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2 Aminopurine

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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 2Aminopurine
    Journal of Luminescence, 2006
    Co-Authors: O J G Somsen, M. Niels De Keijzer, Arie Van Hoek, Gediminas Trinkunas, Herbert Van Amerongen

    Abstract:

    Abstract Fluorescent base analogues such as 2Aminopurine report DNA dynamics on the scale of single bases. We find that the time-dependent fluorescence of various 2Aminopurine-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 2Aminopurine Fluorescence in Dinucleotides
    ChemPhysChem, 2005
    Co-Authors: O J G Somsen, Linda B. Keukens, M. Niels De Keijzer, Arie Van Hoek, Herbert Van Amerongen

    Abstract:

    The fluorescent base analogue 2Aminopurine 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 2Aminopurine 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 duplexes
    Physical Chemistry Chemical Physics, 2004
    Co-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 Amerongen

    Abstract:

    Ultrafast transient-absorption and steady-state fluorescence measurements have been performed on dinucleotides comprising the fluorescent adenine analogue 2Aminopurine and guanine, adenine, cytosine, thymine or hypoxanthine, respectively. Two oligodeoxyribonucleotide duplexes that were site-selectively substituted with a single 2Aminopurine 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 2Aminopurine (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 fluorescence
    Journal of the American Chemical Society, 2007
    Co-Authors: Thomas Lenz, Robert K Neely, Anita C Jones, David T F Dryden, Eleanor Y M Bonnist, Goran Pljevaljcic, Axel J Scheidig, Elmar G Weinhold

    Abstract:

    We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2Aminopurine, 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 2Aminopurine in DNA, and 2Aminopurine is subject to considerable quenching by π-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2Aminopurine 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 methyltransferases
    Nucleic Acids Research, 1998
    Co-Authors: Birgit Holz, Saulius Klimasauskas, Saulius Serva, Elmar G Weinhold

    Abstract:

    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 2Aminopurine 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 2Aminopurine at the target site is dramatically enhanced (54-fold) in the presence of M. Hha I. Duplex oligodeoxynucleotides containing 2Aminopurine adjacent to the target cytosine show little fluorescence increase upon addition of M. Hha I. These results clearly demonstrate that duplex oligodeoxynucleotides containing 2Aminopurine 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 2Aminopurine at the target position, also results in a strongly enhanced fluorescence (13-fold), whereas addition to duplex oligodeoxynucleotides containing 2Aminopurine 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 dna
    Chemical Communications, 2006
    Co-Authors: Takumi Kimura, Kiyohiko Kawai, Mamoru Fujitsuka, Tetsuro Majima

    Abstract:

    2Aminopurine (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 dna
    Chemical Communications, 2004
    Co-Authors: Takumi Kimura, Kiyohiko Kawai, Mamoru Fujitsuka, Tetsuro Majima

    Abstract:

    The substitution of 2Aminopurine (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 2Aminopurine–cytidine–7-deazaguanine (5′-ApCdzG-3′) trimer in B- and Z-DNA
    Chemical Communications, 2003
    Co-Authors: Takumi Kimura, Kiyohiko Kawai, Tetsuro Majima

    Abstract:

    The electron transfer quenching of 2Aminopurine by guanine and 7-deazaguanine was investigated in B- and Z-DNA, and an increase in the fluorescence intensity of 2Aminopurine upon B- to Z-DNA transition was demonstrated.