10.Thu.D.4.pdf
Ultrafast Phenomena 2014 © 2014 OSA
Photoinduced charge transfer occurs naturally in DNA
D. B. Bucher1,2, B. M. Pilles1, T. Carell2 and W. Zinth1
1 BioMolecular Optics and Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538
Munich (Germany)
2 Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13,
81377 Munich (Germany)
Abstract: We show by femtosecond IR spectroscopy that excited states in oligonucleotides
decay with high yields by charge transfer to delocalized charged radicals. For the 6-4 lesion,
charge transfer protects the DNA from Dewar formation.
1. Introduction
Charge transfer in DNA has been extensively investigated in the past decade for special DNA constructs [1].
Mainly motivated by DNA electronics or by trying to understand oxidative damage, the molecular mechanism
was investigated by photoinduced charge injection [2]. In many experiments, excitation of artificial DNA bases
or intercalating chromophores initiated the charge transport, which was followed by time resolved UV/Visspectroscopy.
Recently, we could directly show by UV-pump/IR-probe spectroscopy that photoinduced charge transfer is also
an inherent process in natural DNA strands. We observe long-living charge separated states in high yields in
oligonucleotides after photo-excitation. This is in strong contrast to the situation found in single nucleotides,
where the excited state decays ultrafast to the ground state, thus impeding photochemical damage formation.
Base stacking in the biologically important oligonucleotides opens a new decay channel, which generates charge
separated states. The charge is delocalized along stacked domains and recombines on the 100 ps time scale. The
formation of reactive charged radicals along DNA strands might induce chemical reactions – such as damage
formation or repair - currently not considered in DNA photochemistry. Charge transfer is not only observed in
intact DNA strands. Excitation of the 6-4 chromophore, a photolesion between two adjacent pyrimidines,
normally leads with high yields to the Dewar-lesion, a secondary photoproduct in DNA [3]. Our time-resolved
experiments show that Dewar formation is efficiently quenched in stranded DNA by charge transfer with a
neighboring base.
In all of these ultrafast experiments, we took advantage of the fingerprint spectra in the mid IR which enables us
not only to distinguish between different nucleobases, but also to identify the charge transfer states.
Fig. 1. A) Selective excitation of mC in the trinucleotide mCAU leads to a bleach of all three bands (see marker bands) which recovers on a
100 ps time scale. B) Decay spectra of the 100 ps living states of the dinucleotide mCU shows characteristic positive marker bands, which
can be assigned to the mC-cation (bottom).
10.Thu.D.4.pdf
Ultrafast Phenomena 2014 © 2014 OSA
2. Results and Discussion
The investigated oligonucleotides contain three nucleobases, 2’-deoxyuridine (U), 2’-deoxyadenosine (A), 5methyl-2’deoxycytidine (mC). The red shifted absorbance of mC in comparison to A and U allows selective
excitation with UV-light at 295 nm. In the IR, the contribution of each base in the excited state can be deduced
from characteristic marker bands at 1625 cm-1 (A), 1655 cm-1 (U) and 1667 cm-1 (mC). This approach is
illustrated by using the trinucleotide mCAU (Fig. 1A). Although mC is selectively excited, the U and even the A
bands show a ground state bleach, which recovers on a timescale of 100 ps (Fig. 1A, bottom). This process is not
observable in a mixture of the single nucleobases and is thus a direct consequence of the base stacking in the
oligonucleotides.
In simple dinucleotides we find direct evidence of the molecular nature of these states: The decay associated
·+
spectra of mCU dinucleotide show marker bands which can be assigned to radical cation spectra of mC
(Fig.1B) [4]. Investigation of several different dinucleotides shows that light excitation leads to charge
separation, which is directed by the redox potential of the involved nucleobases. The negative charge moves to
the nucleobase with a higher redox potential and the charges recombine on a time scale of 100 ps. This chargeseparated state is not only located on two neighboring bases but on all three bases.
It can be seen in Fig. 1A that all three bases of mCAU bleach instantaneously. Therefore a charge transfer via a
hopping mechanism can be excluded since it would occur on a much slower time scale. Obviously, the charge is
delocalized over a well stacked domain along the DNA strand. We thus propose the following model (Fig. 2A):
Excitation of a nucleobase in a DNA
strand with stacked bases leads ultrafast
to the charge separated state. The
direction of charge transfer is governed
by the redox potential and is thus
encoded in the DNA sequence. These
ionic
states
decay
by
charge
recombination on the 100 ps time scale
reforming the neutral ground-state.
Fig. 2. A) Model for the excited state decay in DNA oligonucleotides (X is a
natural nucleobase), the charge distribution depends on the sequence. B) Model
for the quenching of the excited state of the 6-4 chromophore by charge
transfer processes
We observe a similar process after
excitation of the 6-4 chromophore in
single and double stranded DNA. The 64 lesion has a characteristic absorbance
band in the UV-A regime at 325 nm
which allows selective excitation. Upon
the decay of the excited state we find
contributions from a guanine, which is in
direct neighborhood of the 6-4 lesion.
Apparently the excited state of the 6-4
lesion is quenched by charge transfer.
This process reduces the quantum yield
of Dewar formation and thus protects the
DNA (Fig. 2B).
3. Conclusion
With the help of time resolved IR-spectroscopy experiments we were able show that charge separation in DNA
plays an important role in natural systems and is major decay channel of photoexcited DNA oligonucleotides.
The identification of radical cation and anionic species after light absorption of DNA adds a new dimension to
DNA photochemistry, which have been known before only from artificial systems.
References
[1] J. C. Genereux and J. K. Barton, “Mechanisms for DNA Charge Transport”, Chem. Rev. 110, 1642-1662 (2010).
[2] H. A.Wagenknecht, “Principles and Mechanisms of Photoinduced Charge Injection, Transport, and Trapping in DNA” in Charge
transfer in DNA (Wiley-VCH, Weinheim, 2005), Chap. 1.
[3] K. Haiser, B. P. Fingerhut, K. Heil, A. Glas, T. T. Herzog, B. M. Pilles, W. J. Schreier, W. Zinth, R. de Vivie-Riedle, T. Carell,
“Mechanism of UV-Induced Formation of Dewar Lesions in DNA”, Angew. Chem. Int. Ed. 51, 408-411 (2012).
[4] D. B. Bucher, B. M. Pilles, T. Pfaffender, T. Carell, W. Zinth, ”Fingerprinting DNA oxidation process: IR characterization of the 5Methyl-2'-deoxycytidine radical cation”, ChemPhysChem, doi:DOI: 10.1002/cphc.201300954 (2014).