Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Ultrafast spectroscopy on 2-aminopurine DNA oligonucleotides provides new insights into mechanism of fluorescence quenching
    Larsen, O.F.A. ; Somsen, O.J.G. ; Stokkum, I.H.M. van; Weerd, F.L. de; Vengris, M. ; Aravindakumar, C.T. ; Grondelle, R. van; Geacintov, N.E. ; Amerongen, H. van - \ 2004
    Biophysical Journal 86 (2004)1. - ISSN 0006-3495 - p. 312a - 312a.
    Ultrafast transient-absorption and steady-state fluorescence measurements on 2-aminopurine substituted dinucleotides and 2-aminopurine substituted DNA duplexes
    Larsen, O.F.A. ; Stokkum, I.H.M. van; Weerd, F.L. de; Vengris, M. ; Aravindakumar, C.T. ; Grondelle, R. van; Geacintov, N.E. ; Amerongen, H. van - \ 2004
    Physical Chemistry Chemical Physics 6 (2004)1. - ISSN 1463-9076 - p. 154 - 160.
    electron-transfer - energy-transfer - charge-transfer - dynamics - base - oligonucleotides - photoionization - spectroscopy - nucleotides - conversion
    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
    Wanorde en stroomgeleidende eigenschappen van DNA
    Larsen, O.F.A. ; Amerongen, H. van - \ 2003
    Nederlands Tijdschrift voor Natuurkunde 69 (2003)11. - ISSN 0926-4264 - p. 348 - 351.
    Electronic states in 2-aminopurine revealed by ultrafast transient absoprtion and target analysis
    Larsen, O.F.A. ; Stokkum, I.H.M. van; Groot, M.L. ; Kennis, J.T.M. ; Grondelle, R. van; Amerongen, H. van - \ 2003
    Chemical Physics Letters 371 (2003)1-2. - ISSN 0009-2614 - p. 157 - 163.
    energy-transfer - dna - dynamics - fluorescence - bases - oligonucleotides - photoionization - distance
    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
    Ultrafast polarized fluorescence measurements on Tryptophan and a Tryptophan-containing peptide
    Larsen, O.F.A. ; Stokkum, I.H.M. van; Pandit, A. ; Grondelle, R. van; Amerongen, H. van - \ 2003
    The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 107 (2003). - ISSN 1520-6106 - p. 3080 - 3085.
    conformational dynamics - excited-state - alpha-helix - hiv-1 rev - proteins - indole - decay - rna - depolarization - spectroscopy
    In this work polarized picosecond fluorescence measurements were performed on isolated tryptophan and tryptophan in a small 22-mer peptide using a streak camera coupled to a spectrograph as a detection system. In both cases the fluorescence decay was multiexponential with decay times of similar to500 ps, and similar to4 ns. Surprisingly, also a short-lived (similar to16 ps) isotropic fluorescence component was found for both tryptophan and the peptide which, to our knowledge. has never been observed before. Fluorescence anisotropy data showed rotational correlation times of 155 ps and 1.5 ns for the peptide, reflecting local and overall peptide dynamics, respectively. Recently it was argued [Lakowicz. J. R. Photochem. Photobiol. 2000, 72, 421] that the nonexponential fluorescence decay of tryptophan in proteins is mainly due to spectral relaxation, whereas for isolated tryptophan it is due to different rotamers. Our results do not support this view. In contrast we conclude in both cases that the different fluorescence decay times should be ascribed to different rotameric states.
    Ultrafast polarized fluorescence measurements on monomeric and self-associated melittin
    Pandit, A. ; Larsen, O.F.A. ; Stokkum, I.H.M. van; Grondelle, R. van; Kraayenhof, R. ; Amerongen, H. van - \ 2003
    The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 107 (2003). - ISSN 1520-6106 - p. 3086 - 3090.
    conformational dynamics - secondary structure - energy-transfer - tryptophan - protein - decay - refinement - excitation - anisotropy - parameters
    The anisotropic and magic-angle fluorescence decay of the single tryptophan (Trp) residue of melittin, a bee venom peptide, was investigated by time-resolved fluorescence anisotropy using a streak camera setup. The peptide was dissolved either in distilled water or in Hepes/NaOH buffer containing low (10 mM) or high (2 M) concentrations of NaCl, the latter resulting in tetramerized melittin. For melittin in distilled water and low NaCl concentration, two anisotropy decay times were found in the order of similar to50 and similar to800 picoseconds, reflecting, local and overall peptide dynamics, respectively, and for tetramerized melittin, two anisotropy decay times of similar to200 and similar to5500 picoseconds were found. Decay-associated spectra of the isotropic fluorescence decay show three time components in the range of similar to20 picoseconds, similar to500 picoseconds, and similar to3500 picoseconds, respectively. The relative amplitudes of the latter two change upon the self-association of melittin. This change can be explained by the existence of different rotamers of Trp in melittin, of which one is more favored in the melittin tetramer than in the melittin monomer.
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