Photophysics of 1-ethynylpyrene-modified RNA base adenine

Förster, Ute; Gildenhoff, Nina; Grünewald, Christian; Engels, Joachim W.; Wachtveitl, Josef

doi:10.1016/j.jlumin.2009.03.033

Cited by 18 publications

(27 citation statements)

References 15 publications

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“…Those spectra were taken for a total of 4 protic and 5 aprotic solvents (data not shown) covering a broad range of polarity. The spectral characteristics in MeOH are similar to those reported for PyA introduced in RNA strands dissolved in buffer [7] and of a silyl-protected derivate of PyA in MeOH [3]. A global analysis revealed that four time constants are necessary for a sufficient description of both data sets.…”

Section: Resultssupporting

confidence: 68%

“…A G-C base pair leads to the intercalation of PyA, whereas A-U base pairs do not show this behavior. To get a further understanding of the processes, the photophysical properties of PyA were investigated with femtosecond pump-probe absorption spectroscopy and time correlated single photon counting (TCSPC) [6,7]. PyA showed the existence of a locally excited (LE) state with sequence dependent lifetimes around 400 ps and presumably a relaxed S1 state with a lifetime around 2 ns.…”

Section: Introductionmentioning

confidence: 99%

“…For the data analysis the solvent background along with the coherent artifact was subtracted and corrected for group velocity dispersion [9]. The quantitative analysis was performed employing a kinetic model describing the data as a sum of exponential decays [7]. …”

Section: Introductionmentioning

confidence: 99%

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Photophysical processes of the spectroscopic RNA probe 2-(1-ethynylpyrene)-adenosine (PyA)

Trojanowski

Plötner

Grünewald

et al. 2013

EPJ Web of Conferences

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Abstract. We examine the photoinduced excited state dynamics of pyrene modified adenosine, a versatile probe for folding and hybridization of ribonucleic acids. Measurements in different solvents revealed complex ultrafast dynamics, but high robustness since the overall fluorescence quantum yield ( f ) is hardly affected. The result is a strong fluorescent RNA-probe whose spectral properties change in a defined way upon environmental changes.

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Section: Resultssupporting

confidence: 68%

Section: Introductionmentioning

confidence: 99%

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Photophysical processes of the spectroscopic RNA probe 2-(1-ethynylpyrene)-adenosine (PyA)

Trojanowski

Plötner

Grünewald

et al. 2013

EPJ Web of Conferences

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show abstract

“…[32,43,46] These strong changes have been attributed to strong coupling of the dye to the base; this results in an intramolecular exciplex with an at least partial charge transfer from the pyrene to the adenine. [15,[47][48][49][50] The strength of this exciplex coupling is strongly dependent on the attachment site of the pyrene to the base. [51] The varying strength of emission for the selected duplexes already indicates strong changes in the pyrene environment depending on the base sequence.…”

Section: Fluorescence Spectramentioning

confidence: 99%

2‐(1‐Ethynylpyrene)‐Adenosine as a Folding Probe for RNA—Pyrene in or out

et al. 2010

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A series of short RNA duplexes containing one or two 1-ethynylpyrene-modified adenine bases was synthesised. The melting behaviour of these duplexes was examined by monitoring temperature-dependent pyrene fluorescence. In the singly modified RNA duplexes, the bases flanking the ethynylpyrene-rA were varied to examine the sequence specificity of the fluorescence change of pyrene upon RNA hybridisation. Because an increase in pyrene fluorescence upon melting of the duplex can be correlated with intercalation of pyrene, and a decrease is usually associated with the position of pyrene outside the strand, a relationship between the flanking bases and the tendency of the dye to intercalate has been established. It was found that pyrene intercalation is less likely to take place if the modified base is flanked only by A-U base pairs. Flanking G-C base pairs, even only in the 5'-direction of the modified base, will favour intercalation. In addition, we examined a doubly modified compound that had a pyrene located on each strand. The spectra indicated that the two pyrenes were close enough for interaction. Upon melting of the strand, a fluorescence blue shift corresponding to the dissociation of the pyrene-pyrene complex could be observed in addition to the intensity effect already known from the singly modified compounds. Two melting curves based on the different properties of the fluorophore could be extracted, leading to different melting points corresponding to the global duplex melting and to the change of local pyrene environment, respectively.

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“…The upconverted light was spatially filtered, passed through a double monochromator (Jobin Yvon Gemini-180), and detected by a single-photon counting detector and a TCSPC counting card (Becker & Hickl, MSA-1000) operating as a gated photon counter (see ref. [59] for details). The experiment was adjusted to an upconversion wavelength of 320 nm, which corresponded to a fluorescence wavelength of 520 nm.…”

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confidence: 99%

The Photocycle of Channelrhodopsin‐2: Ultrafast Reaction Dynamics and Subsequent Reaction Steps

et al. 2010

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The photocycle of channelrhodopsin-2 is investigated in a comprehensive study by ultrafast absorption and fluorescence spectroscopy as well as flash photolysis in the visible spectral range. The ultrafast techniques reveal an excited-state decay mechanism analogous to that of the archaeal bacteriorhodopsin and sensory rhodopsin II from Natronomonas pharaonis. After a fast vibrational relaxation of the excited-state population with 150 fs its decay with mainly 400 fs is observed. Hereby, both the initial all-trans retinal ground state and the 13-cis-retinal K photoproduct are populated. The reaction proceeds with a 2.7 ps component assigned to cooling processes. Small spectral shifts are observed on a 200 ps timescale. They are attributed to conformational rearrangements in the retinal binding pocket. The subsequent dynamics progresses with the formation of an M-like intermediate (7 and 120 μs), which decays into red-shifted states within 3 ms. Ground-state recovery including channel closing and reisomerization of the retinal chromophore occurs in a triexponential manner (6 ms, 33 ms, 3.4 s). To learn more about the energy barriers between the different photocycle intermediates, temperature-dependent flash photolysis measurements are performed between 10 and 30°C. The first five time constants decrease with increasing temperature. The calculated thermodynamic parameters indicate that the closing mechanism is controlled by large negative entropy changes. The last time constant is temperature independent, which demonstrates that the photocycle is most likely completed by a series of individual steps recovering the initial structure.

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Photophysics of 1-ethynylpyrene-modified RNA base adenine

Cited by 18 publications

References 15 publications

Photophysical processes of the spectroscopic RNA probe 2-(1-ethynylpyrene)-adenosine (PyA)

Photophysical processes of the spectroscopic RNA probe 2-(1-ethynylpyrene)-adenosine (PyA)

2‐(1‐Ethynylpyrene)‐Adenosine as a Folding Probe for RNA—Pyrene in or out

The Photocycle of Channelrhodopsin‐2: Ultrafast Reaction Dynamics and Subsequent Reaction Steps

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