intercalation, to the nonalternating Poly(dA) x Poly(dT) duplex through minor groove binding and to the alternating [Poly(dA-dT)]2 duplex by a combination of two binding modes: intercalation at low concentration and dimerization within the minor groove at higher concentration. Dimerization occurs at lower dye concentrations for the [Poly(dI-dC)]2 sequence, consistent with our previous investigations on an analogous monocationic cyanine dye. [Seifert, J.L., et al. (1999) J. Am. Chem. Soc. 121, 2987-2995] These studies illustrate the diversity of DNA binding modes that are available to a given ligand structure.
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Affiliation(s)
- R Cao
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213-3890, USA
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