Dynamics of ultraviolet-induced DNA lesions: Dewar formation guided by pre-tension induced by the backbone

Fingerhut, Benjamin P.; Herzog, Teja T.; Ryseck, Gerald; Haiser, Karin; Graupner, Franziska F.; Heil, Korbinian; Gilch, Peter; Schreier, Wolfgang; Carell, Thomas; Vivie‐Riedle, Regina de

doi:10.1088/1367-2630/14/6/065006

Cited by 27 publications

(38 citation statements)

References 69 publications

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“…The question is then whether it originates from the 64PP that does absorb here. The absorption spectrum of 64PP has a band at 325 nm , in contrast to T n and T<>T. A very close look at our absorption data reveals that the absorbance at 325 nm actually increases although the band is vanishingly small as is evident from Fig. a.…”

Section: Resultssupporting

confidence: 59%

On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA

Baggesen

Hoffmann

Nielsen

2013

Photochem & Photobiology

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Solar light leads to thymine dimers that are mutagenic and primary cause of skin cancer. Here, we report absorption and synchrotron radiation circular dichroism (CD) spectra of Tn single strands with different number n of bases (n = 2-7, 10, 11) recorded after various 254 nm irradiation times. From a principal component analysis of the CD spectra, we extract fingerprint spectra of both the cyclobutane pyrimidine dimer (CPD) and the pyrimidine (6-4) pyrimidone photoadduct (64PP). Extending the CD measurements to the vacuum ultraviolet region in combination with systematic examinations of size effects is a new approach to gain insight on the dimeric photoproducts. We find a simple linear correlation between n and average number of dimers formed after 1 h of irradiation. The probability for a thymine to engage in a dimer increases from 32% for n = 2 to 41% for n = 11, which implies limited effects of terminal thymines, i.e., the reaction does not occur preferentially at the extremities of the single strands as previously stated. It is even possible to form two dimers with only two bridging thymines. Finally, experiments conducted on calf thymus DNA provided a similar signature of the photodimer, but differences are also evident.

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Section: Resultssupporting

confidence: 59%

On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA

Baggesen

Hoffmann

Nielsen

2013

Photochem & Photobiology

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“…This allows to resolve transient reaction intermediates 29–31 , obtain structural details 32 and thus ultimately resolve the reaction mechanism 3,4,33,34 . The UV-Pump - IR-Probe technique has been proven to be a valuable direct probe for complex photoreactions by allowing to identify the real time reaction mechanism leading to the formation of photolesions in DNA nucleobases 3,4,34,35 and other photoreactions 30,31,33,36 .…”

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confidence: 99%

Monitoring Nonadiabatic Dynamics of the RNA Base Uracil by UV Pump–IR Probe Spectroscopy

Fingerhut

Dorfman

Mukamel

2013

J. Phys. Chem. Lett.

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Resolving the excited state dynamics of DNA- and RNA- nucleobases has attracted considerably attention. UV irradiation of the isolated nucleobases leads to the population of an electronic excited state which is quenched by internal conversion mediated by conical intersections on an ultrafast timescale. We present non-adiabatic on-the-fly molecular dynamics simulations of the UV-pump-IR-probe signal of the pyrimidine nucleobase uracil using a novel semiclassical protocol which takes into account the path integral over the excited state vibrational dynamics and properly describes the joint temporal and spectral resolution of the technique. Simulations of vibrational motions of carbonyl fingerprint modes in the electronically excited states reveal clear signatures of different relaxation pathways on a timescale of hundreds of femtoseconds which arise from an ultrafast branching in the excited state. We show that the inherent temporal and spectral resolution of the technique is not purely instrumental but also depends on the vibrational fluctuation timescale.

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“…The DADS of Figure 3, parts b and e, also show contributions from a bleach of the (6−4)-state, indicating that the corresponding short-living state involves the simultaneous excitation of the bases (G and/or C) and the (6−4)-chromophore. 6 and Fingerhut et al 10,11 The model is depicted schematically in Scheme 2 on the right part. For the dimer Tc(6−4)T, the initial excitation of the Franck−Condon region (state (6−4)* FC ) is followed by a rapid relaxation on the excited state potential energy surface toward the minimum (state (6−4)* rel ), where the system resides for about 130 ps.…”

Section: Articlementioning

confidence: 99%

Dewar Lesion Formation in Single- and Double-Stranded DNA is Quenched by Neighboring Bases

2015

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UV-induced Dewar lesion formation is investigated in single- and double-stranded oligonucleotides with ultrafast vibrational spectroscopy. The quantum yield for the conversion of the (6-4) lesion to the Dewar isomer in DNA strands is reduced by a factor of 4 in comparison to model dinucleotides. Time resolved spectroscopy reveals a fast process in the excited state with spectral characteristics of bases which are adjacent to the excited (6-4) lesion. These kinetic components have large amplitudes and indicate that an additional quenching channel acts in the stranded DNA systems and reduces the Dewar formation yield. Presumably relaxation evolves via a charge transfer to the neighboring guanine and the paired cytosine participates in a double-stranded oligomer. Changes in the decay of the relaxed excited electronic state of the (6-4) chromophore point to modifications in the excited state energy landscape which may lead to an additional reduction of the Dewar formation yield.

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Dynamics of ultraviolet-induced DNA lesions: Dewar formation guided by pre-tension induced by the backbone

Cited by 27 publications

References 69 publications

On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA

On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA

Monitoring Nonadiabatic Dynamics of the RNA Base Uracil by UV Pump–IR Probe Spectroscopy

Dewar Lesion Formation in Single- and Double-Stranded DNA is Quenched by Neighboring Bases

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