The Experts below are selected from a list of 219 Experts worldwide ranked by ideXlab platform
Herbert Van Amerongen - One of the best experts on this subject based on the ideXlab platform.
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Structural Heterogeneity in DNA: Temperature Dependence of 2‐Aminopurine Fluorescence in Dinucleotides
ChemPhysChem, 2005Co-Authors: O J G Somsen, Linda B. Keukens, M. Niels De Keijzer, Arie Van Hoek, Herbert Van AmerongenAbstract:The fluorescent base analogue 2-Aminopurine is a sensitive probe for local dynamics of DNA. Its fluorescence is quenched by interaction with the neighboring bases, but the underlying mechanisms are still under investigation. We studied 2-Aminopurine fluorescence in dinucleotides with each of the natural bases. Consistently, two of the four fluorescence-decay components depend strongly on temperature. Our results indicate that these components are due to the excited-state dynamics of a single conformational state. We propose a variation of the gating model in which transient unstacking occurs in the excited state.
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ultrafast transient absorption and steady state fluorescence measurements on 2 Aminopurine substituted dinucleotides and 2 Aminopurine substituted dna duplexes
Physical Chemistry Chemical Physics, 2004Co-Authors: O F A Larsen, Ivo H M Van Stokkum, Frank L De Weerd, Mikas Vengris, Charuvila T Aravindakumar, Rienk Van Grondelle, Nicholas E Geacintov, Herbert Van AmerongenAbstract:Ultrafast transient-absorption and steady-state fluorescence measurements have been performed on dinucleotides comprising the fluorescent adenine analogue 2-Aminopurine and guanine, adenine, cytosine, thymine or hypoxanthine, respectively. Two oligodeoxyribonucleotide duplexes that were site-selectively substituted with a single 2-Aminopurine moiety were also studied. A strong quenching of the steady-state fluorescence was observed in all samples. The transient-absorption spectra were remarkably similar to those of the isolated 2-Aminopurine (Larsen et al.; O. F. A. Larsen, I. H. M. van Stokkum, M.-L. Groot, J. T. M. Kennis, R. van Grondelle and H. van Amerongen, Chem. Phys. Lett., 2003, 371, 157–163), exhibiting both a fluorescent and a non-fluorescent excited state. There was no evidence for significant amounts of charge-separated states in the transient-absorption spectra. The probability that an excitation of 2AP leads to stable charge transfer products was estimated to be very low (∼0.1%). In the systems we studied, the observed fluorescence quenching can largely be explained by a shift of the equilibrium between the two excited states in 2AP, in which the non-fluorescent state is favored.
David T F Dryden - One of the best experts on this subject based on the ideXlab platform.
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2 Aminopurine flipped into the active site of the adenine specific dna methyltransferase m taqi crystal structures and time resolved fluorescence
Journal of the American Chemical Society, 2007Co-Authors: Thomas Lenz, Robert K Neely, David T F Dryden, Anita C Jones, Eleanor Y M Bonnist, Goran Pljevaljcic, Axel J Scheidig, Elmar G WeinholdAbstract:We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-Aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short (∼50 ps) lifetime component associated with fully base-stacked 2-Aminopurine in DNA, and 2-Aminopurine is subject to considerable quenching by π-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-Aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the propo...
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evidence of tautomerism in 2 Aminopurine from fluorescence lifetime measurements
Journal of Physical Chemistry B, 2004Co-Authors: Robert K Neely, Steven W Magennis, David T F Dryden, Anita C JonesAbstract:The fluorescence decay characteristics of 2-Aminopurine (2AP) and 2-Aminopurine riboside (2APr) have been investigated as a function of excitation and emission wavelength in aqueous and ethanolic solutions. Global analysis of the decay data shows that 2AP exists as two emitting species, whereas 2APr exists as a single species. This is attributed to 9H/7H tautomerism of 2AP. The proportion of 7H tautomer is estimated to be 20% in ethanol and 40% in water.
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unusual 2 Aminopurine fluorescence from a complex of dna and the ecoki methyltransferase
Nucleic Acids Research, 2004Co-Authors: Tsueuju Su, Bernard A Connolly, C Darlington, R Mallin, David T F DrydenAbstract:The methyltransferase, M.EcoKI, recognizes the DNA sequence 5¢-AACNNNNNNGTGC-3¢ and methylates adenine at the underlined positions. DNA methylation has been shown by crystallography to occur via a base flipping mechanism and is believed to be a general mechanism for all methyltransferases. If no structure is available, the fluorescence of 2-Aminopurine is often used as a signal for base flipping as it shows enhanced fluorescence when its environment is perturbed. We find that 2-Aminopurine gives enhanced fluorescence emission not only when it is placed at the M.EcoKI methylation sites but also at a location adjacent to the target adenine. Thus it appears that 2-Aminopurine fluorescence intensity is not a clear indicator of base flipping but is a more general measure of DNA distortion. Upon addition of the cofactor S-adenosylmethionine to the M.EcoKI:DNA complex, the 2Aminopurine fluorescence changes to that of a new species showing excitation at 345 nm and emission at 450 nm. This change requires a fully active enzyme, the correct cofactor and the 2-Aminopurine located at the methylation site. However, the new fluorescent species is not a covalently modified form of 2-Aminopurine and we suggest that it represents a hitherto undetected physicochemical form of 2-Aminopurine.
Thomas W Conway - One of the best experts on this subject based on the ideXlab platform.
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2 Aminopurine inhibits the double stranded rna dependent protein kinase both in vitro and in vivo
Journal of interferon research, 1993Co-Authors: Yinghe Hu, Thomas W ConwayAbstract:ABSTRACT The autophosphorylation of interferon (IFN)-induced double-stranded RNA-dependent p68 protein kinase (PKR) and phosphorylation of the α-subunit of the translation initiation factor eIF-2 were inhibited by 10 mM 2-Aminopurine in vitro. High concentrations of ATP overcame the inhibition. Kinetic studies indicated that 2-Aminopurine is a competitive inhibitor with respect to ATP, suggesting that these two molecules bind the same site on the kinase. Treatment of HeLa cells with poly(I):poly(C) stimulated PKR autophosphorylation in vivo. The stimulated activity was inhibited by 10 mM 2-Aminopurine to approximately the same extent as the in vitro inhibition.
Luis Serranoandres - One of the best experts on this subject based on the ideXlab platform.
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2 Aminopurine non radiative decay and emission in aqueous solution a theoretical study
Chemical Physics Letters, 2008Co-Authors: Valdemir Ludwig, A. C. Borin, Marcos Serrou Do Amaral, Zelia Maria Da Costa, Sylvio Canuto, Luis SerranoandresAbstract:Abstract The minimum energy path along the lowest-lying ππ ∗ excited state of 2-Aminopurine was calculated to elucidate the mechanisms of radiationless decay and emission in water. The sequential Monte Carlo quantum mechanics approach with a multiconfigurational and perturbative description of the wave function was employed to compute the minimum, transition state, and conical intersection. It was found that the barrier in the potential energy surface to access the conical intersection funnel increases in aqueous environment, making the system prone to enlarge the emission yield. These results rationalize the observed enhancement of emission in 2-Aminopurine upon increasing of the solvent polarity.
Olha O Brovarets - One of the best experts on this subject based on the ideXlab platform.
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whether 2 Aminopurine induces incorporation errors at the dna replication a quantum mechanical answer on the actual biological issue
Journal of Biomolecular Structure & Dynamics, 2017Co-Authors: Olha O Brovarets, Horacio PerezsanchezAbstract:In this paper, we consider the mutagenic properties of the 2-Aminopurine (2AP), which has intrigued molecular biologists, biophysicists and physical chemists for a long time and been widely studied...
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ir vibrational spectra of h bonded complexes of adenine 2 Aminopurine and 2 Aminopurine with cytosine and thymine quantum chemical study
Optics and Spectroscopy, 2011Co-Authors: Olha O Brovarets, D M HovorunAbstract:Using theoretical study on the B3LYP/6-311++G(d,p) level of theory, we have compared vibrational spectra of 2-Aminopurine (as neutral or protonated at N1 atom species) with adenine and H-bonded complexes of 2-Aminopurine (as neutral or protoned at N1 atom species) · cytosine or 2-Aminopurine · thymine with adenine · cytosine and adenine · thymine base pairs. The nature of the base pairing between adenine, 2-Aminopurine, 2-Aminopurine+ and cytosine or thymine have been investigated by means of quantum-mechanical calculations. We have investigated the effect of the hydrogen bond formation on the vibrational spectra of the investigated base pairs. The main differences in the vibrational spectra as for bases so for base pairs have been observed in the high-frequency region.
