Effects of the Backbone and Chemical Linker on the Molecular Conductance of Nucleic Acid Duplexes

Article abstract of DOI:10.1021/jacs.7b02260

Scanning tunneling microscope break junction measurements are used to examine how the molecular conductance of nucleic acids depends on the composition of their backbone and the linker group to the electrodes. Molecular conductances of 10 base pair long h

Full text of DOI:10.1021/jacs.7b02260

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Article
Effects of the Backbone and Chemical Linker on the
Molecular Conductance of Nucleic Acid Duplexes
Edward Beall, Selma Ulku, Chaoren Liu, Emil Wierzbinski, Y Zhang, Yookyung
Bae, Peng Zhang, Catalina Achim, David N. Beratan, and David H. Waldeck
J. Am. Chem. Soc., Just Accepted Manuscript • Publication Date (Web): 23 Apr 2017
Downloaded from http://pubs.acs.org on April 24, 2017
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Effects of the Backbone and Chemical Linker on the Molecular Conductance of
Nucleic Acid Duplexes
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Edward Beall,α,† Selma Ulku,α,§ Chaoren Liu,‡ Emil Wierzbinski,† Yuqi Zhang,‡ Yookyung Bae,§
Peng Zhang,‡ Catalina Achim,*,§ David N. Beratan,*,‡ and David H. Waldeck*,†
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†Chemistry Department, University of Pittsburgh, Pittsburgh PA 15260
§Chemistry Department, Carnegie Mellon University, Pittsburgh PA 15213
‡Chemistry Department, Duke University, Durham NC 27708
* Address correspondence to achim@cmu.edu, david.beratan@duke.edu, dave@pitt.edu
α The authors contributed equally to this work
Abstract
Scanning tunneling microscopeꢀbreak junction measurements are used to examine how
the molecular conductance of nucleic acids depends on the composition of their backbone and
the linker group to the electrodes. Molecular conductances of 10ꢀbase pair long homoduplexes
of DNA, aegꢀPNA, γꢀPNA, and a heteroduplex of DNA/aegꢀPNA with identical nucleobase
sequence were measured. The molecular conductance was found to vary by 12 to 13 times with
the change in backbone. Computational studies show that the molecular conductance differences
between nucleic acids of different backbones correlate with differences in backbone structural
flexibility. The molecular conductance was also measured for duplexes connected to the
electrode through two different linkers, one directly to the backbone and one directly to the
nucleobase stack. While the linker causes an orderꢀofꢀmagnitude increase in the overall
conductance for a particular duplex, the differences in the electrical conductance with backbone
composition are preserved. The highest molecular conductance value, 0.06 G0, was measured
for aegꢀPNA duplexes with a base stack linker. These findings reveal an important new strategy
for creating longer and more complex electroactive, nucleic acid assemblies.
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Introduction
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The past decade has witnessed important breakthroughs in DNA nanotechnology.1ꢀ3
Researchers have demonstrated how to use WatsonꢀCrick base pairing rules to program the selfꢀ
assembly of nucleic acids into a diverse array of shapes and structures, and it is now possible to
imagine creating a wide range of functional motifs. The use of these nanostructures in electronic
and electrochemical applications will rely on a deeper understanding of their charge transmission
and electron transfer mechanisms.4ꢀ7 Nucleic acids display unusual complexity in their charge
transport properties, with mechanisms that range from coherent tunneling at short distances, to
incoherent hopping at long distances, and coherent ballistic charge transfer via the flickering
resonance mechanism at intermediate distances.4, 8ꢀ10 Moreover, these various regimes and the
transitions between them are known to be sensitive to nucleobase sequence, length, and charge
injection energy. For coherent tunneling, the local energetics of the base stack dominates the
charge transport; whereas for charge hopping and flickering, the electrical conductance is likely
linked to the conformational dynamics of the duplex. For these reasons, understanding the
influence of the molecular backbone on the electron transmission properties of nucleic acids is
important to developing our understanding and eventually to realizing the promise of DNA
molecular electronics.
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The use of DNA nanotechnology in bioelectronics will require that we understand and
control the structural fluctuations of these soft biomaterials and their effect on the molecular
conductance. For example, it has been shown that the conformation of DNA duplexes can lead to
drastic changes in the single molecule electrical conductance.11ꢀ13 Additional strategies that
include incorporating intercalators and metal ions into the base stack have been used to affect the
structure and electrical properties of nucleic acid duplexes.14ꢀ16 Given that orbital overlap of
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adjacent nucleobases dictates nearest neighbor electronic couplings, the ability to access different
conformations can modulate the conductance of a duplex significantly. This work asks how the
single molecule conductance of a duplex depends on its structural flexibility and nucleobase
overlap by examining a set of nucleic acid duplexes that have identical nucleobase sequence and
identical linkers but different backbone structures, which leads to different conformational
flexibility. In particular, the molecular conductance is compared for four different backbone
motifs: the phosphate sugar backbone of DNA, aminoethylglycine peptide nucleic acid (aegꢀ
PNA),17 a gammaꢀmodified (γꢀPNA) backbone,18 and a DNA/aegꢀPNA heteroduplex.
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PNA is a synthetic analogue of DNA that has a neutral aminoethylglycine backbone rather
than the negatively charged, sugar phosphodiester backbone of DNA.17 γꢀPNA has a substituent
at the γꢀposition of the backbone that makes it intrinsically chiral and reduces its conformational
freedom.18 Solution structures obtained by NMR spectroscopy and crystal structures of these
nucleic acid duplexes have shown that homoduplexes of aegꢀPNA and γꢀPNA adopt a Pꢀhelix
structure,19ꢀ21 whereas DNA homoduplexes22 and DNA/PNA heteroduplexes23ꢀ24 adopt a BꢀDNA
helix structure (Figure 1). The fact that both aegꢀPNA and γꢀPNA are more flexible than DNA is
supported by the fact that heteroduplexes of both PNAs with DNA adopt a BꢀDNA structure
characteristic of DNA homoduplexes.23ꢀ25 Examination of the backbone’s chemical structure
suggests that aegꢀPNA is more flexible than γꢀPNA, which in turn is more flexible than DNA;
this inference is supported by NMR studies of these nucleic acids in solution20ꢀ21 and by
molecular dynamics studies.26 Thus, a comparison of the conductance of these molecules should
provide insight into the importance of backbone flexibility on the single molecule conductance.
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Figure 1. Renderings for the four duplexes (A) DNA homoduplex, (B) DNA /aegꢀPNA heteroduplex, (C) aegꢀ
PNA homoduplex, and (D) γꢀPNA homoduplex are shown. In each case the sequence is AGTTTGTACG. The
insets show the chemical structures for the backbones of DNA, aegꢀPNA, and γꢀPNA.
Previous studies have shown that the electrochemical charge transfer rates of nucleic
acids are influenced by their structural flexibility.27ꢀ29 In a study by Wierzbinski and coworkers,
the electrochemical rate constant was measured through aegꢀPNA and γꢀPNA duplexes, and the
γꢀPNA duplexes were shown to have a smaller rate by a factor of two.27 The experimental
observation of larger electrochemical rate constants for aegꢀPNA as compared to those for γꢀ
PNA was rationalized as arising from an increase in the energy level broadening of the hole
mediating superexchange states with the increase in duplex flexibility; or, alternatively, arising
from the ability of the more flexible aegꢀPNA duplexes to access conformations with higher
electronic couplings more often than do γꢀPNA duplexes. As both γꢀPNA and aegꢀPNA adopt a
Pꢀhelix structure,19ꢀ20 the diminished rate is likely to arise from the relative flexibility of the
backbones rather than from differences in the average nucleobase overlaps that might arise for
different helix geometries. The dependence of electron transfer rates on structural fluctuations
was also observed in studies on DNA/LNA hybrids29 and reported for DNA duplexes at different
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temperatures.30 Because the electron transfer rate is directly related to the electrical
conductance,31 it seems plausible that such effects can cause differences between the single
molecule conductance of nucleic acid duplexes.
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In addition to the backbone composition, the effect of changing the chemical linker
between the nucleic acid and the electrode was examined. Figure 2 shows molecular structures
for the two linker types. The propylthiol linker is covalently tethered to the nucleic acid
backbone, whereas the amino thymidine linker is covalently coupled to a nucleobase. In recent
work on DNA conductance, Tao and coworkers showed that the use of an amino thymidine
nucleoside linker significantly increased the conductance relative to a thiol linker.32ꢀ33 This
increased conductance suggests that the amino thymidine linkers enhance the charge injection
into the nucleobase stack, thus enhancing the molecular conductance. The current work examines
whether this linker effect changes the sensitivity of the conductance to the backbone structure. In
the limit that the charge transport proceeds by incoherent hopping (i.e., charge injection onto the
bridge, hopping through the bridge nucleobases, and escape from the bridge to the counter
electrode), one expects the overall resistance of the molecular junction to be a sum of resistances
for each of the three steps; such a mechanism was recently used to describe electrochemical
charge transfer with PNAs.34 In contrast, if the charge transport proceeds coherently, then the
decomposition into resistances for each step is no longer possible; rather the transport should be
viewed as a product of transmission probabilities for each step.35 By contrasting how the single
molecule conductance of DNA and PNA duplexes change with the different linker types, insights
into the nature of the conduction mechanism, incoherent versus coherent, can be ascertained.
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Results
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Although extensive research has examined the dependence of molecular conductance of
nucleic acid duplexes on the sequence of the duplex, this study is the first to examine the
influence of different backbones of nucleic acid duplexes on the molecular conductance of
duplexes that have the same sequence of 10 base pairs, AGTTTGTACG and its complement.
Specifically we compare duplexes that have a pseudopeptide backbone based on aminoethylꢀ
glycine aegꢀPNA, a pseudopeptide backbone based on γꢀhydroxymethyleneꢀaminoethylꢀglycine
γꢀPNA, and sugar diphosphate DNA (Figure 1). We also examine the influence on the molecular
conductance of the linker that connects the duplex to the electrode, through the nucleic acid
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A)
B)
Figure 2. Chemical structure of the linkers that connect PNA to the Au surface. Panel A shows the
propylthiol that is situated at the C end of the single stranded PNA. Panel B shows the thymidine 5ꢀC2
amino linker which can be situated at any position in a single stranded PNA.
backbone (propylthiol) or the nucleobase stack to the electrode (a thymidine 5ꢀC2 amino linker)
(Figure 2).
Conductance Measurements
The electrical conductance properties of the nucleic acid duplexes were investigated by
using the scanning tunneling microscope break junction (STMꢀBJ) method,36 in which a
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triangular waveform bias voltage is applied to the gold STM tip as it is retracted;37 see Figure 3A.
Molecular junctions are formed between a gold substrate and the gold STM tip by way of
terminal linkers positioned on the opposing termini of the duplexes. The current between the
electrodes is monitored as the STM tip is withdrawn from the substrate surface, providing a
currentꢀtime (currentꢀdistance) profile or trajectory. Electrical conduction through a purely
resistive molecular junction manifests in a triangular currentꢀtime waveform response (see
Figure 3B), whereas junctions without such molecules give a more complex (leaky capacitor)
response. The typical tip displacement over one period of the applied triangle wave is 20 pm; < 9%
of an AuꢀS bond length. A large set of trajectories for resistive molecular junctions were
collected and their current responses were fit by an equivalent circuit model to yield a molecular
conductance for each period of the waveform (see Supporting Information). A distribution of
molecular conductance values was measured for each duplex.
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The trajectory shown in Figure 3B was taken for an aegꢀPNA homoduplex with
propanethiol linkers on each strand. It displays two regimes of conductance during the time (~12
periods) that the STM tip is withdrawn and a molecular junction is formed with the substrate.
The multiple modes observed within a conductance distribution could be attributed to different
relative orientations of the linkers with respect to the gold electrodes and/or to different
conformations of the molecule within the molecular junctions.38 At early times, a higher
conductance mode is observed and the current fluctuates between 30 and 60 nA. This fluctuation
can be attributed to the presence of one and two molecules ‘wired’ in parallel in the junction,36 or
to structural variations of the duplex, which have been shown to affect the conductance of the
molecular junction.30, 39 Varying the concentration of the nucleic acid duplexes on the surface
indicated that a higher molecular coverage causes these fluctuations in the current response to
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occur more frequently, supporting the interpretation that two molecules in the junction cause the
fluctuations. At later times, the higher conductance mode transitions to a much lower
conductance regime with a more stable current response. This transition could reflect a change in
the binding of the linker groups to the gold substrate or the partial unraveling of the nucleic acid
strand.40 The latter possibility is less likely, however, as single strand molecules give much lower
currents (<100 pA) than the ones observed here (5 to 10 nA for the lower conductance).31, 41ꢀ42
Although only two conductance modes are observed for some of the systems, the nomenclature
of ‘high’ and ‘medium’ conductance modes is kept for consistency with published data on thiol
linkers.31, 38, 43
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Figure 3. (A) The schematic for the single molecule conductance measurements. (B) Example
currentꢀtime responses for the aegꢀPNA homoduplex showing the triangular wave current response
resulting from a molecular junction (i) and an ‘empty’ current response where a molecular junction
does not occur (ii). For the current response showing the molecular junction, a clear transition occurs
from the high conductance mode (H) to a lower conductance mode (M).
Backbone Comparison: Conductance distributions are shown in Figures 4B through 4E for the
DNA, the aegꢀPNA, the γꢀmodified PNA homoduplexes, and the DNA/aegꢀPNA heteroduplex,
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in each case with propylthiol linker groups. These distributions were obtained from several
thousands of measurements and are normalized to unit area for comparison purposes. For each
duplex type, an example trajectory for one of the molecular junctions is also shown in panel A.
The conductance distributions span several orders of magnitude and have a multimodal character.
The data set for the aegꢀPNA homoduplex (Figure 4C) displays three modes; the data sets of the
other three types of duplexes show two dominant conductance modes. The lowest mode of the
DNA, γꢀmodified PNA, and DNA/aegꢀPNA duplexes were not observed, presumably because of
the sensitivity constraints of the preamplifier. We analyzed and compared the two highest
conductance modes, which are observed for all four duplexes. The plots in Figure 4, show fits to
the data by a sum of two Gaussian functions, which allows a ‘peak’ conductance value to be
assigned for the two higher conductance modes.
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Note that the high conductance mode often presents a shoulder on the high conductance
side of the peak, at roughly twice the conductance of the peak. Analysis of these trajectories
shows that the current response is fluctuating between integer multiples of a single value; i.e., the
junction has two molecules bound across the junction and they act as two parallel resistors.37
Thus, the main peak is attributed to the conductance of a single molecule junction and the
shoulder to a junction containing two or more molecules.
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Figure 4. Panel A shows example current responses for the duplexes. The conductance histograms are
shown for the DNA homoduplex (B), the aegꢀPNA homoduplex (C), the DNA/aegꢀPNA heteroduplex
(D), and the γꢀPNA homoduplex (E). The black curve is a fit of the histogram by a sum of two
Gaussian functions. The peaks in the distributions are associated with major conductance modes,
referred to as high and medium modes.
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The distribution of molecular conductances for the DNA homoduplex is shown in Figure
4B. The conductance at the peak maximum for the high conductance mode (most probable
conductance for the high mode) is 3
x
10ꢀ4 G0, where G0=2e2/h is the quantum of conductance.44
This value agrees with results reported for other 10ꢀmer DNA duplexes with thiol linkers.40, 45ꢀ46
The magnitude of the current responses decreased drastically following roughly 20 angstroms of
retraction, which is consistent with what was reported previously for these molecules.40 This
decrease was attributed to a severing of the hydrogen bonds between the two strands of the
duplex which is the origin of the breakdown mechanism of the molecular junction.
Figure 4C shows the conductance distribution measured for the aegꢀPNA homoduplex.
The entire conductance distribution for the aegꢀPNA is shifted to higher values than that for
DNA (Figure 4B). The distribution for the aegꢀPNA shows three conductance modes. A fit of
these three modes using Gaussians yields most probable conductance values in a ratio of
approximately 54 to 6 to 1 for the high to medium to low modes, respectively (see Supporting
Information). These ratios are similar to those previously reported for alkanedithiols in Au
junctions.38 The values for the high and medium conductance modes of the aegꢀPNA
homoduplex agree well with those that were reported earlier.31 The most probable conductance
for the high mode of the aegꢀPNA duplex is ten times larger than the most probable conductance
for the high mode of the DNA homoduplex.
The conductance distribution for the DNA/aegꢀPNA heteroduplex is shown in Figure 4D
and that for the γꢀPNA homoduplex in Figure 4E. For both duplexes, the most probable
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conductance for the high mode, which is about 4 x 10ꢀ4 G0, falls between the high conductance
mode observed for the DNA and aegꢀPNA homoduplexes. This value is within 25% of the DNA
homoduplex and about 10 times lower than that found for the high conductance mode of aegꢀ
PNA.
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Table 1 summarizes the conductance data for all the duplexes that were studied. The data
show that the DNA/DNA, DNA/aegꢀPNA, and γꢀPNA/γꢀPNA have similar conductances. This
similarity exists despite the fact that the backbones of the duplexes are different in chemical
nature and have different electrostatic charge (see Figure 1). Moreover, the DNA homoduplexes
and the DNA/PNA heteroduplexes form BꢀDNA helixes, whereas aegꢀPNA and γꢀPNA
homoduplexes form a Pꢀtype helix.19ꢀ20, 22ꢀ23
In an earlier study, the γꢀPNA was found to have an electrochemical rate constant smaller
than that of aegꢀPNA by a factor of two,27 and this decrease was attributed to the change in
flexibility of the two duplexes. The difference between the factor of ten in conductance and a
factor of two in electrochemistry experiments may reflect the nonlinear relationship between the
single molecule conductance and electron transfer rate31 as well as the difference in electronic
decoherence between the aegꢀPNA and γꢀPNA.
Linker Study: Figure 5 shows conductance histograms for DNA and PNA homoduplexes with
amino thymidine linkers and a fit to these data by a sum of Gaussians (black line). The DNA
homoduplex has a most probable high conductance value of 1.8 x 10ꢀ3 G0, which is five times
higher than the same mode for the DNA homoduplex with a thiol linker (Figure 4B). Similarly,
the aegꢀPNA homoduplex with the amino thymidine linkers has a most probable high
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conductance mode that is over ten times higher than that observed for the thiol linkers, namely
0.062 G0.
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Figure 5. The conductance histograms for the DNA homoduplex (gray) with amine linkers and PNA
homoduplex (blue) with amine linkers. The peaks in the distributions correspond to major conductance
modes; the overlaid black curves are fits to the histogram by a sum of Gaussian functions.
These findings suggest that the linker strongly affects the conductance of duplexes. With
this increase in overall conductance, the histogram shows the emergence of a low conductance
peak for the DNA duplex, corroborating the earlier supposition that the third, low mode, was not
observed for the thiol linkers because of instrumental limitations. The fact that the conductance
measured for each duplex with amino thymidine linkers is larger than that for the same duplex
with propylthiol linkers is attributed to better electronic coupling between the electrode and the
nucleobase stack mediated by the former linker. It is notable that a conductance value as high as
six percent of G0 has been previously reported only for molecular junctions of a few angstroms,
i.e. much shorter than the 30 angstrom PNA duplex studied here.47ꢀ48
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Summary: Table 1 shows the most probable conductance values for the high (GH) and medium
(GM) conductance modes observed in this study, as well as the ratios of the conductance of the
high mode to medium mode. The conductance for both the high and medium modes increases
from the DNA and γꢀPNA homoduplexes, to the DNA/aegꢀPNA heteroduplex, to the aegꢀPNA
homoduplex. The relative change in the medium conductance peak maximum for the four
duplexes is slightly smaller than the relative change for the high conductance peak maximum;
the more conductive duplexes have a slightly higher ratio. One can postulate that different modes
of the conductance can originate from different nucleic acid duplex conformations and/or from
different linkerꢀgold electrode geometries. The GH/GM ratios reported here for the thiol linker are
in reasonable agreement with previous findings for both nucleic acid duplexes and for
alkanedithiols,31 which suggest that the different conductance modes originate from linkerꢀgold
conformation. The conclusion that different modes originate from changes in the linker group’s
binding geometry are further substantiated by comparison of the different conductance modes for
the same core structures (notably DNA/DNA and aegꢀPNA/aegꢀPNA duplexes) but with
different linkers GH(amine)/GM(amine) and GH(thiol)/GM(thiol) indicates somewhat different
ratios. Since these conductance ratios are somewhat different, this trend cannot be explained
solely by a conformational effect of the molecular backbone because the same ‘high’ to ‘medium’
ratios would be maintained when the linker identity is changed.
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Table 1: Summary of the single molecule conductance measurements for the nucleic acid duplexes.
Linker Type
Duplex
GH /(10-4 G0) GM /(10-4 G0) GH / GM
% GH
9
3.4 ± 1.7
3.6 ± 1.9
4.0 ± 3.3
43 ± 21
0.60 ± 0.32
0.86 ± 0.48
0.92 ± 0.79
5.0 ± 3.0
5.7
4.1
4.4
8.7
47
DNA/DNA
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DNA/aegꢀPNA
γꢀPNA/γꢀPNA
Thiol
aegꢀPNA/aegꢀPNA
18 ± 16
2.5 ± 1.9
59 ± 45
7.2
31
39
DNA/DNA
Amine
620 ± 240
10.5
aegꢀPNA/aegꢀPNA
The relative probabilities of observing the high and medium modes are in reasonable
agreement for the different duplexes. This consistency of the relative amounts of high and
medium modes also supports the notion that the modes arise from different binding geometries,
as one would not expect the relative occurrence of the different linker binding geometries to
change significantly with the molecular backbone. See the Supporting Information for further
discussion.
Computational Results
Computational studies were used to examine features of the backbone changes in the
model system. Molecular dynamics (MD) simulations of the 10ꢀmer duplexes were used to
generate structures for the aegꢀPNA, DNA, DNA/aegꢀPNA, and γꢀPNA duplexes. Quantum
chemistry calculations (with the ZINDO method in Gaussian 0949) of the electronic couplings
were performed on the duplex structures generated by the MD simulations.
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The BüttikerꢀLandauer probe approach was used to calculate the molecular
conductances.50ꢀ52 Büttiker virtual electrodes were introduced to simulate the dephasing induced
by the interaction of the molecule with the environment. In this approach, the conductance was
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calculated with the Hamiltonian
ꢉ
ꢂꢃ ꢄ >< ꢄ + ꢉꢊꢇ ꢅ
ꢄ >< ꢄ + 1 + ℎ. ꢈ.
Eq. 1
∑
|
|
∑
|
|
ꢀꢁ =
ꢃ,ꢃꢆꢇ
ꢃꢋꢇ
ꢃꢋꢇ
where ꢂꢃ is the mean site energy of purine site ꢄ, which is the HOMO energy. These calculations
include the middle six base pairs in the molecular Hamiltonian, while treating the two base pairs
at each end as part of the electrodes. The coupling between electrodes and the terminal molecular
sites is taken to be 0.1 eV. The coupling between Büttiker probes and the molecular sites is set to
0.003 eV for γꢀPNA, DNA/aegꢀPNA, and DNA (indicative of slower dephasing) and 0.01 eV for
aegꢀPNA (indicative of faster dephasing) to reproduce the trend observed in the experimental
measurements. Using this methodology, the calculated conductances were 18.9 × 10ꢊꢌ ꢍꢎ for
aegꢀPNA/aegꢀPNA, 2.26 × 10ꢊꢌ ꢍꢎ for DNA/DNA, 2.67 × 10ꢊꢌ ꢍꢎ for ꢏ ꢀPNA/ ꢏ ꢀPNA, and
1.48 × 10ꢊꢌꢍꢎ for DNA/aegꢀPNA. The conductance for the aegꢀPNA homoduplex was also
calculated using the same Büttiker probe coupling (0.003 eV) that was used for the other
duplexes. In this instance, the calculated conductance is 1.87 × 10ꢊꢌ ꢍꢎ. This indicates that the
increased conductance calculated for the aegꢀPNA homoduplex is representative of the increased
dephasing rate and not an increase in the nucleobase coupling for the aegꢀPNA/aegꢀPNA duplex.
The need for a much faster dephasing rate to capture the experimentally observed conductance
differences supports the notion that backbone flexibility affects the conductance. Faster
dephasing introduces a greater admixture of incoherence in charge/energy transfer, which can
increase the rate of charge53ꢀ55 and energy transfer56ꢀ58 in the weak dephasing regime. When the
dephasing rate increases, a turning point is expected to be found, beyond which the
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charge/energy transfer rates decrease with further increases in the dephasing rate. The
experimental and computational results described here indicate that the dephasing rate in the
nucleic acid molecular systems are in the weaker dephasing regime, where an increase in
dephasing rate produces faster charge transfer rates. Coherent charge transfer may dominate with
some contributions from incoherent channels. The reasons for the rate enhancement produced by
dephasing include: (1) dephasing may suppress destructive coherent interference54 and (2)
dephasing produces spectral broadening and grows the probability of approaching a resonant
mechanism.9, 56 Here, guanines and adenines have a redox potential difference of 0.35 eV.9 The
flickering resonance mechanism, developed to describe the influence of thermal fluctuations on
transient resonant charge transfer, is relevant when thermal fluctuations bring the energies of
molecular species into quasiꢀdegeneracy, enabling charge to move coherently across the system’s
transiently “flat” energy landscape.9 The flickering resonance probability grows for aperiodic
systems as the site energy width grows. Stochastic Schrödinger equation studies of DNA
structures support the idea that fluctuations can accelerate charge transfer in aperiodic systems.59
Exploring the backbone flexibility in the context of helicoidal parameters provides a
framework to understand the electronic dephasing in charge transfer.58ꢀ60 The fluctuations in the
duplex structures were explored by simulating the thermal fluctuations of the structural
parameters. Figure 6 shows the ratio of the structural parameter fluctuations for the aegꢀ
PNA/aegꢀPNA, γꢀPNA/ γꢀPNA, and DNA/aegꢀPNA duplexes relative to DNA/DNA. aegꢀPNA
has systematically higher fluctuation widths in most structural parameters suggesting that aegꢀ
PNA is the most flexible backbone motif. The required Büttiker probe coupling values needed to
reproduce the experimentally determined conductance values appear plausible.59ꢀ60 The γꢀPNA
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Figure 6. The ratio of structural parameter fluctuations (standard deviation of 10,000 MD snapshots,
averaged among the middle 6ꢀmers) between different backbone species as compared to DNA.
duplex has lower parameter fluctuations as compared to aegꢀPNA except for the Buckle metric,
indicating the
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Structural parameters are defined and calculated with x3DNA61. The detailed information about the
parameter means and standard deviations of all base pairs are shown in the Supporting Information.
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effective rigidification associated with γꢀmodification. Pairing a DNA strand with an aegꢀPNA
strand (as in the DNA/aegꢀPNA duplex) rigidifies the whole structure as shown in Figure 6. The
dephasing rate and the induced conductance enhancement are collective features of the systemꢀ
environment interaction, which is represented by the fluctuations of structural parameters in our
case. Dissecting the dephasing rate and the conductance by assigning a weight to each helical
parameter in determining the dephasing rate and conductance is extremely challenging. The
conductance enhancement is only observed in the aegꢀPNA duplex, although the calculated
structural parameter fluctuations of γꢀPNA are slightly smaller than the parameter fluctuation
width in aegꢀPNA (see Figure 6).20 More quantitative descriptions of the nucleic acids’ structural
parameters are limited by available molecular dynamics methods and the force fields. Our
qualitative study found that dephasing due to molecular flexibity is an essential parameter that
influences charge transfer rates, other than the structure of the energy landspace and the
electronic coupling strength. Details on the conductance calculations, based on the Büttikerꢀ
Landauer method, are provided in the supporting information.
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Note that the effective charge injection between the STM tip and the guanine (for the
amine modified structures) is mediated by a thymine base, which should enhance the effective
coupling compared to the case in the thiol modified structures. Finally, we note that the
magnitude of the computed conductances is much less than the measured values. Our model
describes each purine as one localized orbital (the purine HOMO). Including more orbitals may
increase the calculated conductance. The Landauer approach was successfully used to provide
qualitative predictions of molecular conductances, although the numerical conductance values
are significantly lower than the measured values.6, 62
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Conclusions
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The most probable molecular conductance of 10ꢀbase pair nucleic acid duplexes that have
identical nucleobase sequence but different backbones show a 200ꢀfold range. The value of 0.06
G0 measured for the aegꢀPNA duplex is unprecedented for a molecule that is ~ 30ꢀÅ long. The
aegꢀPNA has a high mode conductance that is 13 times higher than that of the corresponding
DNA duplex when the linker is propylthiol linker and 34 times higher than the DNA when the
linker is aminoꢀC2ꢀthymidine. These findings show that both the linker and the nucleic acid
backbone play critical roles in determining the overall magnitude of the measured conductance.
Hence, the molecular conductance for these ~30ꢀÅ long nucleic acid duplexes cannot be
modeled as an incoherent sum of charge injection, charge transport, and charge escape steps, but
must be treated as coherent (or semiꢀcoherent) transport through the molecule.
Methods
Synthesis of PNA monomers and linkers
All reactions were performed under nitrogen atmosphere unless otherwise stated. All
commercially available materials were used without further purification unless otherwise
specified. Anhydrous solvents, purchased from EMD Millipore, such as dimethylformamide
(DMF), dichloromethane (DCM), and tetrahydrofuran (THF), were dried by standard methods
and freshly distilled prior to use. All anhydrous reagents were purchased from Aldrich. Common
reagents were purchased from either ChemꢀImpex or Alfa Aesar. 1HꢀNMR and 13CꢀNMR spectra
were acquired on a Bruker Avance AVꢀ300 or 500 MHz NMR spectrometer.
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The thiol linker was introduced at the Nꢀend of PNA oligomers using 4ꢀ(tritylthio)butyric
acid, which was synthesized by a published procedure,63 Sꢀalkylation of the commercially
available trityl mercaptan. The thiol linker was introduced at the Cꢀend of the PNA oligomers
using 3ꢀaminoꢀ1ꢀpropanethiol hydrochloride, which is commercially available.
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The thymidine 5ꢀC2 amino linker was synthesized using a modified published procedure
according to the general Scheme 1.64 In step (i), commercially available iodouracil 1 was
alkylated at N1 by αꢀethyl bromoacetate in the presence of potassium carbonate in anhydrous
DMF under nitrogen at room temperature for 24 h to give ethyl ester 2 in quantitative yield. In
step (ii), the iodo group of 2 was exchanged with an acryloyl group via a Heck reaction with
acrylic acid to give the carboxylic acid 3 in 60 % yield. In step (iii), coupling of the carboxylic
acid 3 with Bocꢀprotected ethylenediamine was accomplished by activation with HATU in the
presence of DIEA in anhydrous DMF. Hydrolysis of the resulting ethyl ester to carboxylic acid
using LiOH led to the final product 5 in 75% yield over last two steps. Details of the synthesis
are given in the Supporting Information.
O
O
O
O
O
I
NHBoc
HN
HN
HN
N
O
OH
(iii) and (iv)
H
(i)
(ii)
I
HN
O
N
O
N
O
N
O
O
O
O
N
H
1
OEt
OEt
3
OH
5
2
Scheme 1. (i) K2CO3, DMF, αꢀbromo ethyl acetate, DMF, 0oC to room temperature, 24 h, quantitative
yield; (ii) Pd(OAc)2, Bu4NBr, DMF/DIE/H2O, acrylic acid, 80ꢀ90oC, 16h, 60%; (iii)
BocNH(CH2)2NH2.HCl, HATU, DIEA, DMF, 0 oC to room temperature, 12 h; (iv) LiOH, THF, 0oC to rt,
12 h, 75%.
Synthesis of LS-γPNA monomers
Bocꢀprotected LSꢀγPNA monomers were synthesized by adapting the procedures
described by Ly et al. (Scheme 2).18 In order to increase the reaction yield some modifications
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have been made on the first two steps and the last step of the reaction scheme. Specifically,
instead of amidation of the Bocꢀprotected Lꢀserine 6 using N,Oꢀdimethylhydroxylamine
hydrochloride, the carboxylic end of compound 6 was reduced to its alcohol derivative 7 in the
presence of iꢀbuthylchloroformate (IBCF), Nꢀmethyl morpholine (NMP), and sodium
borohydride. The alcohol derivative 7 was converted to aldehyde 8 via Swern oxidation using
oxalyl chloride, dimethylsulsoxide, and triethyl amine. The reaction yield was almost
quantitative. The Swern oxidation provides the product monomers in higher purity than the
previously published procedure and eliminates the use of the expensive reagent CH3NHOCH3ꢀ
HCl. Reductive amination of intermediate 8 with ethyl ester glycine gave Aegꢀbackbone 9 with
40 % yield. Coupling of the aegꢀbackbone with the corresponding nucleobases followed by
hydrolysis led the γꢀmodified monomers 10a-d.
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O
O
BocHN
BnO
BocHN
BnO
BocHN
BnO
BnO
OH
(ii)
OH
(i)
H
O
H
N
BocHN
O
(iii)
NB
6
7
8
9
(iv)
NB
BnO
O
BnO
BocHN
O
O
O
N
N
(v)
BocHN
OH
O
11a-d
10a-d
Scheme 2. Synthesis of γꢀserine modified PNA monomers (i) NMM, ClCO2iꢀBu, DME, NaBH4,
quantitative Yield (ii)DMSO, (COCl)2, Et3N, DCM, N2, ꢀ78oC, % 95(iii) ethyl ester glycine, MeOH, 4 °C,
4 h, then AcOH, NaBH(OAC)3, 30 min., % 40, (iv) carboxymethylnucleobase (B: A, G, C, T), DCC,
DhbtOH, DMF, 40°C, 24 h, %39-63 (v) NaOH/THF (1:1), 30 min., 0oC. %76-96.
Synthesis of PNA oligomers
Boc/Zꢀprotected and Fmoc/Bhoc PNA monomers were purchased from PolyOrg Inc and ASM
Research Chemicals and used without further purification. The oligomers were purified using
reversedꢀphase HPLC and characterized by MALDIꢀTOF. All PNA solutions were prepared in
nanopure water.
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The PNA oligomers containing thymidine 5ꢀC2 amino [T(C2ꢀNH2)] were synthesized
manually on Rinkꢀamide AM resin purchased from Novabiochem following the standard Fmoc
procedures of solidꢀphase peptide synthesis. T(C2ꢀNH2) acetic acid linker was added on the Nꢀend
of a PNA oligomer as the side chain of the BocꢀDAP(Fmoc)ꢀOH (Bocꢀ3ꢀ(Fmocꢀamino)ꢀLꢀ
alanine) amino acid which was purchased from SigmaꢀAldrich. The PNA oligomers were
cleaved from the resin using TFA/DCM/TIS (10:85:5) for 30 min. The deprotection of side chain
was effected by 50% TFAꢀDCM (TIS used as scavenger) for 1 h.
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The PNA oligomers containing a Cꢀend thiol linker were synthesized using 2ꢀchlorotrityl
resin downloaded with 3ꢀAminoꢀ1ꢀpropanethiol hydrochloride by a published protocol65 using
Fmoc strategy. The PNA oligomers with an Nꢀend thiol linker were synthesized on MBHA resin
(purchased from Peptides International) using a Boc strategy. The PNA was cleaved using
TFMSA/TFA/mꢀcresol/thioanisole (20:60:10:10) and TFA/triisopropylsilane/water (95:2.5:2.5)
for Boc and Fmoc strategy, respectively.
LSꢀγPNA oligomers were synthesized manually on methyl benzhydryl amine (MBHA)
resin by standard Bocꢀsolid phase synthesis method. Further details and characterization of the
oligomers are provided in the Supporting Information.
Preparation of samples for conductance measurements
Nucleic Acid Duplexes: The DNA strands were purchased from Integrated DNA Technologies or
Alpha DNA, and the PNA strands were synthesized by the aforementioned procedure. Duplexes
were hybridized by heating a solution containing 20 ꢁM of each nucleic acid strand in a pH = 7.0
o
TrisꢀEDTA buffer and 50 mM NaCl. The solution was heated to 90 C for 10 minutes and then
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allowed to cool back to room temperature over 2ꢀ3 hours. This procedure yields duplexes and
was confirmed by absorbance and circular dichroism spectroscopy.
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Gold Substrates: Ultraflat gold substrates were prepared using the templateꢀstripping process.66
100 nm gold films were evaporated onto freshlyꢀcleaved mica (AJA ATCꢀT Series Thermal
Evaporation System). Piranhaꢀcleaned glass slips (10 mm x 25 mm) were affixed to the gold
films and peeled off to transfer the gold to the slips prior to each experiment. The atomically flat
gold substrates were coated with the solution containing hybridized strands for roughly 10
seconds and then washed with water, washed with ethanol, and dried under an argon stream. The
duplexes bind to the gold substrates via the terminal linker groups and remain on the substrate
following washing and drying.
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Conductance Measurements and Analysis
All measurements were performed using an Agilent 5500 Scanning Probe Microscope
system equipped with an environmental chamber. The chamber was housed in a homemade
acoustically isolated Faraday cage seated on an antiꢀvibrational system (Table Stable) that was
mounted on an optical table. Data collection was performed using a modified version of the
STMꢀcontrolled break junction method.36ꢀ37 An STM tip was repeatedly driven to the surface of
the gold substrates and withdrawn at a constant speed of 10 nm sꢀ1. During the retraction period,
molecular junctions can form as molecules bridge the gap between the gold substrate and the
gold tip. Thousands of trajectories were collected for each duplex, requiring multiple substrates
and STM tips to collect a full set. The gold STM tips (0.25 mm, 99.95% gold wire, Alfa Aesar)
were freshly cut prior to each experiment. All experiments were performed under an argon
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atmosphere and the substrates were immersed in mesitylene. The applied bias was a triangular
waveform with a modulation frequency of 500 Hz (Stanford Research Systems, DS345 Function
Generator). A bias of 50 ± 50 mV was applied in the measurement of every duplex with the
exception of the aegꢀPNA/aegꢀPNA duplex with amine linkers; for these measurements, the
applied bias was 5 ± 5 mV. All measurements were performed using a 10 nA/V preamplifier.
Data filtering and analysis were performed using a custom Matlab code. The currentꢀ
distance trajectories were filtered to remove trajectories that did not display molecular junctions.
The trajectories were partitioned into periods established by the applied bias and fit to current
responses generated using a library of resistance values based on a previous protocol.37 For
certain duplexes, multiple bias ranges were used to ensure that the highest conductance mode
was observable in each instance.
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Molecular Dynamics
The initial structures of DNA are obtained with an x3DNA webserver61. PNA structures
for this sequence were generated by a custom program. The ꢏꢀPNA structures were assembled
by replacing the H2’’ atom on the PNA structures backbone with a C atom. The CHARMM
force field67 was used and CGenFF68 was used to find force field parameters for the amine linker.
DNA/aegꢀPNA was built in GaussView,69 starting from PDB:1PDT.23
For each structure, multiple MD simulations were performed and snapshots were taken at
1frame/ps. Two nucleobases (donor and acceptor bases in coupling calculations) are extracted
from each snapshot. Backbones, solvent molecules, and counterꢀions are removed. Hydrogen
atoms are patched to dangling bonds.26 Coupling calculations were performed with the block
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diagonalization method70 based on the Fock matrix obtained from the ZINDO semiꢀempirical
quantum method embedded in Gaussian 09.49
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Conductance Calculations
To explore the conductivity of the nucleic acids, we used a BüttikerꢀLandauer model,71
where the Büttiker probes perturb the coherence and introduce an incoherent charge transfer
mechanism. The BüttikerꢀLandauer model is widely used to simulate molecular junction
conductance.72ꢀ74 Because the measured conductance arises mainly from hole transfer in our
experiments32ꢀ33 and hole transfer is dominantly mediated by purine bases, we only consider
purine bases (guanine and adenine) in our model.
In our model, the site energy of guanine (HOMO) is 0.35 eV higher than the site energy
of adenine (HOMO).9 The Fermi level of the Au electrodes was placed 0.8 eV higher in energy
than the guanine HOMO.75 The electronic coupling between nearest neighbor purine sites
ꢅꢃ,ꢃꢆꢇ was obtained from quantum calculations and averaged from 1000 MD snapshots. The
coupling calculations for all species are given in Table S9 in the Supporting Information.
Supporting Information
The supporting information provides 1) details on the synthesis and characterization of
the nucleic acid oligomers, 2) details on the synthesis and characterization of the linker moieties,
3) details on the conductance measurements and data analysis, 4) details on the molecular
dynamics simulations of the duplexes, and 5) details on the quantum chemistry calculations.
Acknowledgements
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The authors acknowledge support from the National Science Foundation (1412030 to D.H.W,
1413202 to C.A., and 1413257 to D.N.B.). E.B. acknowledges a fellowship from the Pittsburgh
Quantum Institute during part of this work.
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References
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
1.
2.
3.
Rothemund, P. W. K., Nature 2006, 440, 297ꢀ302.
Pinheiro, A. V.; Han, D.; Shih, W. M.; Yan, H., Nat. Nanotechnol. 2011, 6, 763ꢀ72.
Le, J. D.; Pinto, Y.; Seeman, N. C.; MusierꢀForsyth, K.; Taton, T. A.; Kiehl, R. A., Nano
Lett. 2004, 4, 2343ꢀ2347.
Renaud, N.; Harris, M. A.; Singh, A. P.; Berlin, Y. A.; Ratner, M. A.; Wasielewski, M.
R.; Lewis, F. D.; Grozema, F. C., Nat. Chem. 2016, 8, 1015ꢀ1021.
Paul, A.; Watson, R. M.; Wierzbinski, E.; Davis, K. L.; Sha, A.; Achim, C.; Waldeck, D.
H., J. Phys. Chem. B 2010, 114, 14140ꢀ14148.
Venkatramani, R.; Davis, K. L.; Wierzbinski, E.; Bezer, S.; Balaeff, A.; Keinan, S.; Paul,
A.; Kocsis, L.; Beratan, D. N.; Achim, C.; Waldeck, D. H., J. Am. Chem. Soc. 2011, 133,
62ꢀ72.
Beratan, D. N.; Waldeck, D. H., Nat. Chem. 2016, 8, 992ꢀ993.
Lu, Q.; Liu, K.; Zhang, H.; Du, Z.; Wang, X.; Wang, F., ACS Nano 2009, 3, 3861ꢀ8.
Zhang, Y.; Liu, C.; Balaeff, A.; Skourtis, S. S.; Beratan, D. N., Proc. Natl. Acad. Sci.
U.S.A. 2014, 111, 10049ꢀ10054.
4.
5.
6.
7.
8.
9.
10.
11.
12.
Li, Y.; Artés, J. M.; Hihath, J., Small 2016, 12, 432ꢀ437.
Artes, J. M.; Li, Y.; Qi, J.; Anantram, M. P.; Hihath, J., Nat. Commun. 2015, 6, 8870.
Bag, S.; Mogurampelly, S.; Goddard Iii, W. A.; Maiti, P. K., Nanoscale 2016, 8, 16044ꢀ
52.
Wang, K.; Hamill, J. M.; Wang, B.; Guo, C. L.; Jiang, S. B.; Huang, Z.; Xu, B. Q., Chem.
Sci. 2014, 5, 3425ꢀ3431.
Guo, C.; Wang, K.; ZerahꢀHarush, E.; Hamill, J.; Wang, B.; Dubi, Y.; Xu, B., Nat. Chem.
2016, 8, 484ꢀ490.
Wierzbinski, E.; de Leon, A.; Davis, K. L.; Bezer, S.; Wolak, M. A.; Kofke, M. J.; Schlaf,
R.; Achim, C.; Waldeck, D. H., Langmuir 2012, 28, 1971ꢀ1981.
Liu, S.; Clever, G. H.; Takezawa, Y.; Kaneko, M.; Tanaka, K.; Guo, X.; Shionoya, M.,
Angew. Chem. Int. Ed. 2011, 50, 8886ꢀ8890.
Egholm, M.; Buchardt, O.; Nielsen, P. E.; Berg, R. H., J. Am. Chem. Soc. 1992, 114,
1895ꢀ1897.
DragulescuꢀAndrasi, A.; Rapireddy, S.; Frezza, B. M.; Gayathri, C.; Gil, R. R.; Ly, D. H.,
J. Am. Chem. Soc. 2006, 128, 10258ꢀ67.
Rasmussen, H.; Kastrup, J. S.; Nielsen, J. N.; Nielsen, J. M.; Nielsen, P. E., Nat. Struct.
Biol. 1997, 4, 98ꢀ101.
He, W.; Crawford, M. J.; Rapireddy, S.; Madrid, M.; Gil, R. R.; Ly, D. H.; Achim, C.,
Mol. Biosyst. 2010, 6, 1619ꢀ29.
13.
14.
15.
16.
17.
18.
19.
20.
21.
He, W.; Hatcher, E.; Balaeff, A.; Beratan, D. N.; Gil, R. R.; Madrid, M.; Achim, C., J.
Am. Chem. Soc. 2008, 130, 13264ꢀ73.
Watson, J. D.; Crick, F. H., Nature 1953, 171, 737ꢀ8.
22.
23.
Eriksson, M.; Nielsen, P. E., Nat. Struct. Mol. Biol. 1996, 3, 410ꢀ413.
27
ACS Paragon Plus Environment

Journal of the American Chemical Society
Page 28 of 30
1
2
3
4
5
6
7
8
24.
Yeh, J. I.; Shivachev, B.; Rapireddy, S.; Crawford, M. J.; Gil, R. R.; Du, S.; Madrid, M.;
Ly, D. H., J. Am. Chem. Soc. 2010, 132, 10717ꢀ10727.
Brown, S.; Thomson, S.; Veal, J.; Davis, D., Science 1994, 265, 777ꢀ780.
Hatcher, E.; Balaeff, A.; Keinan, S.; Venkatramani, R.; Beratan, D. N., J. Am. Chem. Soc.
2008, 130, 11752ꢀ61.
25.
26.
9
27.
Wierzbinski, E.; de Leon, A.; Yin, X.; Balaeff, A.; Davis, K. L.; Rapireddy, S.;
Venkatramani, R.; Keinan, S.; Ly, D. H.; Madrid, M.; Beratan, D. N.; Achim, C.;
Waldeck, D. H., J. Am. Chem. Soc. 2012, 134, 9335ꢀ9342.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
28.
29.
O'Neill, M. A.; Barton, J. K., J. Am. Chem. Soc. 2004, 126, 11471ꢀ83.
Thazhathveetil, A. K.; VuraꢀWeis, J.; Trifonov, A.; Wasielewski, M. R.; Lewis, F. D., J.
Am. Chem. Soc. 2012, 134, 16434ꢀ40.
O'Neill, M. A.; Barton, J. K., J. Am. Chem. Soc. 2004, 126, 13234ꢀ5.
Wierzbinski, E.; Venkatramani, R.; Davis, K. L.; Bezer, S.; Kong, J.; Xing, Y.; Borguet,
E.; Achim, C.; Beratan, D. N.; Waldeck, D. H., ACS Nano 2013, 7, 5391ꢀ5401.
Xiang, L.; Palma, J. L.; Bruot, C.; Mujica, V.; Ratner, M. A.; Tao, N., Nat. Chem. 2015,
7, 221ꢀ226.
Liu, C.; Xiang, L.; Zhang, Y.; Zhang, P.; Beratan, D. N.; Li, Y.; Tao, N., Nat. Chem.
2016, 8, 941ꢀ945.
Yin, X.; Wierzbinski, E.; Lu, H.; Bezer, S.; de Leon, A. R.; Davis, K. L.; Achim, C.;
Waldeck, D. H., J. Phys. Chem. A 2014, 118, 7579ꢀ89.
Beratan, D.; Betts, J.; Onuchic, J., Science (Washington, DC, U. S.) 1991, 252, 1285ꢀ
1288.
Xu, B.; Tao, N. J., Science (Washington, DC, U. S.) 2003, 301, 1221ꢀ1223.
Beall, E.; Yin, X.; Waldeck, D. H.; Wierzbinski, E., Nanoscale 2015, 7, 14965ꢀ14973.
Li, C.; Pobelov, I.; Wandlowski, T.; Bagrets, A.; Arnold, A.; Evers, F., J. Am. Chem. Soc.
2008, 130, 318ꢀ326.
Wierzbinski, E.; Arndt, J.; Hammond, W.; Slowinski, K., Langmuir 2006, 22, 2426ꢀ2429.
Bruot, C.; Xiang, L.; Palma, J. L.; Tao, N., ACS Nano 2015, 9, 88ꢀ94.
Guo, X.; Gorodetsky, A. A.; Hone, J.; Barton, J. K.; Nuckolls, C., Nat. Nanotechnol.
2008, 3, 163ꢀ167.
Nogues, C.; Cohen, S. R.; Daube, S.; Apter, N.; Naaman, R., J. Phys. Chem. B 2006, 110,
8910ꢀ8913.
30.
31.
32.
33.
34.
35.
36.
37.
38.
39.
40.
41.
42.
43.
44.
Haiss, W.; Martín, S.; Leary, E.; Zalinge, H. v.; Higgins, S. J.; Bouffier, L.; Nichols, R. J.,
J. Phys. Chem. C 2009, 113, 5823ꢀ5833.
van Wees, B. J.; van Houten, H.; Beenakker, C. W.; Williamson, J. G.; Kouwenhoven, L.
P.; van der Marel, D.; Foxon, C. T., Phys. Rev. Lett. 1988, 60, 848ꢀ850.
Xu, B. Q.; Zhang, P. M.; Li, X. L.; Tao, N. J., Nano Lett. 2004, 4, 1105ꢀ1108.
van Zalinge, H.; Schiffrin, D. J.; Bates, A. D.; Haiss, W.; Ulstrup, J.; Nichols, R. J.,
ChemPhysChem 2006, 7, 94ꢀ98.
Chen, W.; Widawsky, J. R.; Vázquez, H.; Schneebeli, S. T.; Hybertsen, M. S.; Breslow,
R.; Venkataraman, L., J. Am. Chem. Soc. 2011, 133, 17160ꢀ17163.
Yelin, T.; Korytar, R.; Sukenik, N.; Vardimon, R.; Kumar, B.; Nuckolls, C.; Evers, F.;
Tal, O., Nat. Mater. 2016, 15, 444ꢀ449.
45.
46.
47.
48.
49.
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J.
R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.;
Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada,
28
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Page 29 of 30
Journal of the American Chemical Society
1
2
3
4
5
6
7
8
9
M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda,
Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A.; Peralta, J. E.; Ogliaro, F.;
Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.;
Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.;
Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.;
Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.;
Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V.
G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas;
Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J., Gaussian 09, Revision B.01.
Wallingford CT, 2009.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
50.
Venkatramani, R.; Wierzbinski, E.; Waldeck, D. H.; Beratan, D. N., Faraday Discuss.
2014, 174, 57ꢀ78.
Büttiker, M., Phys. Rev. B 1985, 32, 1846ꢀ1849.
51.
52.
53.
54.
Büttiker, M., Phys. Rev. B 1986, 33, 3020ꢀ3026.
Ashkenazi, G.; Kosloff, R.; Ratner, M. A., J. Am. Chem. Soc. 1999, 121, 3386ꢀ3395.
Goldsmith, R. H.; Wasielewski, M. R.; Ratner, M. A., J. Phys. Chem. B 2006, 110,
20258ꢀ20262.
55. Weiss, E. A.; Katz, G.; Goldsmith, R. H.; Wasielewski, M. R.; Ratner, M. A.; Kosloff, R.;
Nitzan, A., J. Chem. Phys. 2006, 124, 074501.
Chin, A. W.; Datta, A.; Caruso, F.; Huelga, S. F.; Plenio, M. B., New J. Phys. 2010, 12,
065002.
56.
57.
58.
59.
60.
61.
62.
Plenio, M. B.; Huelga, S. F., New J. Phys. 2008, 10, 113019.
Patrick, R.; Masoud, M.; Ivan, K.; Seth, L.; Alán, A.ꢀG., New J. Phys. 2009, 11, 033003.
Liu, C.; Beratan, D. N.; Zhang, P., J. Phys. Chem. B 2016, 120, 3624ꢀ3633.
Weiss, U., Quantum Dissipative Systems. World Scientific: Singapore, 1999.
Lu, X.ꢀJ.; Olson, W. K., Nucleic Acids Res. 2003, 31, 5108ꢀ5121.
Xing, Y.; Park, T.ꢀH.; Venkatramani, R.; Keinan, S.; Beratan, D. N.; Therien, M. J.;
Borguet, E., J. Am. Chem. Soc. 2010, 132, 7946ꢀ7956.
Qvit, N.; Reuveni, H.; Gazal, S.; Zundelevich, A.; Blum, G.; Niv, M. Y.; Feldstein, A.;
Meushar, S.; Shalev, D. E.; Friedler, A.; Gilon, C., J. Comb. Chem. 2008, 10, 256ꢀ66.
Oquare, B. Y.; Taylor, J. S., Bioconjug. Chem. 2008, 19, 2196ꢀ204.
Mourtas, S.; Katakalou, C.; Nicolettou, A.; Tzavara, C.; Gatos, D.; Barlos, K.,
Tetrahedron Lett. 2003, 44, 179ꢀ182.
Hegner, M.; Wagner, P.; Semenza, G., Surf. Sci. 1993, 291, 39ꢀ46.
MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M.
J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; JosephꢀMcCarthy, D.; Kuchnir, L.; Kuczera, K.;
Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W.
E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.;
WiórkiewiczꢀKuczera, J.; Yin, D.; Karplus, M., J. Phys. Chem. C 1998, 102, 3586ꢀ3616.
Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian,
E.; Guvench, O.; Lopes, P.; Vorobyov, I.; MacKerell, A. D., J. Comput. Chem. 2010, 31,
671ꢀ690.
63.
64.
65.
66.
67.
68.
69.
Dennington, R.; Keith, T. A.; Millam, J. M., GaussView, Version 6, Semichem Inc.,
Shawnee Mission, KS, 2016.
Scholes, G. D., Annu. Rev. Phys. Chem. 2003, 54, 57ꢀ87.
70.
71.
Qi, J.; Edirisinghe, N.; Rabbani, M. G.; Anantram, M. P., Phys. Rev. B 2013, 87, 085404.
29
ACS Paragon Plus Environment