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DeJaco RF, Roberts MJ, Romsos EL, Vallone PM, Kearsley AJ. Reducing Bias and Quantifying Uncertainty in Fluorescence Produced by PCR. Bull Math Biol 2023; 85:83. [PMID: 37574503 PMCID: PMC10423706 DOI: 10.1007/s11538-023-01182-z] [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: 11/16/2022] [Accepted: 06/20/2023] [Indexed: 08/15/2023]
Abstract
We present a new approach for relating nucleic-acid content to fluorescence in a real-time Polymerase Chain Reaction (PCR) assay. By coupling a two-type branching process for PCR with a fluorescence analog of Beer's Law, the approach reduces bias and quantifies uncertainty in fluorescence. As the two-type branching process distinguishes between complementary strands of DNA, it allows for a stoichiometric description of reactions between fluorescent probes and DNA and can capture the initial conditions encountered in assays targeting RNA. Analysis of the expected copy-number identifies additional dynamics that occur at short times (or, equivalently, low cycle numbers), while investigation of the variance reveals the contributions from liquid volume transfer, imperfect amplification, and strand-specific amplification (i.e., if one strand is synthesized more efficiently than its complement). Linking the branching process to fluorescence by the Beer's Law analog allows for an a priori description of background fluorescence. It also enables uncertainty quantification (UQ) in fluorescence which, in turn, leads to analytical relationships between amplification efficiency (probability) and limit of detection. This work sets the stage for UQ-PCR, where both the input copy-number and its uncertainty are quantified from fluorescence kinetics.
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Affiliation(s)
- Robert F. DeJaco
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Dr., College Park, MD 20742-4454 USA
| | - Matthew J. Roberts
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
- Cost Analysis and Research Division, Institute for Defense Analyses, 730 E. Glebe Rd., Alexandria, VA 22305-3086 USA
| | - Erica L. Romsos
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8314, Gaithersburg, MD 20899-8314 USA
| | - Peter M. Vallone
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8314, Gaithersburg, MD 20899-8314 USA
| | - Anthony J. Kearsley
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, 100 Bureau Dr., MS 8910, Gaithersburg, MD 20899-8910 USA
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2
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DeJaco RF, Majikes JM, Liddle JA, Kearsley AJ. Binding, brightness, or noise? Extracting temperature-dependent properties of dye bound to DNA. Biophys J 2023; 122:1364-1375. [PMID: 36871160 PMCID: PMC10111365 DOI: 10.1016/j.bpj.2023.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
We present a method for extracting temperature-dependent thermodynamic and photophysical properties of SYTO-13 dye bound to DNA from fluorescence measurements. Together, mathematical modeling, control experiments, and numerical optimization enable dye binding strength, dye brightness, and experimental noise (or error) to be discriminated from one another. By focusing on the low-dye-coverage regime, the model avoids bias and can simplify quantification. Utilizing the temperature-cycling capabilities and multi-reaction chambers of a real-time PCR machine increases throughput. Significant well-to-well and plate-to-plate variation is quantified by using total least squares to account for error in both fluorescence and nominal dye concentration. Properties computed independently for single-stranded DNA and double-stranded DNA by numerical optimization are consistent with intuition and explain the advantageous performance of SYTO-13 in high-resolution melting and real-time PCR assays. Distinguishing between binding, brightness, and noise also clarifies the mechanism for the increased fluorescence of dye in a solution of double-stranded DNA compared to single-stranded DNA; in fact, the explanation changes with temperature.
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Affiliation(s)
- Robert F DeJaco
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, Gaithersburg, Maryland; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland.
| | - Jacob M Majikes
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - J Alexander Liddle
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Anthony J Kearsley
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, Gaithersburg, Maryland
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3
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Lim HJ, Hong S, Jin H, Chua B, Son A. A multi-functional reagent suitable for 1-step rapid DNA intercalation fluorescence-based screening of total bacteria in drinking water. CHEMOSPHERE 2023; 313:137541. [PMID: 36526135 DOI: 10.1016/j.chemosphere.2022.137541] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
The prerequisites for rapid screening of total bacteria in drinking water are low detection limit and convenience. Inspired by commercial adenosine 5'-triphosphate (ATP) based total bacterial detection kits, we pursued likewise convenience but with much lower detection limit. Existing intercalation fluorescence-based techniques employ multiple reagents to permeate the cell membrane and intercalate dye into the DNA in discrete sequential steps. A simple multi-functional reagent is proposed to do the same within one step. Surfactants (TritonX and SDS), and intercalating dyes (SYBR green, SYBR gold) were examined for their mutual compatibility and augmented with EDTA. Evaluation was performed with Gram negative Escherichia coli K12 (E. coli K12) and Gram positive Bacillus subtilis (B. subtilis) at serial dilution ratios from 10-6 to 10-2. Comparison was made with absorbance (600 nm) measurements and a commercial ATP kit. Using charge integrated photodetection, the proposed 1-step reagent achieved an LOD (1.00 × 10-6, B. subtilis) that is two orders of magnitude lower than that of ATP kit (LOD = 1.06× 10-4). This means it could detect minute quantity of total bacteria that is otherwise undetected by the ATP kit.
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Affiliation(s)
- Hyun Jeong Lim
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea; Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511, USA
| | - Seungwon Hong
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hyowon Jin
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Beelee Chua
- School of Electrical Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Ahjeong Son
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
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Sharifi-Rad A, Amiri-Tehranizadeh Z, Talebi A, Nosrati N, Medalian M, Pejhan M, Hamzkanloo N, Saberi MR, Mokaberi P, Chamani J. Multi spectroscopic and molecular simulation studies of propyl acridone binding to calf thymus DNA in the presence of electromagnetic force. BIOIMPACTS : BI 2023; 13:5-16. [PMID: 36817002 PMCID: PMC9923809 DOI: 10.34172/bi.2022.23592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 01/09/2023]
Abstract
Introduction: Here, the interaction behavior between propyl acridones (PA) and calf thymus DNA (ct-DNA) has been investigated to attain the features of the binding behavior of PA with ct-DNA, which includes specific binding sites, modes, and constants. Furthermore, the effects of PA on the conformation of ct-DNA seem to be quite significant for comprehending the medicine's mechanism of action and pharmacokinetics. Methods: The project was accomplished through means of absorbance studies, fluorescence spectroscopy, circular dichroism, viscosity measurement, thermal melting, and molecular modeling techniques. Results: The intercalation of PA has been suggested by fluorescence quenching and viscosity measurements results while the thermal melting and circular dichroism studies have confirmed the thermal stabilization and conformational changes that seem to be associated with the binding. The binding constants of ct-DNA-PA complex, in the absence and presence of EMF, have been evaluated to be 6.19 × 104 M-1 and 2.95 × 104 M-1 at 298 K, respectively. In the absence of EMF, the ∆H0 and ∆S0 values that occur in the interaction process of PA with ct-DNA have been measured to be -11.81 kJ.mol-1 and 51.01 J.mol-1K-1, while in the presence of EMF they were observed to be -23.34 kJ.mol-1 and 7.49 J.mol-1K-1, respectively. These numbers indicate the involvement of multiple non-covalent interactions in the binding procedure. In a parallel study, DNA-PA interactions have been monitored by molecular dynamics simulations; their results have demonstrated DNA stability with increasing concentrations of PA, as well as calculated bindings of theoretical ΔG0. Conclusion: The complex formation between PA and ct-DNA has been investigated in the presence and absence of EMF through the multi spectroscopic techniques and MD simulation. These findings have been observed to be parallel to the results of KI and NaCl quenching studies, as well as the competitive displacement with EB and AO. According to thermodynamic parameters, electrostatic interactions stand as the main energy that binds PA to ct-DNA. Regarding the cases that involve the Tm of ct-DNA, EMF has proved to increase the stability of binding between PA and ct-DNA.
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Affiliation(s)
- Atena Sharifi-Rad
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri-Tehranizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atiye Talebi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Niknaz Nosrati
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Morvarid Medalian
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Mahtab Pejhan
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Nazanin Hamzkanloo
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Mohammad Reza Saberi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parisa Mokaberi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran,Corresponding author: Jamshidkhan Chamani, ,
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Alanazi RLB, Zaki M, Bawazir WA. Synthesis and characterization of the new ligand, 1,2,4-triazino[5,6-b]indol-3-ylimino methyl naphthalene-2-ol and its Ni(II) and Cu(II) complexes: comparative studies of their in vitro DNA and HSA Binding. Biometals 2022; 35:1199-1223. [PMID: 36074281 DOI: 10.1007/s10534-022-00437-x] [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: 11/04/2021] [Accepted: 08/16/2022] [Indexed: 12/14/2022]
Abstract
A new ligand 1,2,4-triazino[5,6-b]indol-3-ylimino methyl naphthalene-2-ol (HL) was derived from 5H-[1,2,4]triazino[5,6-b]indol-3-amine and 2-hydroxy-1-naphthaldehyde. The metal complexes of the type [Ni(L)(Bipy)]1/2SO4 (1), [Cu(L)(Bipy)(H2O)2]1/2SO4 (2), [Ni(L)(Phen)]1/2SO4 (3) and [Cu(L)(Phen)(H2O)2]1/2SO4 (4) were synthesized. The ligand (HL) and complexes 1-4 were thoroughly characterized by elemental analysis and spectroscopic methods (FT-IR, ToF-MS, 1H NMR, 13C NMR), molar conductance and magnetic moment determination. The Ni(II) complexes 1 and 3 adopt the square planar geometry and Cu(II) complexes 2 and 4 acquire distorted octahedral arrangement. In vitro DNA binding behavior of ligand (HL) and metal complexes 1-4 was explored by fluorescence spectral and ethidium bromide studies. The outcomes reveal that the complexes interact with DNA via non-covalent groove binding and electrostatic interactions. The higher binding constant (K) values of 4.35 × 104 and 9.12 × 104 M-1 for complexes 2 and 4 indicate stronger binding ability with DNA. Moreover, in vitro human serum albumin (HSA) binding experiment with HL and complexes 1-4 reveals conformational modulations in the Trp-214 microenvironments in the subdomain IIA pocket.
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Affiliation(s)
- Reem L B Alanazi
- Department of Chemistry, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
| | - Mehvash Zaki
- Department of Chemistry, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia.
| | - Wafa A Bawazir
- Department of Chemistry, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
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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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7
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Sakamoto T, Yu Z, Otani Y. Dual-Color Fluorescence Switch-On Probe for Imaging G-Quadruplex and Double-Stranded DNA in Living Cells. Anal Chem 2022; 94:4269-4276. [PMID: 35234461 DOI: 10.1021/acs.analchem.1c04804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A tripodal quinone-cyanine dye having one donor and three acceptors, that is, one quinone and three N-methylbenzothiazolium moieties, QCy(MeBT)3, was synthesized by simple Knoevenagel condensation between 2-hydroxybenzene-1,3,5-tricarbaldehyde and N-methyl-2-methylbenzothiazolium iodide. The 700 nm (λex, 570 nm) and 600 nm (λex, 470 nm) fluorescence emission of QCy(MeBT)3 was significantly and individually enhanced with the addition of G-quadruplex (G4) DNA and double-stranded DNA (dsDNA), respectively. The results of docking simulations and the response against the viscosity change revealed that the dual-fluorescence response was caused by the difference in the binding mode of QCy(MeBT)3 depending on the DNA structure. The results of fluorescence microscopy imaging experiments using QCy(MeBT)3 suggested that G4 DNAs and dsDNAs in the cell nucleus can be imaged with near-infrared (NIR, 700 nm) and red (600 nm) fluorescence emissions. Furthermore, pyridostatin-induced G4 formation in the living cells can be imaged with NIR fluorescence. The results indicated that QCy(MeBT)3 has huge potential to be a NIR-fluorescent molecular probe for analyzing the structural dynamics of nucleic acids in living cells with a normal fluorescence microscope.
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Affiliation(s)
- Takashi Sakamoto
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan.,Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Zehui Yu
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Yuto Otani
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
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Chiriboga M, Diaz SA, Mathur D, Hastman DA, Melinger JS, Veneziano R, Medintz IL. Understanding Self-Assembled Pseudoisocyanine Dye Aggregates in DNA Nanostructures and Their Exciton Relay Transfer Capabilities. J Phys Chem B 2021; 126:110-122. [PMID: 34962787 DOI: 10.1021/acs.jpcb.1c09048] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Progress has been made using B-form DNA duplex strands to template chromophores in ordered molecular aggregates known as J-aggregates. These aggregates can exhibit strong electronic coupling, extended coherent lifetimes, and long-range exciton delocalization under appropriate conditions. Certain cyanine dyes such as pseudoisocyanine (PIC) dye have shown a proclivity to form aggregates in specific DNA sequences. In particular, DX-tiles containing nonalternating poly(dA)-poly(dT) dinucleotide tracks (AT-tracks), which template noncovalent PIC dye aggregates, have been demonstrated to exhibit interesting emergent photonic properties. These DNA-based aggregates are referred to as J-bits for their similarity to J-aggregates. Here, we assemble multifluorophore DX-tile scaffolds which template J-bits into both contiguous and noncontiguous linear arrays. Our goal is to understand the relay capability of noncontiguous J-bit arrays and probe the effects that orientation and position have on the energy transfer between them. We find that linearly contiguous J-bits can relay excitons from an initial AlexaFluor 405 donor to a terminal AlexaFluor 647 acceptor across a distance of up to 16.3 nm. We observed a maximum increase in energy transfer of 41% in the shortest scaffold and an 11% increase in energy transfer across the maximum distance. However, in nonlinear arrays, exciton transfer is not detectable, even when off-axis J-bit-to-J-bit transfer distances were <2 nm. These results, in conjunction with the previous work on PIC-DNA systems, suggest that PIC-DNA-based systems may currently be limited to simple 1-D designs, which prevent isolating J-bits for enhanced energy-transfer characteristics until further understanding and improvements to the system can be made.
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Affiliation(s)
- Matthew Chiriboga
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,Volgenau School of Engineering, Department of Bioengineering, Institute for Advanced Biomedical Research George Mason University, Manassas, Virginia 22030, United States
| | - Sebastian A Diaz
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
| | - Divita Mathur
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - David A Hastman
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,A. James Clark School of Engineering, Fischell Department of Bioengineering, University of Maryland College Park, College Park, Maryland 20742, United States
| | - Joseph S Melinger
- Electronics Science and Technology Division Code 6800, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
| | - Remi Veneziano
- Volgenau School of Engineering, Department of Bioengineering, Institute for Advanced Biomedical Research George Mason University, Manassas, Virginia 22030, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
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Antimicrobial activity and DNA/HSA interaction of fluorinated 3,6,9-trisubstituted acridines. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01079-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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10
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Guarra F, Busto N, Guerri A, Marchetti L, Marzo T, García B, Biver T, Gabbiani C. Cytotoxic Ag(I) and Au(I) NHC-carbenes bind DNA and show TrxR inhibition. J Inorg Biochem 2020; 205:110998. [DOI: 10.1016/j.jinorgbio.2020.110998] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/18/2019] [Accepted: 01/12/2020] [Indexed: 02/07/2023]
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11
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Ethanol effect on gold nanoparticle aggregation state and its implication in the interaction mechanism with DNA. J Colloid Interface Sci 2018; 529:65-76. [DOI: 10.1016/j.jcis.2018.05.108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 01/08/2023]
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12
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Pronkin PG, Tatikolov AS. Influence of the interaction with DNA on the spectral-fluorescent and photochemical properties of some meso-substituted polymethine dyes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 202:269-275. [PMID: 29800889 DOI: 10.1016/j.saa.2018.05.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
Spectral-fluorescent and photochemical properties of meso-substituted thiacarbocyanine dyes 3,3'-dimethyl-9-phenylthiacarbocyanine and 3,3'-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine in solutions and their interaction with DNA were studied. The dyes form noncovalent complexes with DNA, which is accompanied by changes in the absorption spectra and an increase in the fluorescence intensity of the dyes. The data obtained suggest that the dyes are in the form of trans-isomers both in solvents of different polarity and in complexes with DNA. It was shown that the interaction of the dyes with DNA is a complex process involving monomeric dye molecules and aggregates of the dyes. The primary photochemical processes of the dyes in solutions and in complexes with DNA were studied by flash photolysis technique. Upon flash photoexcitation in solutions, the formation and decay of the photoisomers of the dyes were observed, with no generation of the triplet states. In the complex with DNA, no signal of photoisomers was detected; in the absence of oxygen, the formation of the triplet state of the dyes was observed. The decay kinetics of the triplet state of the dyes were two-exponential. The process of quenching of the triplet state of the dyes by oxygen in a complex with DNA was studied, the respective quenching rate constants were estimated, being lower than the diffusion-controlled value.
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Affiliation(s)
- Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia.
| | - Alexander S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia
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13
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Halder D, Purkayastha P. A flavonol that acts as a potential DNA minor groove binder as also an efficient G-quadruplex loop binder. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Tatikolov АS, Akimkin TM, Panova IG, Yarmoluk SM. Spectral-fluorescent study of the interaction of the polymethine dye probe Cyan 2 with chondroitin-4-sulfate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 177:93-96. [PMID: 28129579 DOI: 10.1016/j.saa.2017.01.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 01/12/2017] [Accepted: 01/16/2017] [Indexed: 06/06/2023]
Abstract
The noncovalent interaction of the polymethine dye probe 3,3',9-trimethylthiacarbocyanine iodide (Cyan 2) with chondroitin-4-sulfate (C4S) in buffer solutions with different pH and in water in the absence of buffers has been studied by spectral-fluorescent methods. It has been shown that in all media studied, at relatively high concentrations, the dye is bound to C4S mainly as a monomer, which is accompanied by a steep rise of fluorescence (the intermediate formation of dye aggregates on the biopolymer is also observed). From the dependence of the fluorescence quantum yield on the concentration of C4S, the parameters of binding of the dye monomer to C4S were obtained: the effective binding constant K, the number of the monomeric C4S units n per one dye monomer bound to C4S, and the fluorescence quantum yield of the bound dye monomer Φfb. The dependence of Φfb (and K) on рН of the medium is not monotonic: it has a minimum in the region of neutral pH and a growth in the regions of acid and basic pH. This can be explained by changing the charge of a C4S macromolecule as a function of pH and related conformational alterations in the biopolymer, which can affect the rigidity of a dye molecule and the energy of its interaction with the biopolymer.
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Affiliation(s)
- Аlexander S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia.
| | - Timofey M Akimkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia
| | - Ina G Panova
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Vavilov St. 26, Moscow 119334, Russia
| | - Sergiy M Yarmoluk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, ul. Zabolotnogo 150, Kiev 252143, Ukraine
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15
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Jansson L, Koliana M, Sidstedt M, Hedman J. Blending DNA binding dyes to improve detection in real-time PCR. ACTA ACUST UNITED AC 2017; 14:34-37. [PMID: 28459006 PMCID: PMC5397098 DOI: 10.1016/j.btre.2017.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/10/2017] [Accepted: 02/12/2017] [Indexed: 11/19/2022]
Abstract
The success of real-time PCR (qPCR) analysis is partly limited by the presence of inhibitory compounds in the nucleic acid samples. For example, humic acid (HA) from soil and aqueous sediment interferes with amplification and also quenches the fluorescence of double-stranded (ds) DNA binding dyes, thus hindering amplicon detection. We aimed to counteract the HA fluorescence quenching effect by blending complementary dsDNA binding dyes, thereby elevating the dye saturation levels and increasing the fluorescence signals. A blend of the four dyes EvaGreen, ResoLight, SYBR Green and SYTO9 gave significantly higher fluorescence intensities in the presence and absence of HA, compared with the dyes applied separately and two-dye blends. We propose blending of dyes as a generally applicable means for elevating qPCR fluorescence signals and thus enabling detection in the presence of quenching substances.
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Affiliation(s)
- Linda Jansson
- Applied Microbiology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
| | - Marianne Koliana
- Applied Microbiology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
| | - Maja Sidstedt
- Applied Microbiology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
- Swedish National Forensic Centre, Linköping, SE-591 94, Sweden
| | - Johannes Hedman
- Applied Microbiology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
- Swedish National Forensic Centre, Linköping, SE-591 94, Sweden
- Corresponding author at: Applied Microbiology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden.Applied MicrobiologyDepartment of ChemistryLund UniversityLundSE-221 00Sweden
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Aydinoglu S, Biver T, Figuccia S, Fiore T, Montanaro S, Pellerito C. Studies on DNA interaction of organotin(IV) complexes of meso-tetra(4-sulfonatophenyl)porphine that show cellular activity. J Inorg Biochem 2016; 163:311-317. [PMID: 27393277 DOI: 10.1016/j.jinorgbio.2016.06.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/21/2016] [Accepted: 06/28/2016] [Indexed: 12/29/2022]
Abstract
The interaction of the diorgano- and triorganotin(IV) derivatives of meso-tetra-(4-sulfonatophenyl)porphine (Me2Sn)2TPPS, (Bu2Sn)2TPPS, (Me3Sn)4TPPS and (Bu3Sn)4TPPS to natural DNA was analysed (together with free meso-tetra-(4-sulfonatophenyl)porphine (TPPS4-) for comparison purposes). Particular attention was paid to (Bu3Sn)4TPPS, a species that shows significant cellular action. Preliminary tests were done on the solution properties of the organotin(IV) compounds (pKA and possible self-aggregation). Spectrophotometric and spectrofluorometric experiments showed that all the investigated organotin(IV) derivatives strongly interact with DNA, the binding energy depending on the dye steric hindrance. In all cases experimental data concur in indicating that external binding mode prevails. Interestingly, fluorescence quenching and viscosity experiments show that the Bu-containing species, and in particular (Bu3Sn)4TPPS, are able to noticeably alter the DNA conformation.
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Affiliation(s)
- Sabriye Aydinoglu
- Department of Analytical Chemistry, Faculty of Pharmacy, Cukurova University, 01330 Adana, Turkey
| | - Tarita Biver
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 13, 56124, Pisa, Italy.
| | - Stefania Figuccia
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 13, 56124, Pisa, Italy
| | - Tiziana Fiore
- Dipartimento di Fisica e Chimica (DiFC), Università di Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy
| | - Sonia Montanaro
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 13, 56124, Pisa, Italy
| | - Claudia Pellerito
- Dipartimento di Fisica e Chimica (DiFC), Università di Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy
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17
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Biancardi A, Biver T, Burgalassi A, Mattonai M, Secco F, Venturini M. Mechanistic aspects of thioflavin-T self-aggregation and DNA binding: evidence for dimer attack on DNA grooves. Phys Chem Chem Phys 2015; 16:20061-72. [PMID: 25130260 DOI: 10.1039/c4cp02838d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Thioflavin-T (TFT) is a fluorescent marker widely employed in biomedical research but the mechanism of its binding to polynucleotides has been poorly understood. This paper presents a study of the mechanisms of TFT self-aggregation and binding to DNA. Relaxation kinetics of TFT solutions show that the cyanine undergoes dimerization followed by dimer isomerisation. The interaction of TFT with DNA has been investigated using static methods, such as spectrophotometric and spectrofluorometric titrations under different conditions (salt content, temperature), fluorescence quenching, viscometric experiments and the T-jump relaxation method. The combined use of these techniques enabled us to show that the TFT monomer undergoes intercalation between the DNA base pairs and external binding according to a branched mechanism. Moreover, it has also been observed that, under dye excess conditions, the TFT dimer binds to the DNA grooves. The molecular structures of intercalated TFT and the groove-bound TFT dimer are obtained by performing QM/MM MD simulations.
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Affiliation(s)
- A Biancardi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Risorgimento 35, 56126 Pisa, Italy.
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18
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Busto N, Cano B, Tejido R, Biver T, Leal JM, Venturini M, Secco F, García B. Aggregation features and fluorescence of Hoechst 33258. J Phys Chem B 2015; 119:4575-81. [PMID: 25759973 DOI: 10.1021/jp512306c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The functionality of the bisbenzimide Hoechst 33258 in solution has been largely exploited in the quantification of DNA. Understanding of its behavior is essential to promote its widespread application and learning of biological processes. A detailed study of the dimerization process of the fluorescent blue dye Hoechst 33258 is carried out by isothermal titration calorimetry, absorbance, fluorescence, differential scanning calorimetry and T-jump kinetic measurements. The dimer/monomer ratio depends on the dye concentration and the ionic strength. The dimerization constant determined under physiological conditions (pH = 7.0; I = 0.10 M), KD = 3 × 10(4) M(-1), conveys that only micromolar concentrations of the dye can ensure reasonably high amounts of the monomer species in solution. For instance, for 10 μM dye content, the dimer prevails for I > 0.08 M, whereas the monomer is observed at low ionic strength, a key issue to be elucidated as long as the dimer species is more fluorescent than the monomer and the fluorescence intensity strongly relies on the ionic strength and the dye concentration.
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Affiliation(s)
- Natalia Busto
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Beatriz Cano
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Rocío Tejido
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Tarita Biver
- ‡Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - José M Leal
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Marcella Venturini
- ‡Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Fernando Secco
- ‡Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Begoña García
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
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Biancardi A, Burgalassi A, Terenzi A, Spinello A, Barone G, Biver T, Mennucci B. A Theoretical and Experimental Investigation of the Spectroscopic Properties of a DNA-Intercalator Salphen-Type ZnIIComplex. Chemistry 2014; 20:7439-47. [DOI: 10.1002/chem.201304876] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Indexed: 01/22/2023]
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20
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Synthesis and spectral properties of novel hemicyanine dyes. Russ Chem Bull 2014. [DOI: 10.1007/s11172-014-0496-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Pérez-Arnaiz C, Busto N, Leal JM, García B. New insights into the mechanism of the DNA/doxorubicin interaction. J Phys Chem B 2014; 118:1288-95. [PMID: 24417409 DOI: 10.1021/jp411429g] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Doxorubicin (DOX) is an important anthracycline antibiotic whose intricate features of binding to DNAs, not yet fully understood, have been the object of intense debate. The dimerization equilibrium has been studied at pH = 7.0, I = 2.5 mM, and T = 25 °C. A thermodynamic and kinetic study of the binding of doxorubicin to DNA, carried out by circular dichroism, viscometry, differential scanning calorimetry, fluorescence, isothermal titration calorimetry, and T-jump relaxation measurements, has enabled us to characterize for the first time two different types of calf thymus DNA (ctDNA)/DOX complexes: PD1 for C(DOX)/C(DNA) < 0.3, and PD2 for higher drug content. The nature of the PD1 complex is described better in light of the affinity of DOX with the synthetic copolymers [poly(dA-dT)]2 and [poly(dG-dC)]2. The formation of PD1 has been categorized kinetically as a two-step mechanism in which the fast step is the groove binding in the AT region, and the slow step is the intercalation into the GC region. This bifunctional nature provides a plausible explanation for the high PD1 constant obtained (K1 = 2.3 × 10(8) M(-1)). Moreover, the formation of an external aggregate complex ctDNA/DOX (PD2) at the expense of PD1, with K2 = 9.3 × 10(5) M(-1), has been evinced.
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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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23
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Ghosh D, Chattopadhyay N. Equilibrium and dynamic effects on ligand binding to biomacromolecules and biomimetic model systems. INT REV PHYS CHEM 2013. [DOI: 10.1080/0144235x.2013.782683] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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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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25
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26
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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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27
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Cruz C, Boto REF, Almeida P, Queiroz JA. Study of specific interaction between nucleotides and dye support by nuclear magnetic resonance. J Mol Recognit 2012; 24:975-80. [PMID: 22038804 DOI: 10.1002/jmr.1144] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The binding between four matrices (beaded cellulose, cellulose acetate, cellulose triacetate and Sepharose CL-6B) and beaded cellulose derivatized with a thiacarbocyanine dye with 5'-mononucleotides is investigated by Saturation Transfer Difference Nuclear Magnetic Resonance (STD-NMR) technique. This procedure intends to identify unspecific interactions between 5'-mononucleotides and matrices commonly used in affinity chromatography systems and also clarify the contribution of a thiacarbocyanine dye immobilized onto cellulose beads in a biorecognition process. The differences between non-derivatized and derivatized beaded cellulose evidence the contribution of thiacarbocyanine dye in the observed interaction. STD-NMR experiments show that Sepharose CL- 6B interact less with the 5'-mononucleotides comparatively with beaded cellulose. Indeed, beaded cellulose shows nonspecific interactions with almost all 5'-mononucleotides that compromises the specificity of the interaction between the thiacarbocyanine dye immobilized with the 5'-mononucleotides. The cellulose matrices where the hydroxyl groups are replaced by acetate and triacetate groups do not exhibit binding response to the 5'- mononucleotides, whereas the thiacarbocyanine dye contribution is evidenced by the reinforcement of the interactions with the sugar moiety of 5'-GMP and 5'-UMP and with base of 5'-AMP, 5'-CMP and 5'-TMP. This screening of the nucleotide atoms involved in the binding to the supports can be very useful in chromatography evaluations in which dye-affinity chromatography supports may be used, such as purification of nucleic acids.
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Affiliation(s)
- Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal.
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29
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Ilg T, Cramer J, Lutz J, Noack S, Schmitt H, Williams H, Newton T. The characterization of Lucilia cuprina acetylcholinesterase as a drug target, and the identification of novel inhibitors by high throughput screening. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 41:470-483. [PMID: 21530657 DOI: 10.1016/j.ibmb.2011.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 04/06/2011] [Accepted: 04/13/2011] [Indexed: 05/30/2023]
Abstract
Acetylcholinesterase (AChE, EC3.1.1.7.) is the molecular target for the carbamate and organophosphate pesticides that are used to combat parasitic arthropods. In this paper we report the functional heterologous expression of AChE from Lucilia cuprina (the sheep blowfly) in HEK293 cells. We show that the expressed enzyme is cell-surface-exposed and possesses a glycosyl-phosphatidylinositol membrane anchor. The substrates acetyl-, propionyl- and butyrylthiocholine (AcTC, PropTC, ButTC), and also 11 further thiocholine and homo-thiocholine derivatives were chemically synthesized to evaluate and compare their substrate properties in L. cuprina AChE and recombinant human AChE. The Michaelis-Menten constants K(M) for AcTC, PropTC and ButTC were found to be 3-7-fold lower for the L. cuprina AChE than for the human AChE. Additionally, 2-methoxyacetyl-thiocholine and isobutyryl-thiocholine were better substrates for the insect enzyme than for the human AChE. The AcTC, PropTC and ButTC specificities and the Michaelis-Menten constants for recombinant L. cuprina AChE were similar to those determined for AChE extracted from L. cuprina heads, which are a particularly rich source of this enzyme. The median inhibition concentrations (IC(50) values) were determined for 21 organophosphates, 23 carbamates and also 9 known non-covalent AChE inhibitors. Interestingly, 11 compounds were 100- to >4000-fold more active on the insect enzyme than on the human enzyme. The substrate and inhibitor selectivity data collectively indicate that there are structural differences between L. cuprina and human AChE in or near the active sites, suggesting that it may be possible to identify novel, specific L. cuprina AChE inhibitors. To this end, a high throughput screen with 107,893 compounds was performed on the L. cuprina head AChE. This led to the identification of 195 non-carbamate, non-organophosphate inhibitors with IC(50) values below 10μM. Analysis of the most potent hit compounds identified 19 previously unknown inhibitors with IC(50) values below 200nM, which were up to 335-fold more potent on the L. cuprina enzyme than on the human AChE. Some of these compounds may serve as leads for lead optimization programs to generate fly-specific pesticides.
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Affiliation(s)
- Thomas Ilg
- Intervet Innovation GmbH, Zur Propstei, 55270 Schwabenheim, Germany.
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30
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Biancardi A, Biver T, Marini A, Mennucci B, Secco F. Thiazole orange (TO) as a light-switch probe: a combined quantum-mechanical and spectroscopic study. Phys Chem Chem Phys 2011; 13:12595-602. [DOI: 10.1039/c1cp20812h] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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31
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Prado-Gotor R, Grueso E. A kinetic study of the interaction of DNA with gold nanoparticles: mechanistic aspects of the interaction. Phys Chem Chem Phys 2010; 13:1479-89. [PMID: 21132199 DOI: 10.1039/c0cp00901f] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A kinetic study of the interaction of gold nanoparticles capped with N-(2-mercaptopropionyl)glycine with double stranded DNA was carried out in water and in salt (NaCl) solutions. The kinetic curves are biexponential and reveal the presence of three kinetic steps. The dependence of the reciprocal fast and slow relaxation time, on the DNA concentration, is a curve and tends to a plateau at high DNA concentrations. The simplest mechanism consistent with the kinetic results involves a simple three-step series mechanism reaction scheme. The first step corresponds to a very fast step that is related to a diffusion controlled formation of an external precursor complex (DNA, AuNPs); the second step involves the formation of a (DNA/AuNPs)(I) complex, as a result of the binding affinity between hydrophilic groups of the tiopronin and the DNA grooves. Finally, the third step has been interpreted as a consequence of a conformational change of the (DNA/AuNPs)(I) complex formed in the second step, to a more compacted form (DNA/AuNPs)(II). The values of the rate constants of each step decrease as NaCl concentration increases. The results have been discussed in terms of solvation of the species and changes in the viscosity of the solution.
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Affiliation(s)
- Rafael Prado-Gotor
- Department of Physical Chemistry, Faculty of Chemistry, University of Sevilla, C/Profesor García González s/n, 41012 Sevilla, Spain
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Reuter M, Dryden DTF. The kinetics of YOYO-1 intercalation into single molecules of double-stranded DNA. Biochem Biophys Res Commun 2010; 403:225-9. [PMID: 21073861 DOI: 10.1016/j.bbrc.2010.11.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 11/04/2010] [Indexed: 12/01/2022]
Abstract
The cyanine dye, YOYO-1, has frequently been used in single DNA molecule imaging work to stain double-stranded DNA as it fluoresces strongly when bound. The binding of YOYO-1 lengthens the DNA due to bis-intercalation. We have investigated the kinetics of binding, via this increase in DNA length, for single, hydrodynamically-stretched molecules of lambda DNA observed via Total Internal Reflection Fluorescence (TIRF) microscopy. The rate and degree of lengthening in 40mM NaHCO(3) (pH 8.0) buffer depend upon the free dye concentration with the reaction taking several minutes to reach completion even in relatively high, 40nM, concentrations of YOYO-1. In the absence of overstretching of the DNA molecule, we determine the second order rate constant to be 3.8±0.7×10(5)s(-1)M(-1), the dissociation constant to be 12.1±3.4nM and the maximum DNA molecule extension to be 36±4%. The intercalation time constant (inverse of the pseudo-first order rate constant), τ, decreased from 309 to 62s as YOYO-1 levels increased from 10 to 40nM. The kinetics of binding help with interpretation of the behavior of DNA-YOYO-1 complexes when overstretched and establish defined conditions for the preparation of DNA-YOYO-1 complexes.
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Affiliation(s)
- Marcel Reuter
- School of Chemistry and COSMIC, The University of Edinburgh, West Mains Road, The King's Buildings, Edinburgh EH9 3JJ, UK
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33
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García B, Leal JM, Ruiz R, Biver T, Secco F, Venturini M. Change of the binding mode of the DNA/proflavine system induced by ethanol. J Phys Chem B 2010; 114:8555-64. [PMID: 20524626 DOI: 10.1021/jp102801z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The equilibria and kinetics of the binding of proflavine to poly(dG-dC).poly(dG-dC) and poly(dA-dT).poly(dA-dT) were investigated in ethanol/water mixtures using spectrophotometric, circular dichroism, viscometric, and T-jump methods. All methods concur in showing that two modes of interaction are operative: intercalation and surface binding. The latter mode is favored by increasing ethanol and/or the proflavine content. Both static and kinetic experiments show that, concerning the poly(dG-dC).poly(dG-dC)/proflavine system, intercalation largely prevails up to 20% EtOH. For higher EtOH levels surface binding becomes dominant. Concerning the poly(dA-dT).poly(dA-dT)/proflavine system, melting experiments show that addition of proflavine stabilizes the double stranded structure, but the effect is reduced in the presence of EtOH. The DeltaH degrees and DeltaS degrees values of the melting process, measured at different concentrations of added proflavine, are linearly correlated, revealing the presence of the enthalpy-entropy compensation phenomenon (EEC). The nonmonotonicity of the "entropic term" of the EEC reveals the transition between the two binding modes. T-jump experiments show two relaxation effects, but at the highest levels of EtOH (>25%) the kinetic curves become monophasic, confirming the prevalence of the surface complex. A branched mechanism is proposed where diffusion controlled formation of a precursor complex occurs in the early stage of the binding process. This evolves toward the surface and/or the intercalated complex according to two rate-determining parallel steps. CD spectra suggest that, in the surface complex, proflavine is bound to DNA in the form of an aggregate.
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Affiliation(s)
- Begoña García
- Chemistry Department, University of Burgos, 09001 Burgos, Spain.
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Biver T, García B, Leal JM, Secco F, Turriani E. Left-handed DNA: intercalation of the cyanine thiazole orange and structural changes. A kinetic and thermodynamic approach. Phys Chem Chem Phys 2010; 12:13309-17. [PMID: 20842298 DOI: 10.1039/c0cp00328j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conditions under which different structures of left-handed DNA (poly(dG-me(5)dC)·poly(dG-me(5)dC)) can exist are investigated by spectrofluorometric, spectrophotometric, circular dichroism and calorimetric measurements and the kinetics of the transformations are analysed. The effects of temperature, salt and ethanol content on the transitions are also studied. The left-handed structure obtained by addition of either Mg(2+) ions or EtOH corresponds to Z-DNA, whereas the structure obtained using the mixture Mg(2+)/EtOH corresponds to the aggregate Z*-DNA. Upon addition of the fluorescent cyanine Thiazole Orange (TO), the transition Z → B immediately starts, whereas Z*-DNA retains its left-handed configuration in the presence of TO provided that the ratio [dye]/[polymer] ≤ 0.1. The equilibria and kinetics of the TO binding to Z*-DNA are investigated under the above conditions using the T-jump technique. The reaction mechanism consists of two series steps, the first one being characterized by the formation of an external electrostatic complex and the second corresponding to the dye penetration between the base pairs. A comparison with the B-DNA/TO system is drawn.
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Affiliation(s)
- Tarita Biver
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
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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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36
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El-Shishtawy RM, Asiri AM, Basaif SA, Rashad Sobahi T. Synthesis of a new beta-naphthothiazole monomethine cyanine dye for the detection of DNA in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 75:1605-1609. [PMID: 20227908 DOI: 10.1016/j.saa.2010.02.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 01/22/2010] [Accepted: 02/11/2010] [Indexed: 05/28/2023]
Abstract
Novel monomethine cyanine dye (MC) derived from beta-naphthothiazole and benzothiazole has been prepared and characterized by (1)H and (13)C NMR, FTIR, ESIMS, elemental analyses, absorption and fluorescence spectroscopy. The dye was conveniently synthesized by the condensation of two sulfate heterocyclic quaternary salts. The interaction between calf thymus DNA (ct-DNA) in tris(hydroxymethyl)aminomethane-HCl (Tris-HCl) aqueous buffer solution and MC has been studied with spectral fluorescence method. The binding constant value has been determined by fluorescence titration of MC with ct-DNA concentrations. The result obtained is consistent with an intercalative binding interaction between MC and ct-DNA. Compared with ethidium bromide (EB), MC showed a huge fluorescence enhancement upon mixing with ct-DNA.
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Affiliation(s)
- Reda M El-Shishtawy
- Faculty of Science, Chemistry Department, King Abdul-Aziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia.
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37
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Ghosh R, Bhowmik S, Bagchi A, Das D, Ghosh S. Chemotherapeutic potential of 9-phenyl acridine: biophysical studies on its binding to DNA. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 39:1243-9. [DOI: 10.1007/s00249-010-0577-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 12/14/2009] [Accepted: 01/13/2010] [Indexed: 10/19/2022]
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38
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ACHYUTHAN KE, WHITTEN DG, BRANCH DW. Supramolecular Self-Assembling Cyanine as an Alternative to Ethidium Bromide Displacement in DNA-Drug Model Interactions during High Throughput Screening. ANAL SCI 2010; 26:55-61. [DOI: 10.2116/analsci.26.55] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | - David G. WHITTEN
- Department of Chemical and Nuclear Engineering, University of New Mexico
| | - Darren W. BRANCH
- Biosensors and Nanomaterials Department, Sandia National Laboratories
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39
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Biver T, Boggioni A, García B, Leal JM, Ruiz R, Secco F, Venturini M. New aspects of the interaction of the antibiotic coralyne with RNA: coralyne induces triple helix formation in poly(rA)*poly(rU). Nucleic Acids Res 2009; 38:1697-710. [PMID: 20008509 PMCID: PMC2836573 DOI: 10.1093/nar/gkp1146] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The interaction of coralyne with poly(A)*poly(U), poly(A)*2poly(U), poly(A) and poly(A)*poly(A) is analysed using spectrophotometric, spectrofluorometric, circular dichroism (CD), viscometric, stopped-flow and temperature-jump techniques. It is shown for the first time that coralyne induces disproportionation of poly(A)*poly(U) to triplex poly(A)*2poly(U) and single-stranded poly(A) under suitable values of the [dye]/[polymer] ratio (C(D)/C(P)). Kinetic, CD and spectrofluorometric experiments reveal that this process requires that coralyne (D) binds to duplex. The resulting complex (AUD) reacts with free duplex giving triplex (UAUD) and free poly(A); moreover, ligand exchange between duplex and triplex occurs. A reaction mechanism is proposed and the reaction parameters are evaluated. For C(D)/C(P)> 0.8 poly(A)*poly(U) does not disproportionate at 25 degrees C and dye intercalation into AU to give AUD is the only observed process. Melting experiments as well show that coralyne induces the duplex disproportionation. Effects of temperature, ionic strength and ethanol content are investigated. One concludes that triplex formation requires coralyne be only partially intercalated into AUD. Under suitable concentration conditions, this feature favours the interaction of free AU with AUD to give the AUDAU intermediate which evolves into triplex UAUD and single-stranded poly(A). Duplex poly(A)*poly(A) undergoes aggregation as well, but only at much higher polymer concentrations compared to poly(A)*poly(U).
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Affiliation(s)
- Tarita Biver
- University of Pisa, Chemistry and Industrial Chemistry Department, 56126 Pisa, Italy
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40
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Pronkin PG, Tatikolov AS. Electronic excitation energy transfer between molecules of carbocyanine dyes in complexes with DNA. HIGH ENERGY CHEMISTRY 2009. [DOI: 10.1134/s0018143909060101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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Chang E, Congdon EE, Honson NS, Duff KE, Kuret J. Structure-activity relationship of cyanine tau aggregation inhibitors. J Med Chem 2009; 52:3539-47. [PMID: 19432420 DOI: 10.1021/jm900116d] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A structure-activity relationship for symmetrical cyanine inhibitors of human tau aggregation was elaborated using a filter trap assay. Antagonist activity depended on cyanine heterocycle, polymethine bridge length, and the nature of meso- and N-substituents. One potent member of the series, 3,3'-diethyl-9-methylthiacarbocyanine iodide (compound 11), retained submicromolar potency and had calculated physical properties consistent with blood-brain barrier and cell membrane penetration. Exposure of organotypic slices prepared from JNPL3 transgenic mice (which express human tau harboring the aggregation prone P301L tauopathy mutation) to compound 11 for one week revealed a biphasic dose response relationship. Low nanomolar concentrations decreased insoluble tau aggregates to half those observed in slices treated with vehicle alone. In contrast, high concentrations (> or =300 nM) augmented tau aggregation and produced abnormalities in tissue tubulin levels. These data suggest that certain symmetrical carbocyanine dyes can modulate tau aggregation in the slice biological model at concentrations well below those associated with toxicity.
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Affiliation(s)
- Edward Chang
- Center for Molecular Neurobiology, Department of Molecular and Cellular Biochemistry, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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42
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Liang M, Liu X, Nakamura K, Chen X, Cheng D, Liu G, Dou S, Wang Y, Rusckowski M, Hnatowich DJ. A convenient thiazole orange fluorescence assay for the evaluation of DNA duplex hybridization stability. Mol Imaging Biol 2009; 11:439-45. [PMID: 19444399 DOI: 10.1007/s11307-009-0221-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 01/06/2009] [Accepted: 01/16/2009] [Indexed: 11/25/2022]
Abstract
OBJECTIVE A simple and rapid method for measuring the hybridization stability of duplexes of DNAs and other oligomers in different environments is described. When added to an oligomer duplex, the thiazole orange (TO) dye intercalates and in this state is fluorescent. Therefore, when duplex dissociation occurs, the release of TO results in a detectable change in fluorescence intensity. This assay was developed primarily to screen antisense oligomer duplexes that are stable in serum and in the cytoplasm but unstable in the presence of their target messenger RNA (mRNA). METHODS The two antisense oligomers of this investigation were both 25 mer phosphorothioate (PS) DNAs, one directed against the RIalpha mRNA and the other directed against the mdr1 mRNA. The former duplex was first used in the solution studies, in most cases duplexed with a 16 mer phosphodiester (PO) complementary DNA (i.e., PS-DNA25/PO-cDNA16). Both duplexes were then tested in a series of cell studies using SK-BR-3 (RIalpha+), KB-G2 (mdr1++), and KB-31 (mdr1+/-) cells. RESULTS Preliminary measurements in solution showed that maximum fluorescence was achieved when more than ten TO molecules were bound to each duplex. When a 25 mer PO-DNA or PO-RNA with the base sequence of the RIalpha mRNA was added, the dramatic change in fluorescence intensity that followed signified dissociation of the antisense DNA from the study duplex and reassociation with the target DNA. Kinetic measurements showed that this process was completed in about 3 min. Fluorescent measurements of SK-BR-3 (RIalpha+) cells incubated at 37 degrees C with the anti-RIalpha study duplex over time showed a maximum at the point where the loss of fluorescence due to dissociation of the study duplex, probably by an antisense mechanism, began to dominate over the increasing fluorescence due to continuing cellular accumulation. A similar result was observed in the KB-G2 (mdr1+) cells incubated with the anti-mdr1 study duplex. CONCLUSIONS When study duplexes shown to be stable in serum were incubated with their target cells, the assay successfully detected evidence of dissociation, most likely by an antisense mechanism. Thus, a TO fluorescence assay has been developed that is capable of detecting the dissociation of DNA duplexes.
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Affiliation(s)
- Minmin Liang
- Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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43
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Singh MP, Jennings TL, Strouse GF. Tracking spatial disorder in an optical ruler by time-resolved NSET. J Phys Chem B 2009; 113:552-8. [PMID: 19099435 DOI: 10.1021/jp808997h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For biomolecular applications, potential interactions between newly developed dye molecules and the biomolecule of interest can dramatically influence the accuracy of optical ruler techniques. By utilizing nanometal surface energy transfer (NSET), an optical technique is developed that allows the nature of interactions between dyes and a biomolecule, namely DNA, to be directly assessed. To demonstrate the method, interactions between well-known molecular dyes based on carboxyfluorescein (FAM, noninteracting) and Cy5 (known intercalator) with DNA is probed. The results demonstrate that FAM exhibits no interactions with the DNA backbone and is adequately represented as a solvent exposed dye, while the commonly used near-IR dye Cy5 exhibits two discrete interactions that depend on the site of appendage and the length of the linker arm. The exact population and nature of Cy5 interaction with the DNA indicates a 37% ratio of intercalation for the internal C(6), a 42% ratio for an internal C(3) spacer length, and no evidence of interaction for terminal labeling. The results allow quantitative assignment of the site occupation of donors to be analyzed providing a powerful set of information for use of dyes in FRET based optical ruler technologies without the need of single molecule methods or the assumption of an averaged site occupation for the donor.
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Affiliation(s)
- Mani Prabha Singh
- Department of Chemistry and Biochemistry, Molecular Biophysics Program, Florida State University, Tallahassee, Florida 32306-4390, USA
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Zhang G, Liu M. Acidichromism and chiroptical switch based on the self-assembly of a cyanine dye on the PLGA/PAH LbL film. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b817782a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Itsko M, Zaritsky A, Rabinovitch A. Thermodynamics of unstable DNA structures from the kinetics of the microgene PCR. J Phys Chem B 2008; 112:13149-56. [PMID: 18795769 DOI: 10.1021/jp8045142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microgene polymerization reaction (MPR) generates head-to-tail tandem repeats from homoduplexes (HDs). In MPR initiation, one HD putatively aligns two others in the proximity required to form a nucleation complex, thus allowing the DNA polymerase to skip the intertemplate gap and generate an initial doublet (ID) prone to repeat propagation. The current investigation refines this stage by additional thermodynamic considerations and elucidates the fundamental mechanism underlying propagation. Four different HD types were designed to extend the range of melting temperatures and to simultaneously modify the stabilities of their secondary structures. Following the propagation kinetics with these, using real-time PCR at different temperatures revealed a new stage in the MPR, amplification of an ID by an original HD, and enabled us to decipher the biphasic kinetics of the process. This amplification merges with the propagation stage if the lifetime of the staggered conformation of the ID is sufficiently long for DNA polymerase to fill in the overhangs. The observed increase with temperature of thermodynamically unfavorable conformations of singlet and doublet HDs that underlies, respectively, MPR initiation and propagation is well correlated with simulations by UNAFold.
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Affiliation(s)
- Mark Itsko
- Departments of Life Sciences and Physics, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
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46
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Biver T, Secco F, Venturini M. Mechanistic aspects of the interaction of intercalating metal complexes with nucleic acids. Coord Chem Rev 2008. [DOI: 10.1016/j.ccr.2007.10.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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47
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Ghasemi J, Ahmadi S, Ahmad AI, Ghobadi S. Spectroscopic Characterization of Thiazole Orange-3 DNA Interaction. Appl Biochem Biotechnol 2008; 149:9-22. [DOI: 10.1007/s12010-007-8124-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2007] [Accepted: 12/06/2007] [Indexed: 10/22/2022]
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48
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Biological properties of 4-methyl-2,7-diamino-5,10-diphenyl-4,9-diazapyrenium hydrogensulfate (ADAP). Cancer Chemother Pharmacol 2007; 62:595-604. [DOI: 10.1007/s00280-007-0643-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Accepted: 10/31/2007] [Indexed: 02/02/2023]
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49
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García B, Secco F, Ibeas S, Muñoz A, Hoyuelos FJ, Leal JM, Senent ML, Venturini M. Structural NMR and ab initio study of salicylhydroxamic and p-hydroxybenzohydroxamic acids: evidence for an extended aggregation. J Org Chem 2007; 72:7832-40. [PMID: 17887699 DOI: 10.1021/jo0709798] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The acid-base behavior and self-aggregation of salicylhydroxamic (SHA) and p-hydroxybenzohydroxamic acids (PHBHA)have been investigated by UV and 1HNMR spectroscopy, respectively. The acid-base parameters, measured in H2O at 25 degrees C and I=0.1 M, were pK1=7.56, pK2=9.85 for SHA and pK1=8.4, pK2=9.4 for PHBHA. The 1H NMR signals for salicylhydroxamic and p-hydroxybenzohydroxamic acids measured in acetone indicate that both acids self-aggregate according to a mechanism where two monomers produce planar E-E dimers stabilized by horizontal H-bonds. Further dimer aggregation yields sandwich-like tetramer structures stabilized by vertical H-bonds and pi-pi interactions. The p-hydroxybenzohydroxamic tetramers, less stable than those of salicylhydroxamic, contain two water molecules in their structures. The gas-phase structures of salicylhydroxamic acid and its anions were investigated by ab initio calculations using the density functional theory at the B3LYP/AUG-cc-pVDZ level. The SHA most stable gas-phase conformer is the A-Z amide, a structure with all three phenolate (OP), carboxylate (OC), and hydroxamate (OH) oxygen atoms in the cis position. The B-Z amide, with the OP oxygen trans to OC, lies 5.4 kcal above the A-Z amide. The most stable monoanion is the N-deprotonated A-Z amide.
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Affiliation(s)
- Begoña García
- Universidad de Burgos, Departamento de Química, 09001 Burgos, Spain.
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50
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Bazzicalupi C, Bencini A, Bianchi A, Biver T, Boggioni A, Bonacchi S, Danesi A, Giorgi C, Gratteri P, Ingraín AM, Secco F, Sissi C, Valtancoli B, Venturini M. DNA Binding by a New Metallointercalator that Contains a Proflavine Group Bearing a Hanging Chelating Unit. Chemistry 2007; 14:184-96. [PMID: 17853515 DOI: 10.1002/chem.200601855] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The new bifunctional molecule 3,6-diamine-9-[6,6-bis(2-aminoethyl)-1,6-diaminohexyl]acridine (D), which is characterised by both an aromatic moiety and a separate metal-complexing polyamine centre, has been synthesised. The characteristics of D and its ZnII complex ([ZnD]) (protonation and metal-complexing constants, optical properties and self-aggregation phenomena) have been analysed by means of NMR spectroscopy, potentiometric, spectrophotometric and spectrofluorimetric techniques. The equilibria and kinetics of the binding process of D and [ZnD] to calf thymus DNA have been investigated at I=0.11 M (NaCl) and 298.1 K by using spectroscopic methods and the stopped-flow technique. Static measurements show biphasic behaviour for both D-DNA and [ZnD]-DNA systems; this reveals the occurrence of two different binding processes depending on the polymer-to-dye molar ratio (P/D). The binding mode that occurs at low P/D values is interpreted in terms of external binding with a notable contribution from the polyamine residue. The binding mode at high P/D values corresponds to intercalation of the proflavine residue. Stopped-flow, circular dichroism and supercoiled-DNA unwinding experiments corroborate the proposed mechanism. Molecular-modelling studies support the intercalative process and evidence the influence of NH+...O interactions between the protonated acridine nitrogen atom and the oxygen atoms of the polyanion; these interactions play a key role in determining the conformation of DNA adducts.
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Affiliation(s)
- Carla Bazzicalupi
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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