Enhancing excess electron transport in DNA

Article abstract of DOI:10.1039/c3cc43887b

The efficiency of excess electron transport in duplex DNA can be enhanced by limiting the pathways available for migration and using a donor of moderate strength that suppresses radical recombination through selective electron transfer to distal pyrimidines rather than proximal purines.

Full text of DOI:10.1039/c3cc43887b

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Enhancing excess electron transport in DNA†
Fazel Fakhari,z Yun-Yun K. Chen and Steven E. Rokita*z
Cite this: Chem. Commun., 2013,
4
9, 7073
Received 23rd May 2013,
Accepted 26th June 2013
DOI: 10.1039/c3cc43887b
www.rsc.org/chemcomm
The efficiency of excess electron transport in duplex DNA can be
enhanced by limiting the pathways available for migration and
using a donor of moderate strength that suppresses radical recom-
bination through selective electron transfer to distal pyrimidines
rather than proximal purines.
Charge transport (CT) in DNA contributes to a range of natural
processes and has recently been integrated into nanostructures
1
,2
and sensing devices. However, challenges still remain before
DNA may be widely applied to nanoelectronics, and much effort
has focused on identifying and optimizing parameters that limit
CT efficiency between defined donors and acceptors. The inter-
vening nucleotide sequence, helical structure and conformational
Fig. 1 Freedom of charge migration may influence the efficiency of its transport
from a donor (D) to an acceptor (A) in DNA.
3
dynamics are all crucial in optimizing long distance CT. The
selection of appropriate donors and acceptors is also equally
important for successful CT.
The number of pathways available for charge migration in initial charge injection into DNA. Both experimental and
DNA is another variable that is expected to influence the apparent theoretical investigations have demonstrated that increasing
efficiency of transport between a specific donor–acceptor pair, but the distance between these counter ions will suppress their
Transport of charge from a donor to acceptor also competes
against rapid recombination of the proximal ion pair formed by
4
–6
1
2
1
3
direct study of this has been minimal. Most model systems are non-productive recombination. Judicious choice of donors and
0
based on DNA with a charge donor appended to the 5 -terminus of a their surrounding nucleotide sequence may reduce this back
4
,14
duplex strand. For example, hairpin systems are typically capped electron transfer as illustrated previously with hole transport.
7
with a terminal donor. Likewise, most double-stranded systems This same strategy has now been tested as described below for
using organic and organometallic donors rely on their attachment enhancing excess electron transfer (EET) initiated by single
2,8
near to a helical terminus as well. Alternative placement of a donor electron transfer from a photoexcited donor to DNA.
at an internal position within helical DNA has received less attention Our model system for comparing donor placement and
and offers an intrinsic competition between charge migration in two electron injection relied on dU as an electron acceptor. This
Br
9
–11
directions (Fig. 1).
The efficiency of delivering an electron from a is easily incorporated into DNA by standard phosphoramidite
Br
donor in the middle of a duplex to an acceptor ( dU) has now been chemistry and acts with a trapping efficiency near unity by
compared directly to an equivalent system with the donor at the rapidly eliminating bromide and generating a transient uridinyl
0
1
duplex terminus in order to restrict electron migration.
radical that oxidizes its 5 neighboring deoxyribose and creates a
0,15,16
site of alkaline lability.
A methylated derivative of the
chosen diaminonaphthyl donor (DN) had originally been syn-
Department of Chemistry and Biochemistry, University of Maryland, College Park,
Maryland 20742, USA
1
0
thesized using a norbornyl protection strategy, but the parent
donor lacking the methyl groups could only be isolated in low
yield under equivalent conditions. Substituting the norbornyl
group with a phthalimide group facilitated deprotection and
provided high yields of the desired donor (a, Chart 1 and ESI†).
The donor was easily coupled through its hydroxylamine group
†
Electronic supplementary information (ESI) available: Synthesis and oligo-
nucleotide conjugation of electron donors, HPLC and absorption spectra of
conjugates, thermal denaturation of duplex DNA, initial rate of strand scission
induced by excess electron transfer. See DOI: 10.1039/c3cc43887b
‡
Current address: Department of Chemistry, Johns Hopkins University, Baltimore,
MD 21218, USA. E-mail: rokita@jhu.edu; Tel: +1 410-516-5793.
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Br
Fig. 3 EET from donors (DN and AA) to dU in DNA1–DNA4 as indicated by strand
scission after UV irradiation and piperidine treatment. Initial scission rates (v) were
i
obtained by linear fitting of % scission vs. time (ESI†). Each analysis was repeated a
minimum of three times and error bars represent their standard deviation.
signal-to-noise for an additional test of donor placement and
electron migration. For these duplexes, the G/C base pair adjacent to
the donor was replaced with an A/T to avoid the likely suppression
of electron migration encountered from an intermediate cytosine
Chart 1 Duplex DNA alternatively containing donors of (a) diaminonaphthalene
and (b) aminoanthracene for EET studies.
to abasic sites in oligonucleotides that resulted from deglycosylation radical that is stabilized by proton transfer from its hydrogen
1
7
5,11,18
of the uridine-containing parents (ESI†).
bonding partner guanine.
This change of sequence was
Br
Restricting the potential migration of an excess electron in DNA sufficient to enhance the efficiency of CT to the acceptor dU
was expected to enhance the efficiency of CT from donor to by more than 100% (Fig. 3), and the trend of efficiency versus
acceptor. This was confirmed after reaction was initiated by irradia- donor position remained constant. Each example illustrates the
tion of the donor DN (l > 335 nm) in duplexes DNA1a and DNA2a benefit of limiting the migration of the injected electron by
that contained identical nucleotide sequences but alternative place- placing the donor at a helix terminus.
Br
ment of the donor DN and acceptor dU within the duplex as indi-
The reducing potential of the electron donor is another
0
0
cated in Chart 1. However, the sequence and the 5 to 3 orientation variable that may affect the efficiency of delivering charge to
between these redox active centers remained constant. The charac- its acceptor within DNA. Initial selection of these donors was
teristic strand scission resulting from electron trapping by dU was guided by the original uncertainty that excess electron transport
Br
quantified after gel electrophoresis and monitored over time of was even possible in DNA. Thus, a very strong photoexcited
irradiation (Fig. 2). Initial rates of scission were indeed enhanced donor (E * below ꢀ3 V vs. SCE) was selected at first for injecting
ox
1
0
2
-fold for the duplex with DN at a terminal versus an internal an electron indiscriminately into any of the nucleobases. This
position (Fig. 3). However, the signal-to-noise ratio for this first com- strategy became unnecessary and unsuitable once back electron
parison was only moderate due to the relatively low efficiency of CT. transfer from the initial charge-separated species was found to
1
2
A second set of duplexes (DNA3a and DNA4a, Chart 1) was limit long distance transport. Alternative application of a more
subsequently prepared with an expectation of increasing the selective donor provided an opportunity to suppress radical
recombination by placing an unreactive nucleobase between
4
,14
the initial pair of charges.
In order to investigate this strategy,
a derivative of 1-aminoanthracene (AA) was chosen as a close
analog of DN for comparison. Unlike the excited state of DN, the
excited state of AA is capable of only reducing pyrimidines and
1
9,20
not purines due to its moderate potential of ꢀ2.25 V vs. SCE.
Consequently, surrounding AA with purines enforced a distance
between charged species that should enhance excess electron
transport between donor and acceptor in DNA (Fig. 4).
The donor AA was prepared and conjugated to DNA by the same
methods used for the DN derivative (ESI†). Transport efficiency was
then measured within identical nucleotide sequences (Chart 1) to
establish direct comparisons between AA, DN and the trends
already established by DN. In each example, the AA conjugates
supported a greater level of transport than their equivalent DN
conjugates (Fig. 3, ESI†). The enhancement ranged from a low
of approximately 50% for DNA2 to a high of 250% for DNA4.
In addition, preferential transport from donors placed at a
terminal rather than central region of a duplex was confirmed
Fig. 2 Phosphoimagery of 20% denaturing polyacrylamide gels showing strand
scission of DNA1a and DNA2b after UV irradiation (l > 335 nm) and piperidine
treatment. Arrows indicate the scission sites caused by electron trapping by the
Br
dU residue.
7
074 Chem. Commun., 2013, 49, 7073--7075
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Br
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1
1
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Br
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5
,11,18
base pairing,
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1
1
2
2
judicious choice of donor potential and DNA sequence. Such
considerations should be incorporated into future systems that
rely on excess electron transport through DNA to convey a
signal, trigger an actuator or initiate other related applications
of nanosystems based on DNA.
Authors would like to thank Dr Neil P. Campbell, Timothy J.
Simons and Angel Li for initial studies and useful discussions.
Financial support from NSF (CHE-0517498) and the Howard
Hughes Medical Institute Undergraduate Science Education
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This journal is c The Royal Society of Chemistry 2013
Chem. Commun., 2013, 49, 7073--7075 7075