Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays
Adrian Keller,1,2† Jenny Rackwitz,3 Emilie Cauët,4 Jacques Liévin,4 Thomas Körzdörfer,3 Alexandru
Rotaru,5 Kurt V. Gothelf,1 Flemming Besenbacher,1 Ilko Bald1,3,6*
1
Interdisciplinary Nanoscience Center (iNANO) and Danish National Research Foundation: Centre for
DNA Nanotechnology (CDNA), Aarhus University, 8000 Aarhus C, Denmark
2
Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf,
Dresden, Germany
3
Institute of Chemistry – Physical Chemistry, University of Potsdam, Potsdam, Germany
4
Service de Chimie quantique et Photophysique, Université Libre de Bruxelles, 1050 Brussels, Belgium
5
Center of Advanced Research in Bionanoconjugates and Biopolymers, ‘‘Petru Poni’’ Institute of
Macromolecular Chemistry, 700487 Iasi, Romania
6
BAM Federal Institute of Materials Research and Testing, Berlin, Germany
*e-mail: ilko.bald@uni-potsdam.de
† present address: Technical and Macromolecular Chemistry, University of Paderborn, Paderborn,
Germany
1. Alternative DNA nanoarray design:
The DNA origami based DNA nanorray technique can also be used to compare three different
nucleotide sequences within one irradiation experiment. For this, we prepared triangular DNA
nanoarrays with the three 5-bromouracil (BrU) containing sequences TT(ABrUA)3TT, TT(CBrUC)3TT
and TT(GBrUG)3TT. To avoid recording the complete fluence dependence we have used σSSB of the
TT(GBrUG)3TT sequence as a reference, which we have determined in a previous experiment (see
main text). To distinguish the three different positions on the DNA origami triangle by AFM we
introduced an additional Bt-SAv marker, which rendered the DNA nanoarray asymmetric making an
identification of the three different oligonucleotide sequences possible. The σSSB values determined
after 18 eV electron irradiation are similar to the values reported above (must be recalculated!) and
confirm the reliability of the measurements and the method in general. A larger error has to be
accounted for the nanoarrays with three different sequences, since the number of analysed
structures was far less than for the nanoarrays shown in figure 1.
Figure S1: Alternative DNA origami design that allows for comparison of three different DNA
strands. (a) Scheme of triangular DNA origami platform with 9 protruding strands and an
asymmetric biotin marker for sequence identification. (b,c) AFM images of a control (b) and a
sample irradiated with 18 eV electrons (c). (d) Higher magnification of individual DNA origami
structures from the samples shown in (b) (top image) and (c) (lower image). (e) Absolute cross
sections for DNA single strand breaks inuced by 18 eV electrons (σSSB) for TT(YBrUY)3TT.
2. Comparison of theoretical methods (MP2 and GW):
In terms of the IP, there is one major difference between the MP2 and GW results. In GW, the IP
follows the clear trend T > C > A > G, both for T and BrU as the central units, with a difference in IP of
0.9 eV between T and G. This is not the case in the MP2 calculations, where ATA shows the lowest IP
of all XTX structures. Interestingly, changing the central unit T by BrU does not seem to play a major
role except for this particular structure for which the IP increases by 0.5 eV.
The use of single configuration approaches like MP2 and GW is conditioned by the fact that no
configuration mixing usually occurs around the stationary point geometries and that the ground state
is well separated energetically from the excited states of the system. However, the characterization
of excited states requires the use of a multiconfigurational treatment. To elucidate the particularity
of the results obtained for the ATA structure, we thus decided to calculate the IP of the ATA and GTG
structures using multi-configuration ab initio methods with the 6-311++G(d,p) basis set. All these
calculations have been achieved with the MOLPRO program suite. Complete active space selfconsistent field (CASSCF) calculations have been performed in which the molecular orbitals playing
an active role in the description of the ground and the first low-lying excited states of the structures
were optimized. A state-averaging procedure has been used to optimize a common molecular orbital
basis set describing the electronic states of the structures. Main configuration state functions (CSFs)
defining the low-lying states have been accounted for in a restricted active orbital space correlating a
minimal number of electrons. This space was defined by the two highest occupied molecular orbitals
(HOMO, and HOMO-1) and the two lowest unoccupied molecular orbitals (LUMO and LUMO+1), in
which three electrons were distributed to form the CASSCF wave functions. Because a significant
amount of computer time was required for variationally optimizing the (closed shell + active) orbitals,
we decided to freeze the lowest occupied molecular orbitals arising from the 1s and 2s orbitals of
oxygen, carbon, and nitrogen, which were optimized at the SCF level. In order to introduce the
remaining dynamical correlation, the CASSCF calculations have been followed by second-order
perturbation theory (CASPT2) calculations. The RS2 approach has been adopted in which 61 electrons
were correlated.
The CASPT2 IP values, calculated for GTG and ATA structures, are 7.06 and 6.96 eV, respectively. Let
us note that these values are smaller than the MP2 and GW ones. This difference corresponds to the
change in the number of correlated electrons. These results show that ATA has the lowest IP with a
difference in IP of 0.1 eV between ATA and GTG. The CASPT2 energy difference between the ground
and first excited states is 0.51 eV for the GTG structure while it is severely reduced for ATA; only 0.03
eV. This small difference suggests us that the energy of the ionic species obtained by a single
configuration approach could easily converge to the first excited state of the cation leading to an IP
value slightly larger.