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Pandey MP, Sasidharan S, Raghunathan VA, Khandelia H. Molecular Mechanism of Hydrotropic Properties of GTP and ATP. J Phys Chem B 2022; 126:8486-8494. [PMID: 36251789 DOI: 10.1021/acs.jpcb.2c06077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hydrotropes are small amphiphilic compounds that increase the aqueous solubility of hydrophobic molecules. Recent evidence suggests that adenosine triphosphate (ATP), which is the primary energy carrier in cells, also assumes hydrotropic properties to prevent the aggregation of hydrophobic proteins, but the mechanism of hydrotropy is unknown. Here, we compare the hydrotropic behavior of all four biological nucleoside triphosphates (NTPs) using molecular dynamics (MD) simulations. We launch all atom MD simulations of aqueous solutions of NTPs [ATP, guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP)] with pyrene, which acts both as a model hydrophobic compound and as a spectroscopic reporter for aggregation. GTP prevents pyrene aggregation effectively. Dissolution is not achieved in the presence of CTP and UTP. The higher stability of the base stacking in guanine is responsible for the higher hydrotropic efficiency of GTP. Consistent with the simulations, spectroscopic measurements also suggest that the hydrotropic activity of GTP is higher than ATP. Stacking of aromatic pyrene with the aromatic base of NTPs is a characteristic feature of this hydrotropic property. Both ATP and GTP also dissolve clusters of di- and tripeptides containing tryptophan but with equal potency. Importantly, the presence of aromatic amino acids is a necessary condition for the hydrotropic potency of ATP and GTP. Our results can have broad implications for hydrotrope design in the pharmaceutical industry, as well as the possibility of cells employing GTP as a hydrotrope to regulate the hydrophobic protein aggregation in membrane-less biological condensates.
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Affiliation(s)
- Mayank Prakash Pandey
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense5230, Denmark
| | | | | | - Himanshu Khandelia
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense5230, Denmark
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Garo F, Häner R. A DNA-based light-harvesting antenna. Angew Chem Int Ed Engl 2011; 51:916-9. [PMID: 22162263 DOI: 10.1002/anie.201103295] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 10/18/2011] [Indexed: 12/20/2022]
Affiliation(s)
- Florian Garo
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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Akbay N, Seferoğlu Z, Gök E. Fluorescence interaction and determination of calf thymus DNA with two ethidium derivatives. J Fluoresc 2009; 19:1045-51. [PMID: 19557506 DOI: 10.1007/s10895-009-0504-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 06/05/2009] [Indexed: 10/20/2022]
Abstract
In this paper, we reported the syntheses and investigation of the modes of binding to DNA of the two new ethidium derivatives containing benzoyl and phenylacetyl groups of both amines at 3-and 8- positions. The interactions between calf thymus DNA (ct-DNA) and the two derivatives, 3,8-dibenzoylamino-5-ethyl-6-phenylphenantridinium cloride (E2) and 3,8-diphenylacetylamino-5-ethyl-6-phenylphenantridinium chloride (E3), were investigated by fluorescence quenching spectra and UV-vis absorption spectra. The Stern-Volmer quenching constants, binding constants, binding sites and the corresponding thermodynamic parameters DeltaH, DeltaS and DeltaG were calculated at different temperatures. The results indicated the formation of E2 and E3-DNA complexes and van der Waals interactions as the predominant intermolecular forces in stabilizing for each complex. In addition, increasing nucleophilicity of the functional groups at 3- and 8- positions exhibited the respectable increment the DNA binding affinities of derivatives. The results of absorption, ionic strength and iodide ion quenching suggested that the interaction mode of E2 and E3 with ct-DNA was intercalative binding. The limit of detection (LOD) of ct-DNA were 7.49 x 10(-8) (n = 4) and 4.18 x 10(-8) mol/l (n = 7) in presence of E2 and E3, respectively.
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Affiliation(s)
- Nuriye Akbay
- Department of Chemistry, Hacettepe University, 06800 Beytepe, Ankara, Turkey
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Cuomo F, Palazzo G, Ceglie A, Lopez F. Quenching efficiency of pyrene fluorescence by nucleotide monophosphates in cationic micelles. J Photochem Photobiol A Chem 2009. [DOI: 10.1016/j.jphotochem.2008.10.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Lopez F, Cuomo F, Ceglie A, Ambrosone L, Palazzo G. Quenching and dequenching of pyrene fluorescence by nucleotide monophosphates in cationic micelles. J Phys Chem B 2008; 112:7338-44. [PMID: 18503268 DOI: 10.1021/jp8003344] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fluorescence behavior of pyrene solubilized in the hexadecyltrimethylammonium bromide aqueous micellar solution in the presence of adenosine 5'-monophosphate (AMP) and uridine 5'-monophosphate (UMP) was investigated. AMP and UMP were found to influence oppositely the fluorescence of micellized pyrene. UMP acts as quencher, while AMP acts as dequencher. Both effects saturate at high nucleotide concentration (about 40 mM). Dequenching of micellized pyrene fluorescence is induced also by addition of disodium hydrogen orthophosphate (Na 2HPO 4), while loading with sodium bromide (NaBr) quenches the fluorescence. Furthermore, in absence of micelles, pyrene fluorescence depends on the UMP, according to the Stern-Volmer relation, but is unaffected by AMP. Dynamic light scattering experiments showed that the size and shape of aggregates is not affected by different types of nucleotide loaded into the solution; thus, we conclude that the opposite photophysical effect exploited by AMP and UMP are uncorrelated to any change in micellar microstructure. The whole fluorescence data set was successfully accounted for by assuming that the anionic nucleotides compete with the surfactant counterion (bromide) for the surface of the micelle. Accordingly, substitution of bromide with the more effective quencher UMP results in a strong decrease of the pyrene fluorescence, while the substitution of bromide with the nonquencher AMP results in an increase in the pyrene fluorescence.
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Affiliation(s)
- Francesco Lopez
- Consorzio Interuniversitario per lo sviluppo dei Sistemi a Grande Interfase (CSGI), c/o Department of Food Technology (DISTAAM), University of Molise, I-86100 Campobasso, Italy.
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Bichenkova EV, Savage HE, Sardarian AR, Douglas KT. Target-assembled tandem oligonucleotide systems based on exciplexes for detecting DNA mismatches and single nucleotide polymorphisms. Biochem Biophys Res Commun 2005; 332:956-64. [PMID: 15913549 DOI: 10.1016/j.bbrc.2005.05.048] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Accepted: 05/10/2005] [Indexed: 11/15/2022]
Abstract
We report the first exciplex-based split-probe system for DNA detection. The detector is split at a molecular level into signal-silent components which, before a signal is generated, must be assembled correctly into a particular three-dimensional arrangement. The model system comprises of two 8-mer oligonucleotides, complementary to neighbouring sites of a 16-mer DNA target, each equipped with moieties able to form an exciplex on correct, contiguous hybridization. The exciplex emits at approximately 480 nm with a large Stokes shift (135 nm). The extremely rigorous structural demands for exciplex formation and emission were achieved by careful structural design and by the discovery that high levels of certain organic solvents (especially trifluoroethanol) specifically favour emission of the DNA-mounted exciplex, probably the net result of the particular duplex structure and specific solvation of the exciplex partners. Inserts and mismatches can be effectively detected by this exciplex construct giving potential for single nucleotide polymorphism detection.
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Affiliation(s)
- Elena V Bichenkova
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester M13 9PL, UK
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Heinlein T, Knemeyer JP, Piestert O, Sauer M. Photoinduced Electron Transfer between Fluorescent Dyes and Guanosine Residues in DNA-Hairpins. J Phys Chem B 2003. [DOI: 10.1021/jp0348068] [Citation(s) in RCA: 195] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas Heinlein
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Jens-Peter Knemeyer
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Oliver Piestert
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Markus Sauer
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
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Brodkorb A, Kirsch-De Mesmaeker A, Rutherford T, Keene F. Stereoselective Interactions and Photo-Electron Transfers between Mononucleotides or DNA and the Stereoisomers of a HAT-Bridged Dinuclear RuII Complex (HAT = 1,4,5,8,9,12-hexaazatriphenylene). Eur J Inorg Chem 2001. [DOI: 10.1002/1099-0682(200108)2001:8<2151::aid-ejic2151>3.0.co;2-m] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Rogers JE, Kelly LA. Nucleic Acid Oxidation Mediated by Naphthalene and Benzophenone Imide and Diimide Derivatives: Consequences for DNA Redox Chemistry. J Am Chem Soc 1999. [DOI: 10.1021/ja9841299] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Widengren J, Dapprich J, Rigler R. Fast interactions between Rh6G and dGTP in water studied by fluorescence correlation spectroscopy. Chem Phys 1997. [DOI: 10.1016/s0301-0104(97)00014-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Tuite E, Kelly JM. The interaction of methylene blue, azure B, and thionine with DNA: Formation of complexes with polynucleotides and mononucleotides as model systems. Biopolymers 1995. [DOI: 10.1002/bip.360350502] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Geacintov NE, Zhao R, Kuzmin VA, Kim SK, Pecora LJ. Mechanisms of quenching of the fluorescence of a benzo[a]pyrene tetraol metabolite model compound by 2'-deoxynucleosides. Photochem Photobiol 1993; 58:185-94. [PMID: 8415908 DOI: 10.1111/j.1751-1097.1993.tb09547.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The hydrophobic interactions of bulky polycyclic aromatic hydrocarbons with nucleic acid bases and the formation of noncovalent complexes with DNA are important in the expressions of the mutagenic and carcinogenic potentials of this class of compounds. The fluorescence of the polycyclic aromatic residues can be employed as a probe of these interactions. In this work, the interactions of the (+)-trans stereoisomer of the tetraol 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (BPT), a hydrolysis product of a highly mutagenic and carcinogenic diol epoxide derivative of benzo[a]pyrene, were studied with 2'-deoxynucleosides in aqueous solution by fluorescence and UV spectroscopic techniques. Ground-state complexes between BPT and the purine derivatives 2'-deoxyguanosine (dG), 2'-deoxyadenosine (dA), and 2'-deoxyinosine (dI) are formed with association constants in the range of approximately 40-130 M(-1). Complex formation with the pyrimidine derivatives 2'-deoxythymidine (dT), 2'-deoxycytidine (dC), and 2'-deoxyuridine (dU) is significantly weaker. Whereas dG is a strong quencher of the fluorescence of BPT by both static and dynamic mechanisms (dynamic quenching rate constant k(DYN) = [2.5 +/- 0.4] x 10(9) M(-1)s(-1), which is close to the estimated diffusion-controlled value of approximately 5 x 10(9) M(-1)s(-1), both dA and dI are weak quenchers and form fluorescence-emitting complexes with BPT. The pyrimidine derivatives dC, dU, and dT are efficient dynamic fluorescence quenchers (k(DYN) approximately [1.5-3.0] x 10(9) M (-1)s(-1), with a small static quenching component due to complex formation evident only in the case of dT. None of the four nucleosides dG, dA, dC and dT are dynamic quenchers of BPT in the triplet excited state; the observed lower yields of triplets are attributed to the quenching of single excited states of BPT by 2'-deoxynucleosides without passing through the triplet manifold of BPT. Possible fluorescence quenching mechanisms involving photoinduced electron transfer are discussed. The strong quenching of the fluorescence of BPT by dG, dC and dT accounts for the low fluorescence yields of BPT-native DNA and of pyrene-DNA complexes.
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Affiliation(s)
- N E Geacintov
- Chemistry Department, New York University, New York, NY 10003
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Slama-Schwok A, Jazwinski J, Béré A, Montenay-Garestier T, Rougée M, Hélène C, Lehn JM. Interactions of the dimethyldiazaperopyrenium dication with nucleic acids. 1. Binding to nucleic acid components and to single-stranded polynucleotides and photocleavage of single-stranded oligonucleotides. Biochemistry 1989; 28:3227-34. [PMID: 2742835 DOI: 10.1021/bi00434a017] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The binding of dimethyldiazaperopyrenium dication (1) with nucleosides, nucleotides, and single-stranded polynucleotides has been studied by photophysical methods. It has been shown that 1 may be a potential selective fluorescent probe for A- and/or T-rich polynucleotides. 1 efficiently cleaves oligonucleotides at guanine sites, under illumination with visible light, and therefore may be used as a sequence-specific artificial photonuclease.
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Affiliation(s)
- A Slama-Schwok
- Chimie des Interactions Moléculaires, Collège de France, Paris
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Abramovich M, Prakash AS, Harvey RG, Zegar IS, Lebreton PR. A comparison of the intercalative binding of non-reactive benzo[a]pyrene metabolites and metabolite model compounds to DNA. Chem Biol Interact 1985; 55:39-62. [PMID: 3933843 DOI: 10.1016/s0009-2797(85)80119-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The reversible DNA physical binding of a series of non-reactive metabolites and metabolite model compounds derived from benzo[a]pyrene (BP) has been examined in UV absorption and in fluorescence emission and fluorescence lifetime studies. Members of this series have steric and pi electronic properties similar to the highly carcinogenic metabolite trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) and the less potent metabolite 4,5-epoxy-4,5-dihydrobenzo(a)pyrene (4,5-BPE). The molecules examined are trans-7,8-dihydroxy-7,8-dihydrobenzo[a]-pyrene (7,8-di(OH)H2BP), 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (tetrol) 7,8,9,10-tetrahydrobenzo[a]pyrene (7,8,9,10-H4BP), pyrene, trans-4,5-dihydroxy-4,5-dihydrobenzo[a]pyrene (4,5-di(OH)H2BP) and 4,5-dihydrobenzo[a]pyrene (4,5-H2BP). In 15% methanol at 23 degrees C the intercalation binding constants of the molecules studied lie in the range 0.79-6.1 X 10(3) M-1. Of all the molecules examined the proximate carcinogen 7,8-di(OH)-H2BP is the best intercalating agent. The proximate carcinogen has a binding constant which in UV absorption studies is found to be 2.8-6.0 times greater than that of the other hydroxylated metabolites. Intercalation is the major mode of binding for 7,8-di(OH)H2BP and accounts for more than 95% of the total binding. Details concerning the specific role of physical bonding in BP carcinogenesis remain to be elucidated. However, the present studies demonstrate that the reversible binding constants for BP metabolites are of the same magnitude as reversible binding constants which arise from naturally occurring base-base hydrogen bonding and pi stacking interactions in DNA. Furthermore, previous autoradiographic studies indicate that in human skin fibroblasts incubated in BP, pooling of the unmetabolized hydrocarbons occurs at the nucleus. The high affinity of 7,8-di(OH)H2BP for DNA may play a role in similarly elevating in vivo nuclear concentrations of the non-reactive proximate carcinogen.
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Sharifian HA, Pyun CH, Jiang FB, Park SM. Interactions of several polycyclic aromatic hydrocarbons with DNA base molecules studied by absorption spectroscopy and fluorescence quenching. ACTA ACUST UNITED AC 1985. [DOI: 10.1016/0047-2670(85)85027-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Mantooth D, Georghiou S. Complex formation between ethidium bromide and the nucleotides AMP and GMP. Photochem Photobiol 1983; 38:623-6. [PMID: 6316377 DOI: 10.1111/j.1751-1097.1983.tb03393.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Fick J, Lawaczeck R, Schneider FW. Fluorescence of intramolecular and intermolecular interactions of aminonaphthyl-sulfonate with nucleotides. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 126:367-72. [PMID: 7128595 DOI: 10.1111/j.1432-1033.1982.tb06789.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Fluorescence studies of the intramolecular and intermolecular interactions between aminonaphthylsulfonate and nucleotides of uracil or adenine are described. The fluorescence originates solely from the naphthyl moiety and is intramolecularly quenched by the base, uracil being more effective than adenine. The enzymatic splitting of the molecule into a nucleoside monophosphate and the pyrophosphate product of the aminonaphthylsulfonate removes the intramolecular quenching and, especially in the case of uracil, a drastic increase of the fluorescence intensity results. The intact molecule exists predominantly in the folded form except in cases where electrostatic repulsion exceeds the stacking attraction. This is borne out by the pH dependence and the existence of a pronounced solvent-isotope effect of the fluorescence quantum yield for the uracil derivative at basic pH. At pH values above the pK of the enol proton of the uracil base the fluorescent properties of the intact and phosphodiesterase-digested molecules are very similar. The intermolecular interactions between 1-aminonaphthalene-5-sulfonate with AMP and UMP can be explained on the basis of dynamic quenching (collisional quenching) without any significant participation of ground-state complexes (static quenching). The interaction of the pyrophosphate adduct of 1-aminonaphthalene-5-sulfonate with UMP can best be explained by invoking two interacting nucleotide species: the free nucleotide and a sodium-nucleotide complex.
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