Modulation of Excess Electron Transfer through LUMO Gradients in DNA Containing Phenanthrenyl Base Surrogates

Article abstract of DOI:10.1002/chem.201605846

The modulation of excess electron transfer (EET) within DNA containing a dimethylaminopyrene (C-AP) as an electron donor and 5-bromouracil (^BrdU) as an electron acceptor through phenanthrenyl pairs (phen-R) could be achieved by modifying the phenanthrenyl base surrogates with electron withdrawing and donating groups. Arranging the phenanthrenyl units to form a descending LUMO gradient increased the EET efficiency compared to the electron transfer through uniform LUMOs or an ascending LUMO gradient.

Full text of DOI:10.1002/chem.201605846

DOI: 10.1002/chem.201605846
Communication
&
DNA Modification |Hot Paper|
Modulation of Excess Electron Transfer through LUMO Gradients
in DNA Containing Phenanthrenyl Base Surrogates
Pascal Roethlisberger, Veerabhadrarao Kaliginediand, and Christian J. Leumann*[a]
Herein, we investigated the EET through DNA containing
Abstract: The modulation of excess electron transfer (EET)
phenanthrenyl base surrogates with different reduction poten-
within DNA containing a dimethylaminopyrene (C-AP) as
tials and LUMO energy levels (Figure 1). It is believed that the
an electron donor and 5-bromouracil (BrdU) as an electron
electron transfer within DNA can be modulated by the installa-
acceptor through phenanthrenyl pairs (phen-R) could be
tion of a potential energy gradient.[10] The predicted advantage
achieved by modifying the phenanthrenyl base surrogates
of such a redox/LUMO gradient was envisioned to be the uni-
with electron withdrawing and donating groups. Arrang-
directionality of the electron transfer and therefore a gain in
ing the phenanthrenyl units to form a descending LUMO
efficiency. The installation of the different reduction potentials
gradient increased the EET efficiency compared to the
was deemed to be possible by the introduction of electron-
electron transfer through uniform LUMOs or an ascending
withdrawing (CN) and -donating (NH2) groups at the 7-position
LUMO gradient.
of the phenanthrene (phen). The synthesis of the NH2phen and
phen phosphoramidites applicable for automated DNA synthe-
sis was performed according to published procedures.[11] The
The well-defined double helical structure of DNA with linearly
arranged base pairs is a suitable scaffold for charge transfer
and is therefore subject to intense studies in DNA damage,[1]
sensors,[2] and applications in molecular electronics.[3] Reductive
electron transfer, also called excess electron transfer (EET), in
DNA is a process that is directed through the lowest unoccu-
pied molecular orbital (LUMO) of the DNA bases. Investigations
elucidated that the charge transfer over longer distances
occurs by electron hopping, mostly through thymine bases
(k=1010 sÀ1).[4] In earlier studies it was shown that the replace-
ment of the natural base pairs by non-hydrogen-bonding base
surrogates with extended aromatic surfaces such as phenan-
threne could have beneficial conducting properties and could
overcome the physicochemical limitations of the natural nucle-
obases.[5] Regarding the reduction of such base surrogates the
choice of the electron injector is crucial for the success of the
experiments. Investigations by Grigorenko et al. revealed that
pyrene (PydU, Ered*=À2.2 V vs. NHE)[6] only enables a superex-
change mechanism, whereas phenothiazine (PTZ, Ered*=À2.7 V
vs. SCE)[7] allowed to trigger the system into an electron hop-
ping mechanism with a transport that spreads over longer dis-
tances.[5] A photoexcitable dimethylaminopyrenyl donor at-
tached to a deoxyuracil (APdU, Ered*=À2.2 V vs. NHE)[8] that ex-
hibits suitable redox properties for long range charge transfer
experiments was successfully used by Bꢀtzner et al. to inject an
electron in hydroquinoline base surrogates.[9]
[a] Dr. P. Roethlisberger, Dr. V. Kaliginediand, Prof. Dr. C. J. Leumann
Department of Chemistry and Biochemistry
University of Bern
Freiestrasse 3, 3012 Bern (Switzerland)
E-mail: christian.leumann@dcb.unibe.ch
Figure 1. a) Representation of the EET system, consisting of a photoexcitable
C-AP donor opposite an abasic site, zipper-like stacked phenanthrenyls and
Supporting information and the ORCID identification number(s) for the au-
thor(s) of this article can be found under:
http://dx.doi.org/10.1002/chem.201605846.
a 5-bromouracil (BrdU) as electron acceptor. b) Representation of the ener-
getics in the electron-transfer process of the system consisting of a C-AP
donor, the modified phenanthrenyls and the BrdU acceptor.
Chem. Eur. J. 2017, 23, 1 – 5
1
ꢁ 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
&
&
These are not the final page numbers! ÞÞ

Communication
introduction of a cyano group required a palladium-catalyzed
substitution of the intermediate 9 with copper(I) cyanide. Tri-
tiylation and phosphitilation of the CNphen C-nucleoside oc-
curred under standard conditions and yielded the correspond-
ing phosphoramidite 12 (Supporting Information, Scheme S3).
The redox properties of the building blocks were analyzed by
cyclic voltammetry at the level of the free nucleosides 10
(CNpen, Ered =À1.63 V vs. Ag/AgCl), 13 (NH2phen, Ered =À2.60 V
vs. Ag/AgCl) and 14 (phen, Ered =À2.52 V vs. Ag/AgCl). Further-
more, the density functional theory calculations (B3LYP/6-31G*)
were found to correlate with the experimentally determined
reduction potentials (Supporting Information, Figure S1).
To study the EET properties through phenanthrenyl base sur-
rogates, a a-C-nucleosidic dimethylamino-pyrene (C-AP) was
synthesized that could intercalate well against an abasic site,
which enables an efficient photoinduced electron injection
owing to the close proximity to the phenanthrenyl stack.[12]
The synthesis involved a nucleosidation of the chloro Hofer
sugar and a Gilman cuprate[13] of the 6-bromo-N,N-dimethylpy-
ren-1-amine, which was received from bromination, nitrifica-
tion, reduction, and dimethylation of the amine function of the
pyrene (Supporting Information, Schemes S1, S2). According to
cyclic voltammetry, this donor (6) was found to have suitable
reduction potential in the excited state (Ered*=À2.7 V vs. Ag/
AgCl) to reduce all the phenanthrenyl units.
Figure 2. Representative denaturing PAGE showing the fragmentation of the
duplex D8 after 640 s of irradiation at 420 nm. Conditions: 4 mm duplex,
10 mm NaH2PO4, 0.15m NaCl, pH 7.0. The duplex was exposed to the UV
light for the indicated amount of time and analyzed after subsequent piperi-
dine treatment at 908C for 30 min. Lane 1 contains the control under light
exclusion and without piperidine treatment. The additional lanes show the
specific fragments; a) PO4-ACGC-FAM; b) PO4-TACGC-FAM.
As an electron acceptor, 5-bromouracil (BrdU) was used,
which releases a bromine anion (BrÀ) after encounter and cap-
ture a migrating electron that is injected into the DNA upon
excitation of the C-AP at 420 nm. The formed 5-uracyl radical
abstracts a hydrogen form the 5’ adjacent deoxyribose, which
eventually affords alkali label products under aqueous condi-
tions.[14] The EET efficiency can then be evaluated by fragment
analysis using polyacrylamide gel electrophoresis (PAGE) and
control sequences as markers for the specific fragments (see
Figure 2).
With the phosphoramidites of C-AP, phen, CNphen, NH2phen,
and BrdU, a series of oligonucleotides were synthesized con-
taining either a single (D1–D16) or triple (D17–D29) phenan-
threnyl modifications between the pyrenyl donor and the elec-
tron acceptor. Thermal denaturing studies revealed that single
phen modifications in general lead to a destabilization. On the
other hand, multiple phen modifications stabilized the duplex
compared to the natural base pairs. This effect was observed
in earlier studies with non-hydrogen bonding base surrogates
and was found to be an enthalpy-driven process induced by
the increased hydrophobic interactions of such base surro-
gates.[11,15] An expected decrease in stability was observed for
duplexes containing electron-donating groups, and vice versa
a stabilization of duplexes containing electron-withdrawing
groups.
ment without irradiation occurred owing to the applied
heat.[16] Along with the specific short fragments a low mobility
band occurred in sequences with NH2phen and phen pairs. Ac-
cording to mass spectrometry, the reaction product correlates
to an intrastrand crosslink, as already observed in earlier EET
studies with phen pairs (Supporting Information, Fig-
ure S5, S6).[5]
Electron transfer through single phenanthrenyl (D8, D11,
D14) pairs is less effective than EET through A/T (D7) base
pairs owing to the fact that thymine (À0.95 eV)[17] exhibits
a lower reduction potential compared to all the phenanthrenyl
base surrogates. Additionally, a suppression of hole transfer
processes was found for duplexes with base mismatches[18]
and bulge positions,[19] suggesting that a slight perturbation of
the base stack in the case of single phenanthrenyl pairs is ac-
companied with suppressing effects as well (see Figure 3).[20]
Circular dichroism (CD) spectroscopy revealed that the sec-
ondary structure of natural DNA is not disturbed by the phe-
nanthrenyl or pyrenyl modifications.
Initial EET experiments were performed with duplexes D1,
D2, D3 lacking the donor or D4, D5, D6 without an acceptor.
Both series did not show any fragment formation upon irradia-
tion. In general, a non-specific cleavage after piperidine treat-
Figure 3. DNA cleavage yields for duplexes D7-D16 after 640 s irradiation at
420 nm.
&
&
Chem. Eur. J. 2017, 23, 1 – 5
www.chemeurj.org
2
ꢁ 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
ÝÝ These are not the final page numbers!

Communication
Comparing the EET yield of the different phenanthrenyl
pairs, it was found that the efficiency of the electron transfer
processes correlates with the reducibility of the phenanthrenyl
base surrogates (CNphen>phen>NH2phen). The differences in
yield, however, were found to be within a 6% range. This
could be explained by the fact that electron transfer over short
distances can also occur via hole transfer and therefore lowers
the influence of the reducibility in such processes. Analysis of
the permutated phenanthrenyl sequences (D9, D10, D12, D13)
show no statistically significant difference in EET yield and are
therefore not further discussed (Supporting Information,
Table S4).
Extending the phenanthrenyl units from one to three con-
secutive incorporations for each strand allows the installation
of an electron gradient over longer distance. In this context,
gel electrophoretic analysis of irradiated duplexes D17, D18,
D19, D20, D21, lacking an electron donor, revealed two differ-
ent features: 1) in general no major irradiation dependent
strand cleavage occurred through three consecutive phen
(D17) and CNphen (D19) base pairs; 2) installation of a LUMO
gradient in an ascending manner produced an irradiation de-
pendent fragmentation with a yield of up to 33.7% over 640
seconds without the use of an electron injector. It is assumed
that the consecutive phenanthrenyl units can form an exciplex
and absorb light at higher wavelength. An unexpected domi-
nant strand cleavage product, with a lower mobility than the
5mer, was observed for the NH2phen containing duplex D18. It
occurs in the dark as well as in a time dependent fashion upon
irradiation. The same fragmentation pattern, but in much
lower extent, was observed for duplex D21 having an ascend-
ing LUMO gradient with NH2phen at the 5’ end of the phen
stack. It is not evident from these studies why this fragment is
produced in the absence of irradiation at low temperatures
(48C storage). However, a possible explanation for the frag-
mentation is that a ground-state reaction is enabled by an en-
larged p-stack of NH2phen units, which could stabilize the re-
sulting cationic species on the 5’ NH2phen in a similar way to
what has been observed for guanine rich sequences in hole
transfer (HT) studies.[21]
Figure 4. EET from excited C-AP to BrdU through multiple base surrogates as
a function of time. (D27; purple CNphenphenNH2phen), (D22; yellow TTT),
(D23; blue phenphenphen), (D24; red CNphenCNphenCNphen), (D26; orange
N
H2phenphenCNphen). Conditions are given in the legend of Figure 2.
cess is not solely dependent on the LUMO energy of the par-
ticipants.
Installation of a descending LUMO gradient as in D26 result-
ed in an EET yield that is higher by 4.2% compared to three
CNphen (D24) or 15.0% higher compared to three consecutive
phenanthrene residues (D23; Figure 5). A suppression of back
electron transfer and charge recombination could be used to
explain the increase in EET.[23] Furthermore, an over two-fold
lower transfer performance was observed for the ascending
LUMO gradient (D27, 26.7%) compared to the descending
LUMO gradient (D26, 64.3%), highlighting the importance of
an exergonic process. Interestingly, the EET yield through du-
plexes with mixed ascending and descending strands (D28
and D29) a relative high electron transfer yield (54.7% to
The EET efficiency through three consecutive A–T base
pairs decreased by 13.3% (Figure 4, compare D7 to D22),
while the efficiency through three phen pairs remained the
same (compare D8 and D23). On the other hand, the exten-
sion of the p-stack of CNphen enhanced the EET yield by
+6.3% (compare D24 to D11). Comparing the cleavage prod-
uct yield of homologous duplexes, it was observed that the
electron transfer through CNphen (D24) is 10.7% more efficient
than through unsubstituted phen (D23) and 15.1% higher
than through A–T base pairs (D22). Interestingly the increased
electron-transfer yield through phen units coincides with an in-
creased stability of the DNA duplexes (see the Supporting In-
formation). It is believed that a favorable conformation of a sta-
bilized duplex allows more efficient electron transfer, as de-
scribed in hole transfer studies by Wasielewski and co-work-
ers.[22] The fact that the electron transfer efficiency is higher for
phen stacks than for neutral A–T base pairs that have an intrin-
sic lower reduction potential is implying that the transfer pro-
Figure 5. Comparison of DNA cleavage yields of single strands after 640 sec-
onds irradiation at 420 nm.
Chem. Eur. J. 2017, 23, 1 – 5
www.chemeurj.org
3
ꢁ 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
&
&
These are not the final page numbers! ÞÞ

Communication
[1] a) E. J. Merino, J. K. Barton, Biochemistry 2007, 46, 2805–2811; b) M. E.
NfflÇez, G. P. Holmquist, J. K. Barton, Biochemistry 2001, 40, 12465–
12471; c) D. J. Tan, R. K. Bai, L. J. C. Wong, Cancer Res. 2002, 62, 972–
976.
[2] a) A. L. Furst, M. G. Hill, J. K. Barton, Langmuir 2015, 31, 6554–6562;
b) H. Zhao, Z. Li, N. Y. Lee, J. S. Kim, E.-C. Lee, Curr. Appl. Phys. 2012, 12,
1493–1496.
[3] a) S. O. Kelley, J. K. Barton, N. M. Jackson, M. G. Hill, Bioconjugate Chem.
1997, 8, 31–37; b) A. K. Boal, J. K. Barton, Bioconjugate Chem. 2005, 16,
312–321; c) E. M. Boon, J. K. Barton, Curr. Opin. Struct. Biol. 2002, 12,
320–329; d) S. O. Kelley, N. M. Jackson, M. G. Hill, J. K. Barton, Angew.
Chem. Int. Ed. 1999, 38, 941–945; Angew. Chem. 1999, 111, 991–996.
[4] M. J. Park, M. Fujitsuka, K. Kawai, T. Majima, J. Am. Chem. Soc. 2011, 133,
15320–15323.
53.5%) was observed, assuming that the electron transfer
occurs not solely by electron hopping but also via electron
tunneling to overcome the endergonic migrating steps.
When the electron transfer through single strands was
tested, a circa 50% loss of EET efficiency was observed in
strands with single phen (ON12) and CNphen (ON13) incorpora-
tions, while a loss of about 75% of EET was determined for
thymine- (ON11) and NH2phen- (ON14) containing strands com-
pared to their duplexes. Prolonging the distance between the
donor and acceptor in single strands only led to a positive
effect on the EET yield in the case of CNphen (ON28-ON13,
19.3%) but showed little effect in all other single strands. The
observation that phenanthrene with an intrinsic higher reduc-
tion potential than thymine (À1.05 vs. Ag/AgClO4 or À1.86 vs.
NHE)[17,24] shows a higher electron transfer yield for long-range
migrations, indicate that the electron transfer efficiency cannot
be explained by the driving force solely, even though the
transfer yields increased with decreasing LUMO energies of the
phen units. Okamoto et al. introduced the concept of expand-
ed aromatic systems to increase HT efficiencies by taking the
advantage of the enhanced p-stacking properties. Experimen-
tal findings showed that the expanded aromatic hole mediator
enhance the charge transfer over long distances (20 bp).[25]
Thus, it is believed that inter alia a high driving force, obtained
by the installation of a descending LUMO gradient as well as
the intrinsic large aromatic p-surfaces play a crucial role for the
EET efficiency.
[5] P. Roethlisberger, F. Wojciechowski, C. J. Leumann, Chem. Eur. J. 2013,
19, 11518–11521.
[6] N. A. Grigorenko, C. J. Leumann, Chem. Commun. 2008, 5417–5419.
[7] a) T. Ito, A. Hayashi, A. Kondo, T. Uchida, K. Tanabe, H. Yamada, S. Nishi-
moto, Org. Lett. 2009, 11, 927–930; b) T. Ito, A. Kondo, S. Terada, S.
Nishimoto, J. Am. Chem. Soc. 2006, 128, 10934–10942.
[8] T. Ehrenschwender, W. Schmucker, C. Wellner, T. Augenstein, P. Carl, J.
Harmer, F. Breher, H.-A. Wagenknecht, Chem. Eur. J. 2013, 19, 12547–
12552.
[9] E. Bꢀtzner, Y. Liang, C. Schweigert, A. N. Unterreiner, H. A. Wagenknecht,
ChemPhysChem 2015, 16, 1607–1612.
[10] a) T. Ito, R. Kurihara, N. Utsumi, Y. Hamaguchi, K. Tanabe, S.-i. Nishimoto,
Chem. Commun. 2013, 49, 10281–10283; b) M. Tanaka, K. Oguma, Y.
Saito, I. Saito, Chem. Commun. 2012, 48, 9394–9396.
[11] N. A. Grigorenko, C. J. Leumann, Chem. Eur. J. 2009, 15, 639–645.
[12] T. Ito, S. E. Rokita, J. Am. Chem. Soc. 2004, 126, 15552–15559.
[13] S. Hainke, I. Singh, J. Hemmings, O. Seitz, J. Org. Chem. 2007, 72, 8811–
8819.
[14] H. Sugiyama, Y. Tsutsumi, I. Saito, J. Am. Chem. Soc. 1990, 112, 6720–
6721.
In summary, the C-nucleosidic C-AP donor was found to be
powerful and stable electron donor for EET experiments with
an absorption band around 400 nm allowing for a selective ex-
citation. Introducing modified phen base surrogates allowed
the study of electron transfer through LUMO energy gradients.
Although the interaction of the phenanthrenyl pairs within
DNA could alter their LUMO levels to some extent, it is still
possible to estimate the efficiency of the EET based on the
LUMO levels of the isolated polyaromatic nucleosides. Indeed,
an enhancement of electron transfer was found through a de-
scending gradient compared to flat or ascending LUMO
energy levels. The control of the electron transfer directionality
widens the potential application of devices based on artificial
DNA.
[15] a) C. Brotschi, C. J. Leumann, Angew. Chem. Int. Ed. 2003, 42, 1655–
1658; b) C. Brotschi, A. Haberli, C. J. Leumann, Angew. Chem. Int. Ed.
2001, 40, 3012–3014; Angew. Chem. 2001, 113, 3101–3103.
[16] G. W. Grigg, Nucleic Acids Res. 1977, 4, 969–987.
[17] M. Hintze, K. O. Thiel, A. Vollmer, H. Brunner, C. Donner, Electrochim.
Acta 2010, 55, 8135–8141.
[18] P. K. Bhattacharya, J. K. Barton, J. Am. Chem. Soc. 2001, 123, 8649–8656.
[19] D. B. Hall, J. K. Barton, J. Am. Chem. Soc. 1997, 119, 5045–5046.
[20] P. Roethlisberger, A. Istrate, M. J. Marcaida Lopez, R. Visini, A. Stocker,
J. L. Reymond, C. J. Leumann, Chem. Commun. 2016, 52, 4749–4752.
[21] H. Sugiyama, I. Saito, J. Am. Chem. Soc. 1996, 118, 7063–7068.
[22] W. B. Davis, M. A. Ratner, M. R. Wasielewski, J. Am. Chem. Soc. 2001, 123,
7877–7886.
[23] a) T. Ito, Y. Hamaguchi, K. Tanabe, H. Yamada, S. Nishimoto, Angew.
Chem. Int. Ed. 2012, 51, 7558–7561; b) F. Fakhari, Y. Y. K. Chen, S. E.
Rokita, Chem. Commun. 2013, 49, 7073–7075.
[24] M. P. Scannell, D. J. Fenick, S. R. Yeh, D. E. Falvey, J. Am. Chem. Soc. 1997,
119, 1971–1977.
[25] A. Okamoto, K. Tanaka, I. Saito, J. Am. Chem. Soc. 2003, 125, 5066–
5071.
Acknowledgements
Financial Support by the Swiss National Science Foundation
(grant-No.:200020-130373) is acknowledged.
Manuscript received: December 15, 2016
Accepted Article published: December 19, 2016
Final Article published: && &&, 0000
Keywords: electron
phenanthrene · stacking interactions
transfer
·
oligonucleotides
·
&
&
Chem. Eur. J. 2017, 23, 1 – 5
www.chemeurj.org
4
ꢁ 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
ÝÝ These are not the final page numbers!

Communication
COMMUNICATION
Excess electron transfer (EET) can be
modulated within DNA by introducing
a dimethylaminopyrene (C-AP) base sur-
rogate as an electron donor, 5-bromour-
acil (BrdU) as an electron acceptor, and
by changing the electronic nature of
the phenanthrenyl pair.
&
DNA Modification
P. Roethlisberger, V. Kaliginediand,
C. J. Leumann*
&& – &&
Modulation of Excess Electron Transfer
through LUMO Gradients in DNA
Containing Phenanthrenyl Base
Surrogates
Chem. Eur. J. 2017, 23, 1 – 5
www.chemeurj.org
5
ꢁ 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
&
&
These are not the final page numbers! ÞÞ