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| 2. |
- Holm, Anne I. S., et al.
(författare)
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Electronic coupling between cytosine bases in DNA single strands and i-motifs revealed from synchrotron radiation circular dichroism experiments
- 2010
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 12:14, s. 3426-3430
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Tidskriftsartikel (refereegranskat)abstract
- In this work we have recorded synchrotron radiation circular dichroism (SRCD) spectra from 180 nm to 360 nm of cytosine strands [(dC)(n), n = 1, 2,..., 10] in aqueous solution at different pH values to reveal electronic coupling between bases in different ionisation states. The geometry of the strands is determined by the pH value and the strand length and the local organisation of the cytosines will determine the base-to-base interaction that impacts on the CD signal. At low pH where all bases are protonated, there is no signature of electronic coupling between the bases, and the SRCD spectrum is simply n times that of the n = 1 spectrum. At higher pH where all bases are neutral, the spectra for n > 1 differ from the monomer spectrum, which implies electronic coupling between bases. The correlation between the CD signal and n is linear, and the spatial extent of the excited state wavefunction is therefore over just two stacked bases both in the UV and VUV. At intermediate pH, the low-n spectra are different from the high-n spectra, and a transition is seen to occur at n = 6-8. We ascribe this behavior to the formation of i-motif structures between four (dC)(n) strands for high n.
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| 3. |
- Nielsen, Lisbeth Munksgaard, et al.
(författare)
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Effect of introducing thymine spacers into an adenine strand : Electronic decoupling?
- 2011
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Ingår i: Journal of Photochemistry and Photobiology A. - : Elsevier BV. - 1010-6030 .- 1873-2666. ; 220:1, s. 1-3
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Tidskriftsartikel (refereegranskat)abstract
- Electronic coupling between DNA bases governs the deexcitation pathways after light absorption as well as the ability of the DNA strand to conduct charge. UV excitation of single strands of adenine bases involves two adjacent bases while the spatial extent of the excited state wavefunction following VUV excitation is over eight bases. In this work, we have recorded synchrotron radiation circular dichroism spectra for a series of DNA strands on the form A(n)T(m)A(n), n = 1-5 and m = 1-3, in aqueous solution to study the effect of introducing thymine spacers on the electronic coupling between the adenines. We find that a single thymine spacer is enough to eliminate the strong coupling between the adenine bases for all excitation wavelengths between 175 nm and 330 nm.
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| 4. |
- Ashworth, Eleanor K., et al.
(författare)
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Complexation of Green and Red Kaede Fluorescent Protein Chromophores by a Zwitterion to Probe Electrostatic and Induction Field Effects
- 2022
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 126:7, s. 1158-1167
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Tidskriftsartikel (refereegranskat)abstract
- The photophysics of green fluorescent protein (GFP) and red Kaede fluorescent protein (rKFP) are defined by the intrinsic properties of the light-absorbing chromophore and its interaction with the protein binding pocket. This work deploys photodissociation action spectroscopy to probe the absorption profiles for a series of synthetic GFP and rKFP chromophores as the bare anions and as complexes with the betaine zwitterion, which is assumed as a model for dipole microsolvation. Electronic structure calculations and energy decomposition analysis using Symmetry-Adapted Perturbation Theory are used to characterize gas-phase structures and complex cohesion forces. The calculations reveal a preponderance for coordination of betaine to the phenoxide deprotonation site predominantly through electrostatic forces. Calculations using the STEOM-DLPNO-CCSD method are able to reproduce absolute and relative vertical excitation energies for the bare anions and anion–betaine complexes. On the other hand, treatment of the betaine molecule with a point-charge model, in which the charges are computed from some common electron density population analysis schemes, show that just electrostatic and point-charge induction interactions are unable to account for the betaine-induced spectral shift. The present methodology could be applied to investigate cluster forces and optical properties in other gas-phase ion–zwitterion complexes.
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| 5. |
- Holm, Anne I. S., et al.
(författare)
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Synchrotron Radiation Circular Dichroism of Various G-Guadruplex Structures
- 2010
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 93:5, s. 429-433
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Tidskriftsartikel (refereegranskat)abstract
- Here we report synchrotron radiation circular dichroism spectra of various G-quadruplexes from 179 to 350 nm, and a number of bands in the vacuum ultraviolet (VUV) are reported for the first time. For a tetramolecular parallel structure, the strongest band in the spectrum is a negative band in the VUV at 182 nm; for a bimolecular antiparallel structure with diagonal loops, a new strong positive band is found at 190 nm; for a bimolecular parallel structure with edgewise loops, a strong positive band at 189 nm is observed; and for a self-folded chair-type structure, the strongest band in the spectrum is a positive band at 187 nm. For the tetramolecular parallel structure, the CD signals at all wavelengths are dominated by contributions from quartets of G bases, and the signal strength is approximately proportional to the number of quartets. Our experiments on well-characterized G-quadruplex structures lead us to question past attributions of CD signals to helix handedness and G quartet polarity. Although differences can be observed in the VUV region for the various quadruplex types, there do not appear to be clear-cut spectral features that can be used to identify specific topological features. It is suggested that this is because a dominant positive band in the VUV seen near 190 nm in all quadruplex structures is due to intrastrand guanine guanine base stacking. However, our spectra can serve as reference spectra for the G-quadruplex structures investigated and, not least, to benchmark theoretical calculations and empirical models.
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| 6. |
- Kelly, Orla, et al.
(författare)
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Effects of Charge Location on the Absorptions and Lifetimes of Protonated Tyrosine Peptides in Vacuo
- 2012
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 116:7, s. 1701-1709
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Tidskriftsartikel (refereegranskat)abstract
- Nearby charges affect the electronic energy levels of chromophores, with the extent of the effect being determined by the magnitude of the charge and degree of charge-chromophore separation. The molecular configuration dictates the charge chromophore distance. Hence, in this study, we aim to assess how the location of the charge influences the absorption of a set of model protonated and diprotonated peptide ions, and whether spectral differences are large enough to be identified. The studied ions were the dipeptide YK, the tripeptide KYK (Y = tyrosine; K = lysine) and their complexes with 18-crown-6-ether (CE). The CE targets the ammonium group by forming internal ionic hydrogen bonds and limits the folding of the peptide. In the tripeptide, the distance between the chromophore and the backbone ammonium is enlarged relative to that in the dipeptide. Experiments were performed in an electrostatic ion storage ring using a tunable laser system, and action spectra based on lifetime measurements were obtained in the range from 210 to 310 nm. The spectra are all quite similar though there seems to be some changes in the absorption band between 210 and 250 nm, while in the lower energy band all ions had a maximum absorption at similar to 275 nm. Lifetimes after photoexcitation were found to shorten upon protonation and lengthen upon CE complexation, in accordance with the increased number of degrees of freedom and an increase in activation energies for dissociation as the mobile proton model is no longer operative.
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| 7. |
- Stockett, Mark H., et al.
(författare)
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Photophysics of Isolated Rose Bengal Anions
- 2020
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 124:41, s. 8429-8438
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Tidskriftsartikel (refereegranskat)abstract
- Dye molecules based on the xanthene moiety are widely used as fluorescent probes in bioimaging and technological applications due to their large absorption cross-section for visible light and high fluorescence quantum yield. These applications require a clear understanding of the dye's inherent photophysics and the effect of a condensed-phase environment. Here, the gas-phase photophysics of the rose bengal doubly deprotonated dianion [RB - 2H](2-), deprotonated monoanion [RB - H](-), and doubly deprotonated radical anion [RB - 2H](center dot-) is investigated using photodetachment, photoelectron, and dispersed fluorescence action spectroscopies, and tandem ion mobility spectrometry (IMS) coupled with laser excitation. For [RB - 2H](2-), photodetachment action spectroscopy reveals a clear band in the visible (450-580 nm) with vibronic structure. Electron affinity and repulsive Coulomb barrier (RCB) properties of the dianion are characterized using frequency-resolved photoelectron spectroscopy, revealing a decreased RCB compared with that of fluorescein dianions due to electron delocalization over halogen atoms. Monoanions [RB - H](-) and [RB 2H](center dot-) differ in nominal mass by 1 Da but are difficult to study individually using action spectroscopies that isolate target ions using low-resolution mass spectrometry. This work shows that the two monoanions are readily distinguished and probed using the IMSphoto-IMS and photo-IMS-photo-IMS strategies, providing distinct but overlapping photodissociation action spectra in the visible spectral range. Gas-phase fluorescence was not detected from photoexcited [RB - 2H](2-) due to rapid electron ejection. However, both [RB - H](-) and [RB - 2H](center dot-) show a weak fluorescence signal. The [RB - H](-) action spectra show a large Stokes shift of similar to 1700cm(-1), while the [RB - 2H](center dot-) action spectra show no appreciable Stokes shift. This difference is explained by considering geometries of the ground and fluorescing states.
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