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Matić J, Tandarić T, Radić Stojković M, Šupljika F, Karačić Z, Tomašić Paić A, Horvat L, Vianello R, Tumir LM. Phenanthridine-pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme. Beilstein J Org Chem 2023; 19:550-565. [PMID: 37153642 PMCID: PMC10155618 DOI: 10.3762/bjoc.19.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Two novel conjugate molecules were designed: pyrene and phenanthridine-amino acid units with a different linker length between the aromatic fragments. Molecular modelling combined with spectrophotometric experiments revealed that in neutral and acidic buffered water solutions conjugates predominantly exist in intramolecularly stacked conformations because of the π-π stacking interaction between pyrene and phenanthridine moieties. The investigated systems exhibited a pH-dependent excimer formation that is significantly red-shifted relative to the pyrene and phenanthridine fluorescence. While the conjugate with a short linker showed negligible spectrophotometric changes due to the polynucleotide addition, the conjugate with a longer and more flexible linker exhibited a micromolar and submicromolar binding affinity for ds-polynucleotides and inactivated a mutant of dipeptidyl peptidase enzyme E451A. Confocal microscopy revealed that the conjugate with the longer linker entered the HeLa cell membranes and blue fluorescence was visualized as the dye accumulated in the cell membrane.
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Affiliation(s)
- Josipa Matić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Tana Tandarić
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Marijana Radić Stojković
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Filip Šupljika
- Laboratory for Physical Chemistry and Corrosion, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Croatia
| | - Zrinka Karačić
- Laboratory for Protein Biochemistry and Molecular Modelling, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ana Tomašić Paić
- Laboratory for Protein Biochemistry and Molecular Modelling, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Lucija Horvat
- Laboratory for Molecular Plant Biology and Biotechnology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Lidija-Marija Tumir
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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Yadav P, Verma A, Sharma VP, Singh R, Yadav T, Kumar R, Pal S, Gupta H, Saha S, Tewari AK. The development of a robust folded scaffold as a fluorescent material using butylidine-linked pyridazinone-based systems via aromatic π⋯π stacking interactions. NEW J CHEM 2022. [DOI: 10.1039/d2nj00083k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence-capable robust folded pyridazinone-based homo- and heterodimers linked with butylidine linkers, whose crystals exhibit fluorescence with quantum yields of 11% (1CN) and 28% (2CN) due to intramolecular stacking, were synthesized.
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Affiliation(s)
- Priyanka Yadav
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh-221005, India
| | - Abhineet Verma
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh-221005, India
| | - Vishal Prasad Sharma
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh-221005, India
| | - Rashmi Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh-221005, India
| | - Tarun Yadav
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, Uttar, Pradesh-221005, India
| | - Ranjeet Kumar
- Department of Chemistry, CMP Degree College, Prayagraj, Uttar Pradesh-211002, India
| | - Shiv Pal
- Department of Chemistry, Indian Institute of Technology, Bombay-400076, India
| | - Hariom Gupta
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatics Plants (CSIR-CIMAP), Lucknow-226015, India
| | - Satyen Saha
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh-221005, India
| | - Ashish K. Tewari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh-221005, India
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Saftić D, Radić Stojković M, Žinić B, Glavaš-Obrovac L, Jukić M, Piantanida I, Tumir LM. Impact of linker between triazolyluracil and phenanthridine on recognition of DNA and RNA. Recognition of uracil-containing RNA. NEW J CHEM 2017. [DOI: 10.1039/c7nj02699d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A phenanthridine-triazolyluracilyl multifunctional ligand, linked by a lysine–glycine peptide, binds to poly rA–poly rU with micromolar affinity and selective fluorescence response.
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Affiliation(s)
- Dijana Saftić
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- P.O.B. 180
- HR 10002 Zagreb
| | - Marijana Radić Stojković
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- P.O.B. 180
- HR 10002 Zagreb
| | - Biserka Žinić
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- P.O.B. 180
- HR 10002 Zagreb
| | - Ljubica Glavaš-Obrovac
- Department of Medicinal Chemistry and Biochemistry
- School of Medicine Osijek
- 31000 Osijek
- Croatia
| | - Marijana Jukić
- Department of Medicinal Chemistry and Biochemistry
- School of Medicine Osijek
- 31000 Osijek
- Croatia
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- P.O.B. 180
- HR 10002 Zagreb
| | - Lidija-Marija Tumir
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- P.O.B. 180
- HR 10002 Zagreb
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Kataev EA, Shumilova TA, Fiedler B, Anacker T, Friedrich J. Understanding Stacking Interactions between an Aromatic Ring and Nucleobases in Aqueous Solution: Experimental and Theoretical Study. J Org Chem 2016; 81:6505-14. [PMID: 27314892 DOI: 10.1021/acs.joc.6b01130] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stacking interactions between aromatic compounds and nucleobases are crucial in recognition of nucleotides and nucleic acids, but a comprehensive understanding of the strength and selectivity of these interactions in aqueous solution has been elusive. To this end, model complexes have been designed and analyzed by experiment and theory. For the first time, stacking free energies between five nucleobases and anthracene were determined experimentally from thermodynamic double mutant cycles. Three different experimental methods were proposed and evaluated. The dye prefers to bind nucleobases in the order (kcal/mol): G (1.3) > T (0.9) > U (0.8) > C (0.5) > A (0.3). The respective trend of interaction free energies extracted from DFT calculations correlates to that obtained experimentally. Analysis of the data suggests that stacking interactions dominate over hydrophobic effects in an aqueous solution and can be predicted with DFT calculations.
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Affiliation(s)
- Evgeny A Kataev
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Tatiana A Shumilova
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Benjamin Fiedler
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Tony Anacker
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Joachim Friedrich
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
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Badelin VG, Tyunina EY, Mezhevoi IN, Tarasova GN. Thermodynamic characteristics of molecular interactions between L-tryptophan and nicotinic acid and uracyl in aqueous buffer solutions at 298 K. Russ J Phys Chem 2015. [DOI: 10.1134/s0036024415120031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Semenov VE, Krylova ES, Galyametdinova IV, Chernova AV, Kharlamov SV, Latypov SK, Reznik VS. Synthesis and reactivity of acyclic and macrocyclic uracils bridged with five-membered heterocycles. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.07.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Synthesis and Photophysical Properties of Bispsoralen Derivatives Linked by a Bisamide-polymethylene Chain. B KOREAN CHEM SOC 2007; 28:1715-1719. [DOI: 10.5012/bkcs.2007.28.10.1715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Butterfield SM, Sweeney MM, Waters ML. The recognition of nucleotides with model beta-hairpin receptors: investigation of critical contacts and nucleotide selectivity. J Org Chem 2005; 70:1105-14. [PMID: 15704942 DOI: 10.1021/jo0491105] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] We have investigated the factors that contribute to binding of ATP by a designed 12-residue beta-hairpin peptide, WKWK, and have determined its selectivity for binding to the naturally occurring nucleotide triphosphates. We have previously shown that WKWK creates an ATP binding pocket on one face of the beta-hairpin consisting of two Trp and two Lys residues. Mutation of the two Lys residues on the binding face of the beta-hairpin resulted in a lower affinity, indicating that each is involved in ATP binding and that each residue contributes approximately -1.5 kcal/mol to the energy of complexation. Replacement of either Trp residue of the ATP binding pocket with Phe or Leu destabilizes the complex formed with ATP by approximately 1 kcal/mol, indicating that both Trp residues participate in interactions with ATP. For binding to the nucleotide triphosphates, the order of binding affinity was shown to follow dTTP > GTP > ATP > CTP, with differences in binding energies spanning as much as 1.6 kcal/mol. NMR analysis demonstrates that both aromatic interactions with the Trp side chains and CH-pi interactions between the ribose protons and the Trp residues may contribute significantly to binding. The results from our model system provide useful thermodynamic information regarding protein-nucleic acid interactions that occur at the surface of a beta-sheet.
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Affiliation(s)
- Sara M Butterfield
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Lanver A, Schmalz HG. Microwave-assisted amination of a chloropurine derivative in the synthesis of acyclic nucleoside analogues. Molecules 2005; 10:508-15. [PMID: 18007322 DOI: 10.3390/10020508] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Revised: 02/09/2005] [Accepted: 02/10/2005] [Indexed: 11/17/2022] Open
Abstract
An efficient protocol for the amination of 6-chloropurine derivatives through nucleophilic aromatic substitution under microwave irradiation was developed and applied to the synthesis in two steps of a series of new acyclic nucleosides (acyclovir analogues) starting from commercially available compounds.
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11
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Armstrong S, Merrill AR. Toward the elucidation of the catalytic mechanism of the mono-ADP-ribosyltransferase activity of Pseudomonas aeruginosa exotoxin A. Biochemistry 2004; 43:183-94. [PMID: 14705944 DOI: 10.1021/bi034772u] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The catalytic mechanism for the mono-ADP-ribosyltransferase activity of Pseudomonas aeruginosa exotoxin A was investigated by steady-state and stopped-flow kinetic analyses. The rate constants for binding of the NAD(+) substrate to the enzyme were found to be 4.7 +/- 0.4 microM(-1) s(-1) and 194 +/- 15 s(-1) for k(on) and k(off), respectively. The k(on) and k(off) rate constants for the eEF-2 substrate binding to the enzyme were 320 +/- 39 microM(-1) s(-1) and 131 +/- 22 s(-1), respectively. A potent, competitive inhibitor against the enzyme, 1,8-naphthalimide, bound the enzyme with k(on) and k(off) rates of 82 +/- 9 microM(-1) s(-1) and 51 +/- 6 s(-1), respectively. Furthermore, the binding on and off rates for the reaction products, ADP-ribose and nicotinamide, were too rapid for detection with the stopped-flow technique. Investigation of the pre-steady-state kinetics for the ADP-ribose transferase activity of the toxin-enzyme showed that there is no pre-steady-state complex formed during the catalytic cycle. Binding of NAD+ and smaller compounds representing the various parts of this substrate were investigated by the fluorescence quenching of the intrinsic toxin fluorescence. The binding data revealed a significant structural change in the enzyme upon NAD+ binding that could not be accounted for on the basis of the sum of the structural changes induced by the various NAD+ constituents. Product inhibition studies were conducted with nicotinamide and eEF-2-ADP-ribose, and the results indicate that the reaction involves a random-order ternary complex mechanism. Detailed kinetic analysis revealed that the eEF-2 substrate shows sigmoidal kinetic behavior with the enzyme, and fluorescence resonance energy transfer measurements indicated that wheat germ eEF-2 is oligomeric in solution.
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Affiliation(s)
- Souzan Armstrong
- Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, Department of Chemistry and Biochemistry, University of Guelph, Ontario N1G 2W1 Canada
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Coutouli-Argyropoulou E, Pilanidou P. An entry to new isoxazoline analogues of dideoxynucleosides by bromonitrile oxide 1,3-dipolar cycloaddition. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)00752-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Guckian KM, Schweitzer BA, Ren RXF, Sheils CJ, Tahmassebi DC, Kool ET. Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA. J Am Chem Soc 2000; 122:2213-2222. [PMID: 20865137 DOI: 10.1021/ja9934854] [Citation(s) in RCA: 343] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We report the use of thermodynamic measurements in a self-complementary DNA duplex (5'-dXCGCGCG)(2), where X is an unpaired natural or nonnatural deoxynucleoside, to study the forces that stabilize aqueous aromatic stacking in the context of DNA. Thermal denaturation experiments show that the core duplex (lacking X) is formed with a free energy (37 °C) of -8.1 kcal·mol(-1) in a pH 7.0 buffer containing 1 M Na(+). We studied the effects of adding single dangling nucleosides (X) where the aromatic "base" is adenine, guanine, thymine, cytosine, pyrrole, benzene, 4-methylindole, 5-nitroindole, trimethylbenzene, difluorotoluene, naphthalene, phenanthrene, and pyrene. Adding these dangling residues is found to stabilize the duplex by an additional -0.8 to -3.4 kcal·mol(-1). At 5 μM DNA concentration, T(m) values range from 41.7 °C (core sequence) to 64.1 °C (with dangling pyrene residues). For the four natural bases, the order of stacking ability is A > G ≥ T = C. The nonpolar analogues stack more strongly in general than the more polar natural bases. The stacking geometry was confirmed in two cases (X = adenine and pyrene) by 2-D NOESY experiments. Also studied is the effect of ethanol cosolvent on the stacking of natural bases and pyrene. Stacking abilities were compared to calculated values for hydrophobicity, dipole moment, polarizability, and surface area. In general, hydrophobic effects are found to be larger than other effects stabilizing stacking (electrostatic effects, dispersion forces); however, the natural DNA bases are found to be less dependent on hydrophobic effects than are the more nonpolar compounds. The results also point out strategies for the design nucleoside analogues that stack considerably more strongly than the natural bases; such compounds may be useful in stabilizing designed DNA structures and complexes.
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Affiliation(s)
- Kevin M Guckian
- Contribution from the Department of Chemistry, University of Rochester, Rochester, New York 14627
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14
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Enescu M, Levy B, Gheorghe V. Molecular Dynamics Simulation of Methylene Blue−Guanine Complex in Water: The Role of Solvent in Stacking. J Phys Chem B 2000. [DOI: 10.1021/jp992486f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mironel Enescu
- National Institute of Laser, Plasma and Radiation Physics, P.O. Box MG-36, 76900-Magurele, Romania, Laboratoire de Physico-Chimie des Rayonnements (UMR no.8610), Universite Paris Sud, bat. 350, 91405 Orsay Cedex, France, and Biophysics Department, University of Bucharest, 76900-Magurele, Romania
| | - Bernard Levy
- National Institute of Laser, Plasma and Radiation Physics, P.O. Box MG-36, 76900-Magurele, Romania, Laboratoire de Physico-Chimie des Rayonnements (UMR no.8610), Universite Paris Sud, bat. 350, 91405 Orsay Cedex, France, and Biophysics Department, University of Bucharest, 76900-Magurele, Romania
| | - Victor Gheorghe
- National Institute of Laser, Plasma and Radiation Physics, P.O. Box MG-36, 76900-Magurele, Romania, Laboratoire de Physico-Chimie des Rayonnements (UMR no.8610), Universite Paris Sud, bat. 350, 91405 Orsay Cedex, France, and Biophysics Department, University of Bucharest, 76900-Magurele, Romania
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Pang YP, Miller JL, Kollman PA. Computational and Experimental Studies of (2,2)-Bis(indol-1-yl-methyl)acetate Suggest the Importance of the Hydrophobic Effect in Aromatic Stacking Interactions. J Am Chem Soc 1999. [DOI: 10.1021/ja9828410] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuan-Ping Pang
- Contribution from the Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143
| | - Jennifer L. Miller
- Contribution from the Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143
| | - Peter A. Kollman
- Contribution from the Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143
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Zargarian L, Le Tilly V, Jamin N, Chaffotte A, Gabrielsen OS, Toma F, Alpert B. Myb-DNA recognition: role of tryptophan residues and structural changes of the minimal DNA binding domain of c-Myb. Biochemistry 1999; 38:1921-9. [PMID: 10026273 DOI: 10.1021/bi981199j] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Myb oncoprotein specifically binds DNA by a domain composed of three imperfect repeats, R1, R2, and R3, each containing 3 tryptophans. The tryptophan fluorescence of the minimal binding domain, R2R3, of c-Myb was used to monitor structural flexibility changes occurring upon DNA binding to R2R3. The quenching of the Trp fluorescence by DNA titration shows that four out of the six tryptophans are involved in the formation of the specific R2R3-DNA complex and the environment of the tryptophan residues becomes more hydrophobic in the complex. The fluorescence intensity quenching of the tryptophans by binding of R2R3 to DNA is consistent with the decrease of the decay time: 1.46 ns for free R2R3 to 0.71 ns for the complexed protein. In the free R2R3, the six tryptophans are equally accessible to the iodide and acrylamide quenchers with a high collisional rate constant (4 x 10(9) and 3 x 10(9) M-1 s-1, respectively), indicating that R2R3 in solution is very flexible. In the R2R3-DNA complex, no Trp fluorescence quenching is observed with iodide whereas all tryptophan residues remain accessible to acrylamide with a collisional rate constant slightly slower than that in the free state. These results indicate that (i) a protein structural change occurs and (ii) the R2R3 molecule keeps a high mobility in the complex. The complex formation presents a two-step kinetics: a fast step corresponding to the R2R3-DNA association (7 x 10(5) M-1 s-1) and a slower one (0.004 s-1), which should correspond to a structural reorganization of the protein including a reordering of the water molecules at the protein-DNA interface.
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Affiliation(s)
- L Zargarian
- Laboratoire de Biologie Physico-Chimique, UFR de Biochimie, Université Paris 7, France
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Affiliation(s)
- Otto F. Schall
- Bioorganic Chemistry Program and Department of Molecular Biology & Pharmacology, Washington University School of Medicine, Campus Box 8103, 660 S. Euclid Avenue, St. Louis, Missouri 63110
| | - George W. Gokel
- Bioorganic Chemistry Program and Department of Molecular Biology & Pharmacology, Washington University School of Medicine, Campus Box 8103, 660 S. Euclid Avenue, St. Louis, Missouri 63110
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Seidel CAM, Schulz A, Sauer MHM. Nucleobase-Specific Quenching of Fluorescent Dyes. 1. Nucleobase One-Electron Redox Potentials and Their Correlation with Static and Dynamic Quenching Efficiencies. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp951507c] [Citation(s) in RCA: 805] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Itahara T, Imamura K. Preparation and NMR Study of 7,7′-(α,ω-Alkanediyl)bis[theophylline], 1,1′-(α,ω-Alkanediyl)bis[theobromine], and 1,1′-(α,ω-Alkanediyl)bis[3-methyluracil]. BCSJ 1994. [DOI: 10.1246/bcsj.67.203] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Atkins WM, Cader BM, Hemmingsen J, Villafranca JJ. Time-resolved fluorescence and computational studies of adenylylated glutamine synthetase: analysis of intersubunit interactions. Protein Sci 1993; 2:800-13. [PMID: 8098638 PMCID: PMC2142491 DOI: 10.1002/pro.5560020510] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Adenylylation of Tyr-397 of each subunit of Escherichia coli glutamine synthetase (GS) down-regulates enzymatic activity in vivo. The overall structure of the enzyme consists of 12 subunits arranged as two hexamers, face to face. Research reported in this paper addresses the question of whether the covalently attached adenylyl group interacts with neighboring amino acid residues to produce the regulatory phenomenon. Wild-type GS has two Trp residues (positions 57 and 158) and the adenylylation site lies within 7-8 A of the Trp-57 loop in the adjacent subunit of the same hexameric ring; Trp-158 is about 35 A from the site of adenylylation. Fluorescence lifetimes and quantum yields have been determined for two fluorophores with wild-type and mutant GS. One fluorophore is epsilon-AMP adenylylated GS (at Tyr-397), and the other fluorophore is the intrinsic protein residue Trp-57. These experiments were conducted in order to detect possible intersubunit interactions between adenylyl groups and the neighboring Trp-57 to search for a role for the Trp-57 loop in the regulation of GS. The fluorescence due to epsilon-AMP of two adenylylated enzymes, wild-type GS and the W158F mutant, exhibits heterogeneous decay kinetics; the data adequately fit to a double exponential decay model with recovered average lifetime values of 18.2 and 2.1 ns, respectively. The pre-exponential factors range from 0.66 to 0.73 for the long lifetime component, at five emission wavelengths. The W57L-epsilon-AMP enzyme yields longer average lifetime values of 19.5 and 2.4 ns, and the pre-exponential factors range from 0.82 to 0.85 for the long lifetime component. An additional residue in the Trp-57 loop, Lys-58, has been altered and the K58C mutant enzyme has been adenylylated with epsilon-AMP on Tyr-397. Lys-58 is near the ATP binding site and may represent a link by which the adenylyl group controls the activity of GS. The fluorescence of epsilon-AMP-adenylylated K58C mutant GS is best described by a triple exponential decay with average recovered lifetime values of 19.9, 4.6, and 0.58 ns, with the largest fraction being the median lifetime component. Relative quantum yields of epsilon-AMP-Tyr-397 were measured in order to determine if static quenching occurs from adenine-indole stacking in the wild-type GS. The relative quantum yield of the epsilon-AMP-adenylylated W57L mutant is larger than the wild-type protein by the amount predicted from the difference in lifetime values: thus, no static quenching is evident.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- W M Atkins
- Department of Medicinal Chemistry, University of Washington, Seattle 98195
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Encinas MV, Rojas MC, Goldie H, Cardemil E. Comparative steady-state fluorescence studies of cytosolic rat liver (GTP), Saccharomyces cerevisiae (ATP) and Escherichia coli (ATP) phospho enol pyruvate carboxykinases. Biochim Biophys Acta 1993; 1162:195-202. [PMID: 8448184 DOI: 10.1016/0167-4838(93)90147-j] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Two members of the ATP-dependent class of phospho enol pyruvate (PEP) carboxykinases (Saccharomyces cerevisiae and Escherichia coli PEP carboxykinase), and one member of the GTP-dependent class (the cytosolic rat liver enzyme) have been comparatively analyzed by taking advantage of their intrinsic fluorescence. The S. cerevisiae and the rat liver enzymes show intrinsic fluorescence with a maximum emission characteristic of moderately buried tryptophan residues, while the E. coli carboxykinase shows somewhat more average exposure for these fluorophores. The fluorescence of the three proteins was similarly quenched by the polar compound acrylamide, but differences were observed for the ionic quencher iodide. For the ATP-dependent enzymes, these last experiments indicate more exposure to the aqueous media of the tryptophan population of the E. coli than of the S. cerevisiae enzyme. The effect of nucleotides on the emission intensities and quenching efficiencies revealed substrate-induced conformational changes in the E. coli and cytosolic rat liver PEP carboxykinases. The addition of Mn2+ or of the adenosine nucleotides in the presence of Mg2+ induced an enhancement in the fluorescence of the E. coli enzyme. The addition of guanosine or inosine nucleotides to the rat liver enzyme quenched its fluorescence. From the ligand-induced fluorescence changes, dissociation constants of 40 +/- 6 microM, 10 +/- 0.8 microM, and 15 +/- 1 microM were obtained for Mn2+, MgATP and MgADP binding to the E. coli enzyme, respectively. For the cytosolic rat liver PEP carboxykinase, the respective values for GDP, IDP and ITP binding are 6 +/- 0.5 microM, 6.7 +/- 0.4 microM and 10.1 +/- 1.7 microM. A comparison of the dissociation constants obtained in this work with those reported for other PEP carboxykinases is presented.
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Affiliation(s)
- M V Encinas
- Departamento de Química, Facultad de Ciencia, Universidad de Santiago de Chile
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23
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Giedroc DP, Khan R, Barnhart K. Site-specific 1,N6-ethenoadenylated single-stranded oligonucleotides as structural probes for the T4 gene 32 protein-ssDNA complex. Biochemistry 1991; 30:8230-42. [PMID: 1868096 DOI: 10.1021/bi00247a020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacteriophage T4 gene 32 protein (g32P) is a DNA replication accessory protein that binds single-stranded (ss) nucleic acids nonspecifically, independent of nucleotide sequence. G32P contains 1 mol of Zn(II)/mol of protein monomer, which can be substituted with Co(II), with maintenance of the structure and activity of the molecule. The Co(II) is coordinated via approximately tetrahedral ligand symmetry by three Cys sulfur atoms and therefore exhibits intense S(-)----Co(II) ligand to metal charge-transfer (LMCT) transitions in the near ultraviolet [Giedroc, D. P., et al. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 8452-8456]. A series of fluorescent 1,N6-ethenoadenosine (epsilon A)-containing oligonucleotides conforming to the structure (5'----3') d[(Tp)m epsilon A(pT)l-m-1] where 0 less than or equal to m less than or equal to l - 1 and length (l) six or eight nucleotides have been evaluated as dynamics probes and potential fluorescence energy transfer donors to Co(II) in mapping the spatial proximity of the (fixed) intrinsic metal ion and a variably positioned epsilon A-base in a series of protein-nucleic acid complexes. We provide spectroscopic evidence that the epsilon A-oligonucleotides bind to g32P-(A + B) with a fixed polarity of the phosphodiester chain. A Trp side chain(s) makes close approach to a epsilon A base positioned toward the 3' end of a bound l = 8 oligonucleotide. Six oligonucleotides of l = 8 and m = 0, 1, 3, 5, 6, or 7 were investigated as energy transfer donors to Co(II) at 0.1 M NaCl, pH 8.1, 25 degrees C upon binding to Co(II)-substituted or Zn(II) g32P-(A + B), i.e., in the presence and absence of an energy acceptor, respectively. Detectable quenching of the epsilon A-fluorescence by the Co(II)-LMCT acceptors was found to occur in all epsilon A-oligonucleotide-protein complexes, yielding energy transfer efficiencies (E) of 0.43, 0.31, 0.26, 0.26, 0.28, and 0.41 for l = 8 and m = 0, 1, 3, 5, 6, and 7 epsilon A-oligonucleotides, respectively. The two-dimensional distances R (in A) were found to vary as follows: d[epsilon A(pT)7] (m = 0), 16.0 (15.5-16.9); d[Tp epsilon A(pT)6] (m = 1), 17.7 (16.9-19.1); d[(Tp)3 epsilon A(pT)4] (m = 3), 20.7 (19.5-22.1); d[(Tp)5 epsilon A(pT)2] (m = 5), 20.5 (19.5-21.9); d[(Tp)6 epsilon ApT] (m = 6), 19.0 (18.0-20.4); and d[(Tp)7 epsilon A] (m = 7), 18.6 (17.8-19.8).(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- D P Giedroc
- Department of Biochemistry and Biophysics, Texas A&M University, College Station 77843-2128
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Young T, Kim ST, Van Camp JR, Hartman RF, Rose SD. Transient intermediates in intramolecularly photosensitized pyrimidine dimer splitting by indole derivatives. Photochem Photobiol 1988; 48:635-41. [PMID: 3241836 DOI: 10.1111/j.1751-1097.1988.tb02874.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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27
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Fu X, Phillips N, Jentoft J, Tuazon PT, Traugh JA, Leis J. Site-specific phosphorylation of avian retrovirus nucleocapsid protein pp12 regulates binding to viral RNA. Evidence for different protein conformations. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)39325-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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28
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Saito I, Sugiyama H, Matsuura T, Fukuyama K. Stacking interaction between tryptophan and uracil in a synthetic model compound. Tetrahedron Lett 1985; 26:4467-70. [DOI: 10.1016/s0040-4039(00)88932-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Ishida T, Matsui M, Inoue M, Hirano H, Yamashita M, Sugiyama K. Stacking interaction of indole ring with thiazolium ring and effect for H-D exchange reaction of thiamin. Biochem Biophys Res Commun 1983; 116:486-91. [PMID: 6651823 DOI: 10.1016/0006-291x(83)90549-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
As part of a program to clarify the possible binding mode of tryptophan with thiamin coenzyme, the interaction between the indole and thiazolium rings has been studied by using a model compound, 2-(3,4-dimethylthiazolium-5-)ethyl indole-3-propionate, and the prominent stacking formation between both rings has been evidenced by the spectroscopic and X-ray crystallographic methods. The faster H-D exchange reaction of thiamin C2 proton observed in the presence of indole than in the lack would be resulted from the pi-pi charge-transfer interaction between the indole ring and the thiazolium ring of thiamin.
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Ishida T, Usami H, Inoue M, Yamagata Y, Tomita KU. The stacking interaction in 9-(indole-3-propyl)-1-methyl adeninium iodide crystal, a model study on the interaction between tryptophan residue and adenine base in protein-nucleic acid interactions. Biochem Biophys Res Commun 1982; 107:746-51. [PMID: 7126238 DOI: 10.1016/0006-291x(82)91554-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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32
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Omar SB, Schleich T. Assessment of the exposure and environments of tryptophanyl residues in ribosomal protein S1 by fluorescence quenching. Biochemistry 1981; 20:6371-8. [PMID: 7030389 DOI: 10.1021/bi00525a014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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34
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Behr JP, Lehn JM. A Model for Nicotinamide-Trytophane Charge-Transfer Interactions: The complexation of nicotinamide-ammonium salts by a macrocyclic receptor molecule bearing tryptophane side chains. Helv Chim Acta 1980. [DOI: 10.1002/hlca.19800630737] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ishida T, Mitoguchi S, Miyamoto Y, Tomita KI, Inoue M. X-ray structural and conformational studies of [5'-(tryptaminocarbonyl)-2'-deoxyribofuranosyl]thymine, a model compound for the study of the interaction between indole and thymine rings. Biochim Biophys Acta 1980; 609:158-72. [PMID: 7407182 DOI: 10.1016/0005-2787(80)90209-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The crystal structure of [5'-(tryptaminocarbonyl)-2'-deoxyribofuranosyl]-thymine was determined by an X-ray method in order to elucidate a fundamental feature of interaction between indole and thymine rings. Refinement resulted in a conventional R value of 0.043. The bond lengths and angles are in good agreement with those of the related compounds. The deoxyribose unit has a C2'-endo envelope conformation, and orientation of the thymine base with respect to the sugar is anti. In the crystal, the double layers of the thymidine moieties are formed by the hydrogen bonds around a two-fold screw axis and a single layer of the indole moieties is held together by van der Waals contact, and they are alternately packed parallel to the bc-plane. The conformation of the molecule is an extended form, and the intra- and intermolecular interactions between the indole and thymine rings are not observed in the crystal because the dihedral angle of both rings is approximately a right angle (95.8 degrees), and there is no hydrogen bond or short contact between these rings. It was, however, suggested from the ultraviolet spectroscopic study in dilute solution and from the conformational analysis by energy calculation that the most stable conformation is a folded form with the intramolecular stacking interaction between indole and thymine rings. Therefore, the extended form observed in the crystal might be caused by the packing interaction between the neighboring molecules.
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LaPorte D, Builder S, Storm D. Spectroscopic studies of the cAMP binding sites of the regulatory subunits of types I and II protein kinase. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)85896-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Mildner B, Metz A, Chandra P. Interaction of 4'-6-diamidino-2-phenylindole to nucleic acids, and its implication to their template activity in RNA-polymerase reaction of E. coli bacteria and of Friend-virus infected mouse spleen. Cancer Lett 1978; 4:89-98. [PMID: 348301 DOI: 10.1016/s0304-3835(78)93687-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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38
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Abstract
Optically detected magnetic resonance (ODMR) signals of tryptophan (Trp) have been measured in L-lysyl-L-tryptophyl-L-lysine (Lys-Trp-Lys) and in its complex with poly(riboadenylic acid) [poly(rA)]. Measurements were made with optical narrow band detection through the Trp O-O band. Plots of [D] and [E] vs. lambda are distinctly different for Lys-Trp-Lys and its complex with poly(rA). A reduction of [D], in particular, is consistent with stacking of Trp with adenine in the complex, since this effect is expected from charge-transfer contributions in the excited triplet state. Triplet energy transfer from poly(rA) to Lys-Trp-Lys is nearly complete at 77 K, with a Trp:adenine ratio of 0.1. The energy transfer efficiency is considerably reduced at 4.2 K and below, probably resulting from reduction of the triplet mobility in the polymer. Analysis of the phosphorescence decays shows that the triplet states of poly(rA), Lys-Trp-Lys, and their complex decay nonexponentially. Binding of polylysine to poly(rA) has no effect on the phosphorescence spectrum, but the decay kinetics are changed.
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Chandra P, Mildner B, Dann O, Metz A. Influence of 4'-6'-diamidino-2-phenylindole on the secondary structure and template activities of DNA and polydeoxynucleotides. Mol Cell Biochem 1977; 18:81-6. [PMID: 604784 DOI: 10.1007/bf00280272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interaction between 4'-6-Diamidino-2-Phenylindole-hydrochloride (DAPI) and a variety of DNAs and synthetic polydeoxynucleotides was investigated in order to delineate the nucleic acid structural features necessary for binding. The spectra of DAPI-DNA complexes, measured at various DAPI:DNA molar ratios (r), are hypochromic relative to DNA in the region of its maximum absorption. All the curves pass through an isosbestic point at 268 nm. A new maxima appears in the region of 380-392 nm for DAPI-DNA COMplexes. The magnitude of the peaks in the region are directly proportional to the amount of drug present in the complex. Studies with various DNA types and synthetic polydeoxynucleotides indicate that the drug preferentially binds to dAT-rich regions of DNA. This was also confirmed by enzymatic studies. The inhibition of template action by DAPI in a purified DNA-polymerase reaction was dependent on the dAT-content of the template. The implication of these data to explain a selective binding of DAPI to mitochondrial DNA have been discussed.
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Mestelan G, Crouzel C, Comar D. Synthesis and distribution kinetics in animals of [alpha-11C] 3,4-dimethoxyphenethylamine. Int J Nucl Med Biol 1977; 4:185-93. [PMID: 608804 DOI: 10.1016/0047-0740(77)90138-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Domnina ES, Skvortsova GG, Voronkov MG. Charge-transfer complexes based on indole compounds (review). Chem Heterocycl Compd (N Y) 1977; 13:927-33. [DOI: 10.1007/bf00472439] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bierzynski A, Kozlowska H, Wierzchowski KL. Investigations on purine and pyrimidine bases stacking associations in aqueous solutions by the fluorescence quenching method. I. Autoassociation of 2-aminopurine. Biophys Chem 1977; 6:213-22. [PMID: 880337 DOI: 10.1016/0301-4622(77)85002-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A general equation was derived, describing fluorescence quantum yield and lifetime of an autoassociating compound in liquid solutions. The autoassociation of 2-aminopurine in aqueous solution was examined within the range from 0 to 90 degrees C. The compound seemed to associate cooperatively. The thermodynamic parameters of polymerization change with temperature, so that its free enthalypy deltaG = 0.0797 T2 + 45.4 T - 7893. The dimerization enthalpy and entropy are approximately temperature-independent (deltaH2 = -4.17 kcal/mol deltas2 = -10.9 e.u.), although the function: delta g2 = -0.0308T2 +30.3T - 7213 fits experimental points better. The observed dependences can be explained by the increasing role of the hydrophobic effect with temperature and size of the aggregates. The association rate constants were determined, and a two-step reaction mechanism was demonstrated. The first step is diffusion-controlled. The second is characterized by an activation energy of approximately 2 kcal/mol and an encounter distance of approximately 8.3 angstroms.
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Bierzyński A, Kollowska H, Proba Z, Wierzchowski KL. Investigations on purine and pyrimidine bases stacking associations in aqueous solutions by the fluorescence quenching method. III. Intramolecular association of 9,9'-[1,3-propylene]-bis-2-aminopurine. Biophys Chem 1977; 6:231-7. [PMID: 880339 DOI: 10.1016/0301-4622(77)85004-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
General equations relating fluorescence quantum yield and lifetime of a compound with its intramolecular stacking equilibrium and kinetics were derived. Intramolecular stacking association of 9,9'-[1,3-propylene]-bis-2-aminopurine in aqueous solution was examined within the range of temperatures from 0 to 90 degrees C. A two-state thermodynamic model of the association was verified. The stacking enthalpy and entropy can be taken, with a good approximation, as temperature-independent (deltaH equals - 2.0 kcal/mol, deltaS=-3.25 e.u.) although the function deltaG=-0.00886T2 + 8.847 T - 2876 describes more precisely the observed changes of stacking free enthalpy with temperature. The association rate constants were detemined. Activation energy of the reaction (2 kcal/mol) is the same as in the case of association between free 2-aminopurine molecules. It confirms a two-step mechanism of the process. The advantages and shortcomings of the fluorescence quenching method are discussed.
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Abstract
Fluorometric studies on the binding of benz[a]anthracene and benzo[a]pyrene to human serum albumin are described. The protein molecule appears to have one binding site for the hydrocarbons, but all of the sites on the protein are not fully occupied even in relatively large hydrocarbon concentrations. Equilibrium studies showed that both hydrocarbons bind to the protein to the same extent. Evidence for the energy transfer from the tryptophan residue of the protein to bound hydrocarbons is examined. By using Förster's theory, the mean distance between the tryptophan residue and bound ligand was found to be 15,2 A for benz[a]anthracene and 19.6 A for benzo[a]pyrene. It is concluded that the two hydrocarbons may bind to the same general area on the protein molecule near the tryptophan residue but at different sites. The structural differences of the hydrocarbons, which may greatly affect their orientations on the protein molecule, affect mainly the selection of the binding site rather than the binding equilibrium.
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Helene C. Mechanisms of Quenching of Aromatic Amino Acid Fluorescence in Protein-Nucleic Acid Complexes. In: Pullman B, Goldblum N, editors. Excited States in Organic Chemistry and Biochemistry. Dordrecht: Springer Netherlands; 1977. pp. 65-78. [DOI: 10.1007/978-94-010-1273-7_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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