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NATURE CHEMISTRY | www.nature.com/naturechemistry 2

SUPPLEMENTARY INFORMATIONDOI: 10.1038/NCHEM.2480

This document includes:

Supplementary Text (SI 1-10)

Supplementary Figure 1-10

Supplementary Table 1-4

Related References 1-8

Table of Content

SI-1. Chemicals and Materials………………………………………………………………..... 3

SI-2. Imaging analysis of duplex DNA and DNA-coralyne complex monolayers on Au

surface……………………….…………………………………………………..……………..... 3

SI-3. Structure and energy simulations of intercalating coralyne molecules into DNA……. 4

SI-4. Stability of DNA-coralyne complex……………………………………..……………...... 8

SI-5. Complementary study on poly d(CG) 4 DNA…………………………..……………....... 9

SI-6. Landauer Formalism calculation……………………………………..……………....... 10

SI-7. Theoretical calculations……………………………………..……………....................... 11

SI-8. Microscopic origin of rectification………………………..……………......................... 12

SI-9. Considering incoherent transport………………………..…………….......................... 13

SI-10. Cyclic bias sweeping measurements…………….……………...................................... 15

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SI-1. Chemicals and Materials

Oligonucleotides were ordered from Integrated DNA Technology (IDT, Coralville, IA, USA)

with 3’-thiol linkers. DNA sequences for measurement were 5’-CGC GAA ACG CG-3’

(DNA(A)) and 5’-CGC GTT TCG CG-3’ (DNA(T)), respectively. DNA sequence 5’-CGC GCG

CG-3’ (poly d(CG)4) was also measured as complementary study. Coralyne chloride was

purchased from Sigma-Aldrich (St. Louis, MO, USA) and dissolved in water before use. DNA

was stored in PBS (10 mM phosphate, 100 mM NaCl, pH 7.4) at -20 ˚C.

The concentrations of DNA and coralyne were determined by UV-Vis spectroscopy with the

correspondingextinction coefficients: DNA(A), ε 260 = 105 500 M-1cm-1; DNA(T), ε 260 = 94 200

M-1cm-1; coralyne chloride, ε 420 = 14 500 M-1cm-1.

Absorption spectra were recorded on a UV-1700 spectrophotometer (Shimadzu Scientific

Instruments). Circular dichroism (CD) was measured at 25 °C on Chirascan spectrometer with 1mm optical-path quartz cuvette.

SI-2. Imaging analysis of duplex DNA and DNA-coralyne complex monolayers on Au

surface

Supplementary Figure 1. DNA immobilization on Au (111) surface a , STM image of

Au(111) surface without sample molecules.b , STM image of native DNA monolayer on Au(111) surface.c, STM image of DNA-coralyne complex monolayer on Au (111) surface. Sample

conditions for STM imaging were 10 mM phosphate, 100 mM NaCl, pH 7.4. The obtained STM

images were processed by WSxM software.1

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Supplementary Table 1: Roughness analysis for duplex DNA and DNA-coralyne complex

monolayers on Au surface*.

RMS

Roughness (Å)

Maximum

Value (Å)

Roughness

Average (Å)

Average

Height (Å)

DNA-Coralyne 1.0401 7.9331 0.7971 3.6153

DNA 0.3472 3.4727 0.2715 1.5315

*As duplex DNA and DNA-coralyne complex formed relatively high-packed monolayers on Au

surface, respectively, the measured height from roughness analysis is much smaller than the

actual value.

SI-3. Structure and energy simulations of intercalating coralyne molecules into DNA

The positions of coralyne molecules between the mismatched adenine base pairs were adjusted

to reduce the steric hindrance among the atoms in DNA and coralyne molecules.2 The

mismatched DNA in B-form DNA containing one coralyne (DNA-1C) and two coralynes

(DNA-2C) are shown in Supplementary Figure 2. Here, the DNA-2C containing two coralynes

in symmetric stereoisomer formd in Supplementary Figure 3 is shown as an example for binding

energy comparison with DNA-1C and native DNA. For each structure, the molecular dynamics

simulation of 8 ns equilibration in solvatebox TIP3P was conducted by AMBER 11.3 The binding energies of DNA-1C and DNA-2C were calculated by MM-PBSA method in AMBER

11. The calculated Gibbs free energy change from B-form DNA helix to DNA-1C is -35.9 ± 2.8

kcal/mol, and the reaction process from DNA-1C to DNA-2C has an additional -39.9 ± 2.8

kcal/mol energy change. Both DNA-1C and DNA-2C show big changes in binding energy.

Moreover, the mismatched DNA with two coralyne molecules (DNA-2C) is the most stable

complex among these three structures.

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Supplementary Figure 2. Simulated DNA-coralyne complexes and the binding energies.

The left structure is the B-form DNA with three A-A mismatches. The middle one is the DNA

with one coralyne molecule intercalated between two A-A base pairs. The right one is the DNA

with two coralyne molecules intercalated among three A-A base pairs in stereoisomer formd of

Supplementary Figure 3. The six mismatched (dA) bases are highlighted in yellow, the coralyne

molecules are highlighted with surface representation.

In our single-molecular electrical measurements, the most probable DNA-coralyne complex

structure should be the source of I-V rectification because the core of STM-BJ technique lies on

identifying the statistically most populated ones. It is also important to point out that without

control in molecular orientation, single dominant molecular junction conductance and

unidirectional rectifying I-V are observed for the studied DNA-coralyne complex, which

strongly indicated that the two coralyne molecules are at intercalation sites symmetric to the

center of DNA and the two coralynes are also in a symmetric orientation. The complementary

study on poly d(CG)4 DNA indicates that coralyne intercalating into CG-CG sites does not have

significant impact on the overall charge transport properties of the molecular junction

(Supplementary Figure 6). More importantly, when two coralyne molecules symmetrically

inserted into CG-GC sites, the three mismatched bps would decrease the conductance by several

orders of magnitude,4 which contradicts with the measured DNA-coralyne conductance that is

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comparable with native DNA conductance. Thus, the possible intercalation sites of the two

coralyne molecules could be at AA-AA or AA-CG, though the mismatched AA-AA has been

reported to be more favorable intercalation sites for coralyne molecule.5, 6

To figure out which coralyne stereoisomer forms the most stable, i.e. probable structure, we

performed structural simulation and binding energy calculation on the possible intercalation sites

and coralyne orientation forms. As coralyne has four possible stereoisomers within DNA

(Supplementary Figure 3), there are totally eight possible coralyne stereoisomers with symmetric

orientation for both cases of AA-AA and AA-CG (Supplementary Figure 4). As listed in

Supplementary Table 2, the binding energy calculation suggests that the most stable structure of

the DNA-coralyne complex is the one with two coralyne molecules intercalated into AA-AA

sites which maintain the stereoisomer of d in Supplementary Figure 3. Furthermore, considering

the working principle of STM-BJ technique, solid contact between molecule and the electrodes isnecessary for the formation of molecular junctions. In our experiments, the thiol linker was

modified on the 3’ end of the DNA strand to make contact with Au electrode through Au-S bond.

Thus, it matters whether the 3’ end of the DNA is clearly exposed from the overall DNA

structure. We see from Supplementary Figure 4 that the two 3’ ends of the DNA are clearly

exposed for coralyne intercalation into two symmetric AA-AA sites, which is in sharp contrast to

the coralyne intercalation into AA-CG sites where one of the 3’ end is buried inside the DNA

structure. This means the DNA-coralyne complex with two coralynes intercalated into AA-AAsites are more favorable in terms of molecular junction formation, and therefore more likely to

contribute to the conductance and I-V measurements.

To the best of our efforts, combining all the experimental controls and simulation results, we

are led to the conclusion that DNA with two coralyne molecules intercalated into the mismatched

A-A bps are the most probable source of the rectification behavior, even though this seems to

contradict with the “neighboring exclusion principle”. Given the small difference among the

calculated binding energy of different coralyne stereoisomers and the lack of reliable techniqueto determine the exact location of the coralyne molecules, we would conclude here that the

rectification we observed is from DNA containing two coralyne molecules with a symmetric

overall structure.

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Supplementary Figure 3. Four possible stereoisomers for coralyne.

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Supplementary Figure 5. DNA stability characterization. a, Temperature-dependent UV

(absorption at 260 nm) measurement for the DNA(GAG)-coralyne complex studied in the main

text. The dashed line is the room temperature for our electrical measurements.b, CDmeasurement at 25oC for DNA-coralyne complex. The inset is a magnified view of the signature

bump between 310-350 nm induce by coralyne intercalation into DNA.

SI-5. Complementary study on poly d(CG) 4 DNA

Complementary measurements were performed with another DNA/DNA-molecule system: poly

d(CG)4/poly d(CG)4-coralyne complex. The significance for studying this DNA sequence as a

complementary study is in two aspects. First, we can test the role of coralyne intercalation intomismatched A-A on rectification by removing the mismatched A-A. Second, by using poly

d(CG)4 DNA, an important change from 5’-CGCGAAACGCG-3’ to poly d(CG)4 is the switch of

charge transport regime from coherent tunneling to incoherent hopping. In other word, we also

test if the rectification was mainly associated with the perturbation of charge tunneling process as

suggested by the theoretical calculation in the manuscript. As shown in Supplementary Figure

6a, the Job plot shows an inflection point of 2, suggesting that there are only one coralyne in poly

d(CG)4 DNA. Using STM-BJ technique, the log-scale conductance histogram and I-V curve

were measured (Supplementary Figure 6b and 6c). The conductance of single native poly d(CG)4

DNA molecule increases over two orders of magnitude comparing with DNA(GAG)-coralyne

complex, suggesting a fairly significant influence of the tunneling barrier formed by the

mismatched bps on DNA conductance (Supplementary Figure 6b). What we also see is that the

intercalation of coralyne into poly d(CG)4 induced no obvious change but only a slight increase

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in single-molecule conductance. From Supplementary Figure 6c, we find that the I-V behavior of

native poly d(CG)4 DNA and poly d(CG)4 DNA-coralyne complex are both highly symmetric.

This complementary study is a sharp contrast to the I-V rectification shown in the main text. The

comparison between these two DNA/DNA-coralyne systems suggests that the observed

rectification was essentially caused by coralyne intercalation into sites associated with

mismatched A-A bps and the underlying mechanism should be interpreted within the electron

tunneling regime as stated in the main text.

Supplementary Figure 6. The control experiment on poly d(CG) 4 DNA. a, The Job plot of

DNA-coralyne interaction. The inflection point of 2 indicates that one coralyne molecule was

inserted into formed DNA duplex.b, Log-scale conductance histograms of poly d(CG)4 DNA

with (blue) and without (black) coralyne measured at 0.3V. The conductance histograms were

constructed from around 2000 conductance traces.c, I-V characteristics (-1.1~1.1V) of poly

d(CG)4 DNA with (blue) and without coralyne (black).

SI-6. Landauer Formalism calculation

The electrode-induced level broadening is encoded into the retarded (r) and advanced (a)

self-energy terms, Σ , = 2

| 1,1 ⟩⟨1,1 | , Σ , = 2

|11,2 ⟩⟨11,2| describing the left (L) and

right (R) electrodes, whereΓ is the level broadening, also treated as a fitting parameter. The

next step is to calculate the electronic Green’s function, ( , ) = ( (ℋ + ℋ ) + Σ , ) −1 , (4)

where Σ , = Σ , + Σ , . From the Green’s function the transmission function is calculated

via

( , ) = (Σ Σ ) . (5)

The current is calculated from the transmission function via the Landauer formula

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= 2 ∫ ( , ) �( ) ( ) (6)

where is the electron charge adℎthe planck constant. , are the Fermi functions of the left

and right electrodes, given by

, =

1+exp −±

−1

, with the gold electrode

chemical potential, the Bolzmann constant and the temperature (taken as room

temperature hereafter). While is in principle known for gold, here we allow it to vary and

treat it as a fitting parameter.

SI-7. Theoretical calculations

The tight-binding parameters for the DNA tight-binding calculation are tabled in Ref. 42 of the

main text. The optimization of parameters was performed using a dynamic Metropolis

Monte-Carlo algorithm, which we briefly describe here. We denote byp the set of optimized

parameters ( = {S1,Γ,µ,φ} for the untreated DNA, andp = S n,m, n = 5,6,7,m = 1,2 for the

coralyne-treated DNA). At each iterationn the parameter set is randomly incremented,

pn= p n−1+ δp , and with these parameters the I-V curve was calculated. The difference

between the theoretical I-V curve and the experimental one was then evaluated,ηn=

∫dV� ( ) ( ) 2. If ηn< ηn−1then the new set of parameters is accepted. If

ηn> ηn−1then the new set of parameters is accepted with a probabilityexp ( −η

)δη ,

where δη is the parallel to temperature in the classical Metropolis algorithm, and is used to

avoid local minima. δη is not constant throughout the calculation, but is dynamically changed

allowing the system to “anneal” into the global minima. In addition to the Monte-Carlo

algorithm, we have also used genetic minimization algorithms to find the optimal parameters,

and found qualitatively similar results (although the minimization with the Monte-Carlo

algorithm was superior and yielded a much smallerη ). The resulting optimal parameters of the

minimization are given in the tables below.

Supplementary Table 3: Fitting parameters and best fit values.

Parameter Description value

Energy shift in edge sites 0.3285 eV

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Electrode-induced level broadening 1.1790 eV

Gold electrode chemical potential 5.004 eV

Voltage drop fraction 1.25 × 10 −6

Supplementary Table 4: Values of the local energy shifts, obtained from fitting the

theoretical I-V curves to the experimental one.

Energy shift , , , , , ,

Value [eV] 0.08713 1.04307 0.15724 0.45497 0.52863 0.226474

SI-8. Microscopic origin of rectification

Here we wish to elaborate further on the microscopic mechanism responsible for the observed

rectification, as it emerges from the theoretical calculation. In general, when there is a position

dependent change in the local energies due to a bias voltage (Eq. 3 in the main text), two things

can happen (possibly simultaneously): (i) the energy of the orbitals (i.e. the eigenvalues of the

Hamiltonian) can be changed, (ii) the real-space structure of the wave functions (i.e. the

eigen-vectors of the Hamiltonian) can change. This can be seen by considering the simplest

picture of coherent transport, in which the transport through each orbital is defined via a

transmission function, which is a broadened Lorentzian centered at the orbital energy,

Tn (E, V) = (V)

(V) + (E−E ), with En (V) the orbital energy andΓn (V) is the orbital broadening.

The broadening depends on the weight of the orbital wave-function near the contacts. A change

in either En (V) or Γn (V) due to voltage can result in a change in the transmission function and

hence in the I-V curve. What we find in the calculation is that of the two orbitals which

contribute the most to the current (the HOMO and HOMO-1 orbitals), the transmission function

of the HOMO remains almost unchanged, while the HOMO-1 transmission function is change.

The change is not due to a change in the energy, but due to a change in the wave-function, whichinduces a change in the couplings. This can be seen from Supplementary Figure7 below, in

which we plot the HOMO-1 wave function weights| ψ | 2 (on one strand of the DNA for clarity),

as a function of position along the chain and the bias voltage. The solid lines are guides to the

eye. What can be seen is that as a function of bias, the wave-function weight (on one side)

increases substantially (note that the graph is on a log scale), effectively increasing Γn . The

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change in the wave-function in not symmetric in bias; this is due to the non-symmetric form of

the Hamiltonian (Supplementary Table4).

Supplementary Figure 7. HOMO-1 wave function weights show asymmetry in position and

bias. The wave-function | | 2 of the HOMO-1 orbital (on one DNA strand, for clarity) as a

function of position along the chain and bias voltage. The wave function hardly changes at

positive biases, but changes more substantially for negative biases, resulting in an increased

coupling between the orbital and the electrode and increase in (negative) current.

SI-9. Considering incoherent transportA Central assumption of the calculation is that electronic transport is coherent along the DNA is

coherent. In this section we wish to address this issue, at least from a phenomenological point of

view. To do so, we argue that the simplest situation would be to assume that there is partial

decoherence of the electrons. The extreme limit would be that the transport is only coherent in

the central part of the DNA wire. The rest of the wire, which is incoherent, can then be encoded

into the self-energy of the electrode. The simplest model for this would be a two-level system,

depicted in the upper panel of the figure below. The same 2-site model was very recently used to

analyze the observation of a large negative-differential resistance in molecular junctions with a

single thiolated arylethynylene molecule with a 9,10-dihydroanthracene core.7 The model

Hamiltonian is very simple,ℋ = ∑ ϵn (V)| n n| − t( | 1 2| + |2 1| )n=1 ,2 , such that the left

(right) site energy is shifted by±αV

2. In fact, this model is simple enough such that the

transmission function can be found analytically.

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We assume that t = 0.034 eV , the typical value for the DNA. For the untreated DNA wire we

assume symmetric structure,ϵ1 = ϵ2 = ϵs . We are thus left with the following fitting

parameters: Γ (the level broadening),ϵs and α , which are all obtained by fitting the current to

the data for the untreated DNA. Then, using these parameters, we break the left-right symmetry

by fitting new values forϵ1 ,ϵ2 (but keeping the other parameters fixed).

With the following parameters: ϵs = − 1.37 eV, ϵ1 = − 0.986 eV, ϵ2 = − 1.43 eV, Γ =

0.088 eV, α = 0.7174 we were able to fit all the data rather well, as seen from the

Supplementary Figure 8 below (although the fit is not as good as when considering the full DNA

structure). However, since we do not know the relation between these parameters and the actual

parameters of the DNA, this model sheds only partial light on the mechanism of rectification in

our junctions, and it is hard to relate it to the structure and parameters of the DNA.

If one assumes fully incoherent transport (within the same model), the current can be obtained

by using a rate-equation approach.8 The full expression for the current is then

=2 0 sinh (

2 )

2( + 0 )(cosh (2 1 −2 ) + cosh ( + 2 2

2 )) + (2 + 0 )cosh (2 + − 2 1 + 2 22 ) + ( 2 + 3 0 )cosh (

2 )

Supplementray Figure 8. A simplified two-level model for rectification in DNA. Left:

schematic drawing of the model, which consists of two levels coupled to electrodes. Right:

Experimental data and theoretical fit (see SI text for parameters), showing good fit between even

with such a simplified model.

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Where is the transfer rate from the sites to the electrodes, and0 is the transfer rate between

the two sites (replacing the hopping integral in the coherent case). As can be seen in

Supplementary Figure9 below, we were not able to fit the data – even for the untreated DNA –

with an I-V curve obtained from the rate equations (the parameters in Supplementary Figure 4

are = 3.6 × 10 11 s −1 , 0 = 2 × 10 11 s −1 , 1 = 2 = 1.37 eV ). The reason is that within the

incoherent approach, the I-V curve has an exponential resonant shape. The data, on the other

hand, is ohmic for low biases. This is exactly because of the level broadening, a coherent effect

which cannot be captured by an incoherent calculation.

SI-10. Cyclic bias sweeping measurements

Supplementary Figure 9. Fit of data for untreated DNA with a simplified incoherent

transport model. The fit is substantially worse than the fit with a coherent model, because the

incoherent model cannot capture the coherent-broadening-induced ohmic behavior at low biases.

1.0 0.5 0.0 0.5 1.0

0.5

0.0

0.5

bias V

c u r r e n t

n A

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Supplementary Figure 10. Cyclic bias sweeping measurement by sweeping bias from -1.2V

to 1.2V and then back to -1.2V . The measurement was performed for both native DNA (blue)

and DNA-coralyne complex (red). Note that obvious hysteresis was observed for DNA-coralyne

complex, suggesting an electronic structure change during the bias sweeping.

References:

1. Horcas, I. , et al. WSXM: A software for scanning probe microscopy and a tool fornanotechnology. Rev. Sci. Instrum. 78, 013705 (2007).

2. Joung, I. S. , et al. Molecular dynamics simulations and coupled nucleotide substitutionexperiments indicate the nature of A·A base pairing and a putative structure of thecoralyne-induced homo-adenine duplex. Nucleic Acids Res. 37, 7715-7727 (2009).

3. Case, D. A. , et al. AMBER 11. University of California, San Francisco.; 2010.

4. Hihath, J. , et al. Study of single-nucleotide polymorphisms by means of electrical conductancemeasurements. Proc. Nat. Acad. Sci. USA 102, 16979-16983 (2005).

5. Persil, Ö. , et al. Assembly of an antiparallel homo-adenine DNA duplex by small-molecule binding. J. Am. Chem. Soc. 126, 8644-8645 (2004).

6. Ren, J.&Chaires, J. B. Sequence and structural selectivity of nucleic acid binding ligands. Biochemistry 38, 16067-16075 (1999).

7. Perrin, M. L. , et al. Large negative differential conductance in single-molecule break junctions. Nature Nanotech. 9, 830-834 (2014).

8. Muralidharan, B.&Datta, S. Generic model for current collapse in spin-blockaded transport. Phys. Rev. B 76, 035432 (2007).

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