The Experts below are selected from a list of 270 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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Local diffusive dynamics in DNA: A time-resolved fluorescence and molecular-dynamics study of dinucleotides with 2-Aminopurine
Journal of Luminescence, 2006Co-Authors: O J G Somsen, M. Niels De Keijzer, Arie Van Hoek, Gediminas Trinkunas, Herbert Van AmerongenAbstract:Abstract Fluorescent base analogues such as 2-Aminopurine report DNA dynamics on the scale of single bases. We find that the time-dependent fluorescence of various 2-Aminopurine-containing dinucleotides can be described by only two components: a fast (∼20 ps) exponential decay and a much slower (∼1 ns) stretched exponential. This is much simpler than previously proposed models. The fast component reflects quenching in the stacked equilibrium conformation. The slow stretched exponential indicates diffusive dynamics towards the equilibrium conformation. Depending on the dinucleotide, this migration effectively takes place in a one- or two-dimensional manifold. Molecular-dynamics simulations indicate that it involves twisting and sliding with parallel base planes. Our very simple representation of the data provides a powerful tool to study DNA fluorescence quenching and diffusive dynamics independently.
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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.
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Electronic states in 2-Aminopurine revealed by ultrafast transient absorption and target analysis
Chemical Physics Letters, 2003Co-Authors: O F A Larsen, Ivo H M Van Stokkum, Rienk Van Grondelle, Marie Louise Groot, John T. M. Kennis, Herbert Van AmerongenAbstract:Subpicosecond polarized transient-absorption measurements on the fluorescent adenine analogue 2-Aminopurine have been performed in the wavelength region from 320 to 690 nm. Global target analysis of the data reveals structural heterogeneity of the chromophore in the excited state. Two distinct states with remarkably different spectroscopic properties were resolved. One state does show stimulated emission, whereas the other state does not and exposes a very long excited-state lifetime.
Elmar G Weinhold - 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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2 Aminopurine as a fluorescent probe for dna base flipping by methyltransferases
Nucleic Acids Research, 1998Co-Authors: Birgit Holz, Saulius Klimasauskas, Saulius Serva, Elmar G WeinholdAbstract:DNA base flipping, which was first observed for the C5-cytosine DNA methyltransferase M. Hha I, results in a complete removal of the stacking interactions between the target base and its neighbouring bases. We have investigated whether duplex oligodeoxynucleotides containing the fluorescent base analogue 2-Aminopurine can be used to sense DNA base flipping. Using M. Hha I as a paradigm for a base flipping enzyme, we find that the fluorescence intensity of duplex oligodeoxynucleotides containing 2-Aminopurine at the target site is dramatically enhanced (54-fold) in the presence of M. Hha I. Duplex oligodeoxynucleotides containing 2-Aminopurine adjacent to the target cytosine show little fluorescence increase upon addition of M. Hha I. These results clearly demonstrate that duplex oligodeoxynucleotides containing 2-Aminopurine at the target site can serve as fluorescence probes for base flipping. Another enzyme hypothesized to use a base flipping mechanism is the N6-adenine DNA methyltransferase M. Taq I. Addition of M. Taq I to duplex oligodeoxynucleotides bearing 2-Aminopurine at the target position, also results in a strongly enhanced fluorescence (13-fold), whereas addition to duplex oligodeoxynucleotides containing 2-Aminopurine at the 3'- or 5'-neighbouring position leads only to small fluorescence increases. These results give the first experimental evidence that the adenine-specific DNA methyltransferase M. Taq I also flips its target base.
Tetsuro Majima - One of the best experts on this subject based on the ideXlab platform.
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detection of the g quadruplex tmpyp4 complex by 2 Aminopurine modified human telomeric dna
Chemical Communications, 2006Co-Authors: Takumi Kimura, Kiyohiko Kawai, Mamoru Fujitsuka, Tetsuro MajimaAbstract:2-Aminopurine (Ap) modified human telomere sequences were used to monitor the specific complex formation of the G-quadruplex and 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4).
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fluorescence properties of 2 Aminopurine in human telomeric dna
Chemical Communications, 2004Co-Authors: Takumi Kimura, Kiyohiko Kawai, Mamoru Fujitsuka, Tetsuro MajimaAbstract:The substitution of 2-Aminopurine (Ap) for A7 in the human telomeric sequence d[AGGG(TTAGGG)3] resulted in a significant increase in the fluorescence intensity of Ap for the conformational change from duplex to quadruplex.
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Fluorescence properties of 2-Aminopurine–cytidine–7-deazaguanine (5′-ApCdzG-3′) trimer in B- and Z-DNA
Chemical Communications, 2003Co-Authors: Takumi Kimura, Kiyohiko Kawai, Tetsuro MajimaAbstract:The electron transfer quenching of 2-Aminopurine by guanine and 7-deazaguanine was investigated in B- and Z-DNA, and an increase in the fluorescence intensity of 2-Aminopurine upon B- to Z-DNA transition was demonstrated.
Rajeev K Sinha - One of the best experts on this subject based on the ideXlab platform.
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switching on the fluorescence of 2 Aminopurine by site selective microhydration
Nature Chemistry, 2014Co-Authors: Simon Lobsiger, Rajeev K Sinha, Susan Blaser, Hansmartin Frey, Samuel LeutwylerAbstract:The adenine analogue 2-Aminopurine has been considered as intrinsically fluorescent and is widely used in biochemical assays to probe DNA and RNA structure. It is now shown that the molecule alone is nearly non-fluorescent, however, its fluorescence is increased by up to 95 times through hydrogen bonding to a single water molecule.
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isomer and species selective infrared spectroscopy of jet cooled 7h and 9h 2 Aminopurine and 2 Aminopurine h2o clusters
Journal of Physical Chemistry A, 2012Co-Authors: Rajeev K Sinha, Simon Lobsiger, Samuel LeutwylerAbstract:The infrared (IR) spectra of the supersonic-jet cooled 9H- and 7H-tautomers of 2-Aminopurine (2AP) and of the 9H-2-Aminopurine·H2O monohydrate clusters have been measured by mass- and species-selective IR-UV double resonance spectroscopy in the 3200–3900 cm–1 region, covering the N–H and O–H stretching vibrations. The spectra are complemented by density functional (B3LYP and PW91) and by second-order Moller–Plesset (MP2) calculations of the electronic energies and vibrational frequenciesof the respective 2AP tautomers and clusters. The 9H- and 7H-2-Aminopurine tautomers were definitively identified by the shifts of their NH and NH2 symmetric and asymmetric stretching frequencies and by comparison to the B3LYP/TZVP calculated IR spectra. The H-bond topologies of the two previously observed 9H-2-Aminopurine·H2O isomers (Sinha. R. K.; et al. J. Phys. Chem. A2011, 115, 6208) are definitively identified as the “sugar-edge” isomer A and the “trans-amino-bound” isomer B by comparing their IR spectra to the calcu...
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low lying excited states and nonradiative processes of the adenine analogues 7h and 9h 2 Aminopurine
Journal of Chemical Physics, 2011Co-Authors: Simon Lobsiger, Rajeev K Sinha, Maria Angela Trachsel, Samuel LeutwylerAbstract:We have investigated the UV vibronic spectra and excited-state nonradiative processes of the 7H- and 9H-tautomers of jet-cooled 2-Aminopurine (2AP) and of the 9H-2AP-d4 and -d5 isotopomers, using two-color resonant two-photon ionization spectroscopy at 0.3 and 0.045 cm−1 resolution. The S1 ← S0 transition of 7H-2AP was observed for the first time. It lies ∼ 1600 cm−1 below that of 9H-2AP, is ∼1000 times weaker and exhibits only in-plane vibronic excitations. In contrast, the S1 ← S0 spectra of 9H-2AP, 9H-2AP-d4, and 9H-2AP-d5 show numerous low-frequency bands that can be systematically assigned to overtone and combinations of the out-of-plane vibrations ν1′, ν2′, and ν3′. The intensity of these out-of-plane bands reflects an out-of-plane deformation in the 1ππ*(La) state. Approximate second-order coupled-cluster theory also predicts that 2-Aminopurine undergoes a “butterfly” deformation in its lowest 1ππ* state. The rotational contours of the 9H-2AP, 9H-2AP-d4, and 9H-2AP-d5 000 bands and of eight vibroni...
A. C. Borin - 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, 2020Co-Authors: Valdemir Ludwig, A. C. Borin, Marcos Serrou Do Amaral, Zelia Maria Da Costa, Sylvio Canuto, L. Serrano-andresAbstract:The minimum energy path along the lowest-lying pi pi* 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. (c) 2008 Elsevier B.V. All rights reserved.MEC [CTQ2007-61260]Consolider-Ingenio in Molecular Nanoscience [CSD2007-0010]Universitat de ValenciaFUNDECT-MSConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP
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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.
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adenine and 2 Aminopurine paradigms of modern theoretical photochemistry
Proceedings of the National Academy of Sciences of the United States of America, 2006Co-Authors: Luis Serranoandres, Martha Merchan, A. C. BorinAbstract:Distinct photophysical behavior of nucleobase adenine and its constitutional isomer, 2-Aminopurine, has been studied by using quantum chemical methods, in particular an accurate ab initio multiconfigurational second-order perturbation theory. After light irradiation, the efficient, ultrafast energy dissipation observed for nonfluorescent 9H-adenine is explained here by the nonradiative internal conversion process taking place along a barrierless reaction path from the initially populated 1(ππ* La) excited state toward a low-lying conical intersection (CI) connected with the ground state. In contrast, the strong fluorescence recorded for 2-Aminopurine at 4.0 eV with large decay lifetime is interpreted by the presence of a minimum in the 1(ππ* La) hypersurface lying below the lowest CI and the subsequent potential energy barrier required to reach the funnel to the ground state. Secondary deactivation channels were found in the two systems related to additional CIs involving the 1(ππ* Lb) and 1(nπ*) states. Although in 9H-adenine a population switch between both states is proposed, in 7H-adenine this may be perturbed by a relatively larger barrier to access the 1(nπ*) state, and, therefore, the 1(ππ* Lb) state becomes responsible for the weak fluorescence measured in aqueous adenine at ≈4.5 eV. In contrast to previous models that explained fluorescence quenching in adenine, unlike in 2-Aminopurine, on the basis of the vibronic coupling of the nearby 1(ππ*) and 1(nπ*) states, the present results indicate that the 1(nπ*) state does not contribute to the leading photophysical event and establish the prevalence of a model based on the CI concept in modern photochemistry.
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Adenine and 2-Aminopurine: Paradigms of modern theoretical photochemistry
Proceedings of the National Academy of Sciences, 2006Co-Authors: L. Serrano-andres, Martha Merchan, A. C. BorinAbstract:Distinct photophysical behavior of nucleobase adenine and its constitutional isomer, 2-Aminopurine, has been studied by using quantum chemical methods, in particular an accurate ab initio multiconfigurational second-order perturbation theory. After light irradiation, the efficient, ultrafast energy dissipation observed for nonfluorescent 9H-adenine is explained here by the nonradiative internal conversion process taking place along a barrierless reaction path from the initially populated 1(pipi* La) excited state toward a low-lying conical intersection (CI) connected with the ground state. In contrast, the strong fluorescence recorded for 2-Aminopurine at 4.0 eV with large decay lifetime is interpreted by the presence of a minimum in the 1(pipi* La) hypersurface lying below the lowest CI and the subsequent potential energy barrier required to reach the funnel to the ground state. Secondary deactivation channels were found in the two systems related to additional CIs involving the 1(pipi* Lb) and 1(npi*) states. Although in 9H-adenine a population switch between both states is proposed, in 7H-adenine this may be perturbed by a relatively larger barrier to access the 1(npi*) state, and, therefore, the 1(pipi* Lb) state becomes responsible for the weak fluorescence measured in aqueous adenine at approximately 4.5 eV. In contrast to previous models that explained fluorescence quenching in adenine, unlike in 2-Aminopurine, on the basis of the vibronic coupling of the nearby 1(pipi*) and 1(npi*) states, the present results indicate that the 1(npi*) state does not contribute to the leading photophysical event and establish the prevalence of a model based on the CI concept in modern photochemistry.
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Theoretical electronic spectra of 2-Aminopurine in vapor and in water
International Journal of Quantum Chemistry, 2006Co-Authors: A. C. Borin, L. Serrano-andres, Valdemir Ludwig, Kaline Coutinho, Sylvio CanutoAbstract:The accurate quantum chemical CASSCF and CASPT2 methods combined with a Monte Carlo procedure to mimic solvation effects have been used in the calculation of the spectroscopic properties of two tautomers of 2-Aminopurine (2AP). Absorption and emission spectra have been simulated both in vacuum and in aqueous environment. State and transition energies and properties have been obtained with high accuracy, leading to the assignment of the most important spectroscopic features. The lowest-lying 1 (,*) ( 1 La) state has been determined as responsible for the first band in the absorption spectrum and also for the strong fluorescence observed for the system in water. The combined approach used in the present work gives quantitatively accurate
