Scan Science and Technology
Contact Leading Edge Experts & Companies
The Experts below are selected from a list of 270 Experts worldwide ranked by ideXlab platform
Herbert Van Amerongen – 1st expert on this subject based on the ideXlab platform
Local diffusive dynamics in DNA: A time-resolved fluorescence and molecular-dynamics study of dinucleotides with 2–AminopurineJournal 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.
Structural Heterogeneity in DNA: Temperature Dependence of 2‐Aminopurine Fluorescence in DinucleotidesChemPhysChem, 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.
ultrafast transient absorption and steady state fluorescence measurements on 2 Aminopurine substituted dinucleotides and 2 Aminopurine substituted dna duplexesPhysical 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.
Elmar G Weinhold – 2nd expert on this subject based on the ideXlab platform
2 Aminopurine flipped into the active site of the adenine specific dna methyltransferase m taqi crystal structures and time resolved fluorescenceJournal of the American Chemical Society, 2007Co-Authors: Thomas Lenz, Robert K Neely, Anita C Jones, David T F Dryden, 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…
2 Aminopurine as a fluorescent probe for dna base flipping by methyltransferasesNucleic 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 – 3rd expert on this subject based on the ideXlab platform
detection of the g quadruplex tmpyp4 complex by 2 Aminopurine modified human telomeric dnaChemical 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).
fluorescence properties of 2 Aminopurine in human telomeric dnaChemical 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.
Fluorescence properties of 2–Aminopurine–cytidine–7-deazaguanine (5′-ApCdzG-3′) trimer in B- and Z-DNAChemical 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.