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CORRECTION NOTICE

Nature Nanotechnology http://dx.doi.org/10.1038/nnano.2013.209 (2013)

A general strategy for the DNA-mediated self-assembly

of functional nanoparticles into heterogeneous systems Yugang Zhang, Fang Lu, Kevin G. Yager, Daniel van der Lelie and Oleg Gang

In the version of the Supplementary Information originally published, in the caption for Fig. S3, panels c–f, ‘CdS’ should have read ‘CdSe’. This error has been corrected in this file 23 October 2013.

© 2013 Macmillan Publishers Limited. All rights reserved.

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A general strategy for the DNA-mediated self-assembly of functional nanoparticles into heterogeneous systems

Yugang Zhang*, Fang Lu*, Kevin G. Yager*, Daniel van der Lelie†, and Oleg Gang*

*Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973

†Center for Agricultural and Environmental Biotechnology, Research Triangle Institute

International, Research Triangle Park, NC, 12194

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Contents

Materials and Methods

Synthesis of palladium and iron oxide nanoparticles

DNA functionalization for hydrophilic/hydrophobic nanoparticles

Assembly and crystallization of heterogeneous nanoparticle systems

Quantification of the grafting DNA number

Instrumentation

Calculation of interparticle distance from SAXS data

DNA modeling for calculation of interparticle distances

Modeling of SAXS profiles for assemblies

Table S1-S2

Figure S1-S22

References

Materials and Methods

Synthesis of palladium and iron oxide nanoparticles

The poly-vinyl-pyrrolidone (PVP)-capped palladium nanoparticles, including octahedron-, cube-,

and dodecahedron-like shapes, were synthesized in an aqueous solution by a modified

procedure1. Water soluble inorganic Pd salts (Na2PdCl4) were used as a palladium source. PVP

(typically molecule weight (M.W.) ~50,000) was used both as reducing agent and surfactant.

Alkali metal bromides or iodides, such as NaBr, or NaI, were used as shape-controlling agents.

Bromides were used for the synthesis of Pd nano-octahedrons (PO), cubes (PC), while iodides

were used for the synthesis of dodecahedrons. In a typical synthesis procedure, a mixture of Pd

salt and alkali metal halide was first heated to 80~100 0C with a standard reflux system and kept

at that temperature for ~ 30 minutes. Then a pre-heated PVP solution was injected into the

mixture solution. The reaction was allowed for 3 hours. After the reaction, the nanoparticles

products were collected by centrifugation, and then purified by washing with once with acetone

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and subsequently three times with ethanol or water. The as-obtained nanoparticles were then

dispersed in water. The detailed synthesis parameters for Pd nanoparticles are as following, for

PO, [Na2PdCl4]= 58 mM, mole ratio Na2PdCl4: KBr: PVP=1: 20: 5, and temperature = 800C; for

PC, [Na2PdCl4]= 58 mM, mole ratio Na2PdCl4: KBr: PVP=1: 20: 5, temperature = 1000C; for

PD, [Na2PdCl4]= 58 mM, mole ratio Na2PdCl4: KBr: KI:PVP=1: 20:0.01: 5, temperature =

1000C. The as-synthesized Pd nanoparticles are uniform in shape and size and display the similar

volume comparable to ~11 nm spherical particles.

The oleic acid (OA)-capped Fe2O3 (denoted as FeO) nanoparticles was synthesized according to

the reported methods 2. Briefly, first, 0.5 ml of Fe(CO)5 was mixed with 25 ml octyl ether and

3.2 g of OA at 100°C and the solution was heated up to refluxing temperature for 1 hour. Then,

the solution was cooled down to room temperature and 0.85 g (CH3)3NO was added and heated

to 130 °C for 2 h. Next, the solution was heated to reflux for 1h. Finally, the solution was cooled

to room temperature. After a purification procedure, the resulted ~10nm nanoparticles were well

dispersed in toluene.

The commercial available organic soluble TOPO-capped QD (Invitrogen) were used as the initial

materials for QD.

DNA functionalization for hydrophilic/hydrophobic nanoparticles

Our strategy for nanoparticles (other than Au) functionalization with DNA included three steps:

carboxylic group grafting, streptavidin-conjugation, and biotinylated-DNA attachment. In the

first step, short mercapto acid ligands, such as mercaptoundecanoic acid, and amphiphilic

polymers, such as lipid- PEG carboxylic acid, are adopted for hydrophilic and hydrophobic

nanoparticles respectively (Fig. 1a). The subsequent two steps rely on the 1-Ethyl-3-(3-

dimethylaminopropyl) carbodiimide (EDC crosslinker)-assisted chemistry and on the specific

and strong streptavidin-biotin binding (association constant 2.5*1015 M-1 3). We use streptavidin -

biotin-DNA, rather than amine-terminated DNA 4, in order to achieve a higher grafting density

of DNA, owing to the abundant amine groups on STV and four binding sites for biotin 5.





4

(i) Functionalization of nanoparticles with carboxylic group

Ligand-exchange for hydrophilic nanoparticles: The PVP capped on the surface of shaped Pd

nanoparticles was replaced with 11-mercapto-undecanoic acid (MUA) by a ligand-exchange

process. Briefly, we adjusted the pH value of the freshly prepared PVP-capped Pd nanoparticles

in aqueous solution to ~9 by phosphate buffer, which contains ~ 0.01 % Tween 20. Then, excess

MUA (with mole ratio ~105 times to Pd nanoparticles) in ethanol was mixed with the above

solution. Next, the mixture was incubated at 90 0C for 6 hours with brief sonication. Finally, after

a purification procedure, the MA-capped Pd nanoparticles were well dispersed in phosphate

buffer with pH at 6~9.

Amphiphilic polymers attachment for hydrophobic nanoparticles: FeO or QD dispersed in

toluene were first mixed with amphiphilic polymers, such as lipid-PEG carboxylic acid (DSPE-

PEG(2000) Carboxylic Acid, Avanti Polar Lipids), which have hydrophobic chains interacting

with ligands on the nanoparticles and carboxylic acid group for further functionalization. Then

the mixture was incubated for 2~4 hours at room temperature. After complete evaporation of the

organic solvent, the residual solid was purified by a centrifugation-wash cycle procedure, where

the particles are washed three times by borate buffer with pH 7~9. After purification, the

nanoparticles are dispersed in borate buffer with pH at 7~9.

(ii) Conjugation of nanoparticles with streptavidin

The as-prepared carboxylic group capped nanoparticles were conjugated with streptavidin by

formation of an amide bond between carboxylic groups on the nanoparticles, provided by the

ligand, and primary amine groups of streptavidin through EDC-assisted chemistry. Typically,

concentrated nanoparticles were first diluted by pH ~7 phosphate buffer. Then, the solution was

mixed with fresh prepared EDC (0.5 mg/ml), N-hydroxysulfosuccinimide (NHSS, 0.5 mg/ml)

and streptavidin. The quantity of streptavidin was 40~100 times that of the nanoparticles. The

mixture was allowed to incubate at room temperature for 2 hours. After purification, the

nanoparticles were dispersed in phosphate buffer.

(iii) Functionalization of nanoparticles with biotinylated-DNA





5

The as-prepared streptavidin capped nanoparticles were easily coupled with biotinylated-DNA

because of the strong and specific affinity of biotin to streptavidin. The streptavidin capped

nanoparticles were mixed with excess biotinylated-DNA and incubated for several hours at

room temperature. After the remove of excess DNA by purification, the nanoparticles were

dispersed in phosphate buffer.

The details for functionalization of citrate-capped Au nanoparticlees with thiol-DNA can be

found in reference 6.

Assembly and crystallization of heterogeneous nanoparticle systems

We applied two strategies for nanoparticleassembly: direct hybridization (DH) and linker

hybridization (LH), as schematically illustrated in Fig. 1b. The DH system, denoted as A_BXA_XB,

contains tethered DNAs on nanoparticles A (and B) which includes a 15- base outer recognition

region for a complementary hybridization, and a poly-T spacer of XA (XB) bases separating the

outer part from the nanoparticle surface; thus, particle surfaces are separated by N=XA +XB+15

bases. In a LH system, denoted as A_BLn, the 15- base outer regions are not complementary to

each other but instead complementary to the respective 15-base ends of a ssDNA linker. This

linker has a central noncomplementary (flexible) part with Ln bases separating the two ends, thus,

for LH systems N=XA +XB+Ln+30 bases.

For direct hybridization systems, particle assembly was achieved by mixing an equal mole of

type-A and type-A’ DNA capped nanoparticles in a solution of 10mM phosphate buffer, 0.14 M

NaCl, pH=7.1 at room temperature. For linker systems, the assembly was obtained by mixing

type-A , type-B DNA capped nanoparticles and linkers in a mole ratio of 1:1: 40 (for ~ 10nm

nanoparticles). All DNA sequences are shown in Table S1. The particles were allowed from

several minutes to days to assemble into aggregates, depending on the particle concentration.

Synchrotron-based small-angle X-ray scattering (SAXS, performed at NSLS X-9) was employed

to probe the in-situ structure of particles assemblies. If not specifically mentioned, all the

assemblies were annealed at ~ 1-2 degrees below their melting temperature (Tm) for ten minutes

to several hours, and then slowly cooled down to a room temperature. Tm was determined either

from the UV measurements or from in-situ temperature-dependent SAXS.





6

Quantification of the grafting DNA number

A fluorescence-based method 7 was used to determine a grafting DNA number on the

nanoparticle surface. First, a series of 15-base fluorophore-labeled oligonucleotides reacted with

nanoparticles, which has the complementary 15-base outer recognition regions, under same

hybridization conditions (10mM phosphate buffer, 0.14 M NaCl, pH=7.1) as for nanoparticles

assembly. After reaction, the non-hybridized DNA was removed by three centrifugation-wash

cycles. Then, the hybridized fluorophore-labeled DNA was released into solution by adding 1M

NaOH. Next, the released DNA was separated from nanoparticles by centrifugation and the

resulted DNA solution was neutralized by adding HCl. Finally, the concentrations of hybridized

DNA were determined by fluorescence spectroscopy.

Instrumentation

UV-Visible Spectrophotometry (UV-vis): UV-vis spectra were recorded on a Perkin-Elmer

Lambda 35 spectrometer (200-700 nm). Melting analysis was performed in conjunction with a

Perkin-Elmer PTP-1 Peltier Temperature Programmer and was performed between 20-75 oC

with a temperature ramp of 1 oC/min while stirring, in a 10 mM phosphate buffer, 0.14 M NaCl,

pH=7.1, buffer solution.

Fluorescence Spectrophotometry: PL spectra were measured by a Cary Eclipse Fluorescence

spectrophotometer (Varian, Inc.). Time-resolved PL spectroscopy was measured by the time-

correlated single-photon-counting (TCSPC) method using a FluoTime 200 spectrometer

(Picoquant). Lifetimes were calculated by reconvolution of the instrumental response function

with an exponential model function.

Scanning Electron Microscopy (SEM): SEM experiments were carried out on Hitachi S-4800

Scanning Electron Microscopy with typical 1kV voltage and 10μA emission current. Energy-

dispersive x-ray spectroscopy (EDS) data were collected on Analytical SEM JEOL 7600F. The





7

EDS spatial resolution is about sub-micrometer to micrometer. The sample was prepared by

drop-casting an aqueous nanoparticles solution onto a cleaned silicon substrate.

Transmission Electron Microscopy (TEM): TEM images were collected on a JEOL-1300

microscope operated at 120kV. The high-resolution transmission electron microscopic (HRTEM)

observations were performed on a JEOL 2100 operated at 300kV. The samples were prepared by

drop-casting an aqueous nanoparticle solution onto a carbon coated copper grid.

Small Angle X-ray Scattering (SAXS): SAXS experiments were carried out at the National

Synchrotron Light Source’s (NSLS) X-9A beam line. The scattering data were collected with a

MAR CCD area detector and converted to 1D scattering intensity vs. wave vector transfer,

q = (4π/λ) sin (θ/2), where λ= 0.8551 Å and θ, are the wavelength of incident X-ray and the

scattering angle respectively. The scattering angle was calibrated using silver behenate as a

standard. The structure factor S(q) was calculated as Ia(q)/Ip(q), where Ia(q) and Ip(q) are

background corrected 1D scattering intensities extracted by angular averaging of CCD images

for assembled systems and un-aggregated particles, respectively. The peak positions in S (q) are

determined by fitting a Lorentzian form.





8

Calculation of interparticle distances from SAXS data

The nearest neighbor center-to-center interpartice distances (Dcc) in the assemblies were

determined by the following equations:

�� √6 � p��, where q1 is the first diffraction peak position, for BCC (CsCl with same

components) or FCC lattice

�� √3 � p�� , for CsCl (with different components)

The values for DCC calculated from SAXS data are given in Table S2.

The surface-to-surface interpartice distances (Dss) are calculated as �� , where

rA(B) is the hard core radius of A(B) types of nanoparticles.

The correlation lengths (ξ) was used to estimate the average grain size. According to Scherrer

analysis 8, ξ � �λ

��q�� @ �p�

d ,where K is a dimensionless shape factor and has a typical value of

about 0.9, λ is the x-ray wavelength, � and d are accordingly the line broadening at half the

maximum intensity (FWHM) in radians and in wave vector.

DNA modeling for the calculation of interparticle distance

We employed a Daoud-Cotton (DC) blob model and a worm-like chain (WLC) model to

calculate the tethered DNA thickness and linker length, respectively. The similar method was

previously adopted by our group for single component Au nanoparticle systems 9.

Direct hybridization (DH) system:

�� , where RA(B) and TA(B) are the effective radius (including polymer shell

and streptavidin layers for Pd, FeO, and QD) and effective thickness of tethered DNA shells of A

(B) types of nanoparticles. T was approximated using Daoud-Cotton (DC) blob model as

� � �� σν�� , where �� is the contour length of ssDNA with

�� nucleotides of segment length b=0.65 nm.lk º 2nm is the Kuhn length of

ssDNA; tethering density σ � ��, where f is the grafting DNA number on the nanoparticle

surface, and the typical values are 45~60, 20~40, 15~25 and 3~8 for Au, QD, Pd and FeO,

respectively. kº1 is a constant. The excluded volume parameter ν was estimated using Onsager’s





9

concept as ν � ��, where the ssDNA was considered as a chain of charged cylinders with

a length of Kuhn length lk and effective diameter of ssDNA �� κ��.The Debye

screening length κ��º��, where Ca=0.14 M. The values for R, T, and DCC are given in

Table S2.

Liner hybridization (LH) system:

�� , where the end-to-end distance of the linker Hn is estimated by a

worm-like chain (WLC) model as �� , and the lp =lk/2 is the

persistence length of ssDNA and Ln=nb is the contour length of linker with n nucleotides. R and

T are defined same as DH systems, but for the calculation of T, �� , where ��

�� . The calculated R, T, and DCC are given in Table S2.

The surface-to-surface interpartice distances (Dss) for the above two systems are calculated as

�� , where rA(B) is the hard core radius of A(B) types of nanoparticles.





10

Modeling of SAXS profiles for assemblies

To compute theoretical structure factors, we developed a scattering formalism that simulates

powder SAXS profiles obtained from particles assembled on a regular lattice. Our formalism

accounts for particle size and component within the unit cell. In addition, we explicitly consider

in this modeling factors influencing a disorder, such as particle polydispersity, lattice disorder,

and average grain size. To simulate SAXS profile, we allowed for five adjustable parameters

(overall and lattice scaling factors, Debye-Waller factor, peak shape, and peak width), but as

described below all parameters are highly constrained.

To compute theoretical scattering, we first define F(q) to be the form factor amplitude for the

particles: �� r� �� , where the scattering for reciprocal vector � � �� is

computed by integrating over the volume V of the particle, and Δρ is the electron-density contrast

between the particles and the surrounding medium. Because of the small particle size (~10 nm)

and low aspect ratio (~1) in the present study, we use a spherical particle with an equivalent

volume to calculate particle’s F(q) as, �� p��

�� , where r is the radius

of the sphere. We then define the form factor to be an orientational average of the particle’s form

factor amplitude as, �� ‚| ��|�Ú. This quantity is what is measured experimentally when

the particles are dissociated and thus randomly distributed in solution (for our system, above the

melting temperature of the hybridized DNA). In order to capture the structural order from

packing, we define a lattice factor for an isotropic distribution of grains 10: ��

�� ∑ |�� ∑ ��p��|

��

��

�� , where the inner sum is over the Nj

particles in the unit cell, which have fractional positions�� ; the outer sum is over the

Miller indices (hkl) for the desired lattice type. The function L is a normalized peak shape

(described below).

In order to realistically compare with experimental data, we explicitly consider various kinds of

disorder: polydispersity in particle size, variation in particle positions from their idealized lattice

sites, and average grain size.

Polydispersity is accounted for by replacing the form factor by a form factor averaged over a

Gaussian distribution, ��

��σ �

��

σ√�p, of particles sizes, and r0 is the average particle





11

radius, σ is particle radius standard deviation. The inclusion of polydispersity smears the form

factor, which attenuates lattice peak heights at higher q. This lost scattering intensity appears as

diffuse scattering, requiring the definition of the ratio:

b�� |‚�� Ú|�

‚|��|�Ú� |‚�� Ú|�

��

|��

� �� |�

� |��|��

.

This quantity approaches unity in the limit of small particle size distributions, eliminating diffuse

scattering. For intermediate size distributions, it contributes a modulating envelope to the diffuse

scattering.

Lattice disorder is captured by a Debye-Waller factor: �� σ��, where a is the lattice

constant of the unit-cell, and σD describes the relative variation of particle positions from their

ideal lattice sizes. In the present work, σD, in the range of 0.01 to 0.25 were considered; the

closest-match simulations all had σD in the range of 0.02 to 0.12. The effect of G(q) is to generate

diffuse scattering at the expense of higher-order lattice peaks. Combining polydispersity and

lattice disorder, we use an expression for the scattered intensity of: ��

�� b��=P(q)S(q), where c is a scaling constant. The structure factor S(q) thus

contains a diffuse scattering term )()(1 qGqβ− , and a structural term (lattice peaks)

)(/)()(0 qPqGqcZ .

The average grain size for the lattices is implicitly included in the peak width of L: larger

correlation lengths result in a sharper peak whereas small correlation lengths (ξ) result in broad

peaks. In order to account for variations in aggregate shape, lattice strain, and the form of the

aggregate size distribution 11,12, we employ a generalized peak shape as previously reported in the

literature 10:

�� pd

∏ �� gn�

��n��¶��

p�d��, where δ is the peak width, ν a parameter that controls peak-

shape, and γν is a ratio of gamma functions: gn � p�� G��n ��G�n �� . The effect of ν is to vary L

continuously from a Lorentzian (when nö 0) to a Gaussian (when nö ¶): ��

�

d��p��d�� nö 0

�pd

��

p�d�� nö ¶ . Intermediate values of ν allow for mixed peak shapes, which





12

can account for the convolution of instrumental peak broadening and physical peak broadening

(e.g. aggregate size distribution).

Although our model includes five adjustable parameters, each of these parameters is highly

constrained. For instance, the Debye-Waller factor, is essentially dictated by the scaling of the

minima towards unity in the limit of �ö ¶. The overall and lattice scaling factors are

constrained by the primary peak height; the peak parameters δ and ν are similarly determined by

the primary peak shape. We also note that the experimental I(q) may contain contributions from

free particles, which effectively adds form-factor oscillations to the experimental S(q). These

effects are particularly pronounced at high-q, where the lattice peaks have low intensity. Since

our model does not account for any such free particles, we restrict our analysis to the low-q

regime.

In the case of Pd-Au and Au-Au systems, the CsCl lattices were found to agree with the SAXS

data, as displayed in Figure 2a; for streptavidin-Au systems, the Au FCC lattices match the data,

as shown in Figure 3a(3); for FeO-Au systems, we computed 7 different types of possible

lattices, including three types of diamond-like packing (zinc blende, CaF2, NaTl), CsCl, NaCl,

simple cubic, and Au FCC structures. The results indicate the Au FCC lattices similar to that of

streptavidin-Au systems as the best candidate; for QD-Au systems, the CsCl lattices fit the data,

especially for both short DNA and rigid DNA systems, but compositional disorders are required

to be included for the fit of long DNA systems, as exhibited in Figure 4b. For the systems

without Au, CsCl lattices but of quite different degree of order agree with the experimental data.





13

Table S1. DNA Nomenclature and sequences used in the study.

Name Modification Sequence

DHsystems

XA-15 3’-Thiol for Au 3’-Biotin for others

5’-ATT GGA AGT GGA TAA-(T) XA-3’

XB-15 3’-Thiol for Au 3’-Biotin for others

5’-TTA TCC ACT TCC AAT-(T) XB-3’

LHsystems

XA-15 3’-Thiol for Au 3’-Biotin for others

5’-ATT GGA AGT GGA TAA-(T) XA-3’

XB-15 5’-Thiol for Au 5’-Biotin for others

5’- (T) XB TAA CCT AAC CTT CAT-3’

15-Ln-15

5’-TTA TCC ACT TCC AAT - (T)Ln - ATG AAG GTT AGG TTA-3’

L30C24

L30

5’-TTA TCC ACT TCC AAT - TTT- TCC TCA ACA TCT AAT TCT CAA CTA - TTT - ATG AAG GTT AGG TTA-3’

C24 5’-TAG TTG AGA ATT AGA TGT TGA GGA-3’





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Table S2. The calculation of nearest neighbor center-to-center interpartice distances (Dcc)

from DNA models and experimental SAXS data, all the values in the table are in nm units.

Systems RA TA RB TB Hn DCC_Model DCC_SAXSAu_Au systems CsCl lattice Au_Au15 15 4.4 7.1 4.4 7.1 0 23.0 23.8 PD_Au systems CsCl lattice PD_Au3 15 12.0 1.7 4.4 7.1 0 25.2 23.3 PD_Au15 15 12.0 3.5 4.4 7.1 0 27.0 25.3 PD_AuL0 12.0 4.6 4.4 8.8 0 29.8 29.8 PD_Au35 35 12.0 6.3 4.4 11.4 0 34.1 32.1 PD_AuL30 12.0 4.6 4.4 8.8 6.1 35.9 34.6 PD_AuL70 12.0 4.6 4.4 8.8 9.4 39.2 41.3

PD_Au65_65 12.0 8.8 4.4 16.7 0 41.9 38.8 FeO_Au systems CsCl lattice, DCC is the distance between FeO and Au

FeO_Au0_15 9.5 1.1 4.4 7.1 0 22.1 30.9

FeO_Au15_15 9.5 3.0 4.4 7.1 0 24.0 33.3 FeO_Au35 35 9.5 5.3 4.4 11.4 0 30.6 42.7 FeO_Au65 65 9.5 8.5 4.4 16.7 0 39.1 55.7

Au FCC lattice (Phase_D), DCC is the distance between Au and Au a=180

0 a=1090

FeO_Au0 15 2.25 1.6 4.4 7.1 0 30.7 24.9 30.9 FeO_Au15 15 2.25 4.4 4.4 7.1 0 36.3 29.5 33.3 FeO_Au35 35 2.25 7.1 4.4 11.4 0 50.3 40.9 42.7 FeO_Au65_65 2.25 10.3 4.4 16.7 0 67.3 54.7 55.7

streptavidin_Ausystems

Au FCC lattice, DCC is the distance between Au and Au

a=1800

a=1090

streptavidin_Au0_15 2.25 1.6 4.4 7.02 0 30.7 24.9 30.53

streptavidin_Au15_1

5 2.25 4.4 4.4 7.02 0 36.3 29.5 30.90

FeO systems FeO FCC lattice (Phase_F) Sys_FeO 9.5 0 9.5 0 0 19.0 22.5 QD_Au systems CsCl lattice Q7_Au0_15 11.0 1.5 4.4 7.1 0 24.0 23.0 Q7_Au3_15 11.0 2.1 4.4 7.1 0 24.6 23.9 Q7_Au15_15 11.0 4.2 4.4 7.1 0 26.7 27.0





15

Q7_Au35_35 11.0 7.4 4.4 11.4 0 34.2 35.7

Q7_Au65 65 11.0 11.5 4.4 16.7 0 43.6 42.2 Q6_Au0 15 9.0 1.7 4.4 7.1 0 22.2 22.3 Q6_Au15_15 9.0 4.6 4.4 7.1 0 25.1 25.9

Q6_Au35_35 9.0 8.0 4.4 11.4 0 32.8 29.7 Q6_Au65_65 9.0 12.3 4.4 16.7 0 42.4 38.9 Q5_Au0 15 7.0 2.0 4.4 7.1 0 20.5 21.3 Q5_Au15 15 7.0 5.2 4.4 7.1 0 23.7 25.9 Q5_Au35 35 7.0 8.8 4.4 11.4 0 31.6 28.8 Systems without Au

QD_QD systems CsCl lattice Q7_Q73 3 11.0 2.1 11.0 2.1 0 26.2 26.4 Q7_Q715 15 11.0 4.2 11.0 4.2 0 30.4 30.6 Q5_Q515 15 7.0 5.2 7.0 5.2 0 24.4 24.9 Q7_Q53 3 11.0 2.1 7.0 2.7 0 22.8 24.6 Q7_Q515 15 11.0 4.2 7.0 5.2 0 27.4 29.8 Pd_Pd systems CsCl lattice PC_PC15 15 11.5 3.6 11.5 3.6 0 30.2 32.1 PD_PD15 15 12.0 3.6 12.0 3.6 0 31.2 32.8 PC_PD15_15 11.5 3.6 12.0 3.6 0 30.7 33.4 QD_Pd systems CsCl lattice Q7_PC15_15 11.0 4.2 11.5 3.6 0 30.3 31.6 Q7_PD15 15 11.0 4.2 12.0 3.6 0 30.8 32.4





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Figure S1. Characterization of Pd nanoparticles by SEM and TEM. SEM and TEM images

for biotinylated DNA-tethered (a,b,c) Pd cubes (PCs), (d,e,f) octahedrons (POs), and (g,h,i)

dodecahedrons (PDs). (a,d,g) and (b,e,h) are low- and high-magnification SEM images,

respectively. (e,f,i) are TEM images.





17

Figure S2. Characterization of iron oxide nanoparticles by SEM. Low- and high-

magnification SEM images for biotinylated DNA-tethered (a-b) iron oxide (FeO) nanoparticles.





18

Figure S3. Characterization of QD by SEM. Low- and high-magnification SEM images for

biotinylated DNA-tethered (a-b) CdSe/Te@ZnS, (QD705, denoted by Q7) , (c-d) CdSe@ZnS,

(QD605, denoted by Q6), and (e-f) CdSe@ZnS, (QD525, denoted by Q5).





19

Figure S4. Characterization of Au nanoparticles by SEM. Low- and high-magnification SEM

images for thiolated DNA-tethered Au nanoparticles with size of (a-b) 10 nm, (c-d) 15 nm, and

(e-f) 20 nm. Au nanoparticles with DNA formed close-packing structures (FCC lattice) on Si

wafer after solution evaporation. Due to dry, the thickness of 30-bases DNA shell tethered on 10

nm Au particles is significantly reduced by about 10nm compared with that in solution state.





20

Figure S5. Thermal stability of DNA-functionalized nanoparticles. (a) Digital photos for ~15

nM QD605 in 10 mM phosphate buffer under UV light (~380nm) at ~25 and 70 0C, incubated

for one hour. For the scenario when the lipid-carboxyl- streptavidin-DNA are desorbed from QD

surface at 70 0C, the original hydrophobic ligands (trioctylphosphine oxide) will be exposed to

aqueous solution, and this will result in QD aggregation. However, it is not the case in our

experiments. The homogeneous fluorescence emission from QD in the solution shows no

aggregation, which indicates the thermal stability of DNA- QD conjugates at the elevated

temperatures. (b) UV-Vis spectra for streptavidin-biotin-DNA solution (blue curve) and the

supernatant collected from the solution containing aggregates of DNA functionalized Fe2O3, at

room temperature (black curve) and at 70 0C after incubation for one hour (red curve). The

absence of the peak at ~260 nm for the supernatant of the incubated DNA-particles further

demonstrates the thermal stability of DNA-iron oxide nanoparticle conjugates using the

described lipid-carboxyl approach..





21

Figure S6. SAXS scattering profiles for the mixtures of non-complementary nanoparticles,

(a) Au, (b) dodecahedron (PD), octahedrons (PO), and cubes (PC), (c) QD525 (Q5), QD605

(Q6), and QD525 (Q5), (d) iron oxide (FeO) capped with oleic acid (OA) and functionalized

with DNA, (e) Au with each of PD, PO and PC, (f), Q7 with PD and PC, (g), Au with each of

Q7, Q6, and Q5, (h), Au with FeO. All systems except iron oxide do not exhibit aggregation, as

evident from the absence of the diffraction peaks, and only the form factor features are present in

the SAXS profiles. Note, the DNA functionalized iron oxide particles form aggregates due to

non-specific interactions, as discussed in the text. This structure is unchanged when non-

complementary Au nanoparticles are introduced, but it transforms when complementary Au

nanoparticles are added (see text) to the solution. The control experiments demonstrate that DNA

is a driving force for assembly.





22

Figure S7. Characterization of PD-Au assemblies by SAXS, SEM and EDS. (a) Structure

factor of systems for dodecahedron (PD) -shaped Pd and 10 nm Au nanoparticles, including DH

systems PD_Au15_15, PD_Au35_35, PD_Au65_65 and LH systems PD_AuL0, PD_AuL30. (b1) Low-

and (b2) high-magnification SEM images for dried system PD_Au15_15 on Si wafer. The dotted

circle regions in (b2) show weak ordering although this sample almost lost its structure in

solution after dry. (c) EDS analysis for system PD_Au15_15. The EDS was taken from the purple

rectangle region in SEM image (c1), the spectrum (c2) with energy from 0 to 4 keV, and the EDS

mapping for elements (c3) Pd and (c4) Au. The elements P, O, and N could come from phosphate

buffer, DNA, and streptavidin. The mapping displays the homogeneous distribution of Pd and

Au elements in the sample, which indicates that there are no phase separations of Au and PD

nanoparticles. The quantitative EDS analysis gives the atomic ratio of Au to Pd is ~ 1:1.2.

Considering the similar particle size and similar lattice constants of the both FCC structures of

Au and Pd nanoparticles, their particle ratio is approximately 1:1, which consists with the CsCl

structure of binary Au-PD supperlattice.





23

Figure S8. The effect of DNA length on the degree of structural order for PD-Au systems.

DNA length-dependent evolution of the correlation length (ξ ) in (a) DH and (b) LH PD (Pd

dodecahedron)-Au nanoparticle systems. A remarkable increase of ξ with DNA length was

observed both in DH and LH systems.





24

Figure S9. Characterization of short-DNA FeO-Au assemblies by temperature-dependent

SAXS measurements, and by SEM and EDS. (a) Temperature-dependent structure evolution

of a FeO_Au15_15 DH system assembled by iron oxide (FeO) and 10 nm Au nanoparticles. t and

tC denote heat-up and cool-down temperature, respectively. This system consisting of Phase-D

reveals a thermal-reversible dissociation-association behavior, indicating that this phase was a

DNA-driven assembly by FeO and Au nanoparticles. (b1) Low- and (b2) high-magnification

SEM images for dried system FeO_Au15_15 on Si wafer. (c) EDS analysis for system

FeO_Au15_15. The EDS was taken from the purple rectangle region in SEM image (c1), the

spectrum (c2) with energy from 0 to 4 keV, and the EDS mapping for elements (c3) Fe and (c4)

Au. Fe and Au were evenly distributed in the whole sample. The quantitative EDS analysis

gives a value of ~ 6 for the atomic ratio of Fe to Au, and their particle ratio are estimated as ~ 18.

This result supports our structural analysis for system FeO-Au, which was assigned as a FeO

surrounding-Au nanoparticle lattice.





25

Figure S10. Reversible structure conversion in FeO-Au systems. The reversible

conversion process between Phase-F (FeO aggregate) and Phase-D (binary FeO-Au

superlattices ). Introducing Au nanoparticle into the solution of (a) Phase-F leads to (b)

Phase-D. (c) Increasing system (b) temperature above DNA melting, (Tm, typically ~55 0C),

results in the dissociation of FeO and Au nanoparticles. (d) keeping system in melting state

(c) for several hours generates Phase-F, (e) while cooling system directly from (c) leads to

Phase-D.





26

Figure S11. Characterization of long-DNA FeO-Au assemblies by T-dependent SAXS.

Temperature-dependent structure evolution of a FeO_AuL130 LH system assembled by iron

oxide (FeO) and 10 nm Au nanoparticles. t and tC denote heat-up and cool-down

temperatures, respectively. This system consists of a phase mixture, Phase-F and Phase-D,

and the non-dissociation thermal behavior of phase-F indicates that non-specific interaction

is an origin of assembly.





27

Figure S12. The effect of DNA length on the degree of structural order for FeO-Au LH

systems. A structure factor S(q) of LH systems for iron oxide (FeO) and 10 nm Au

nannoparticles, including FeO_AuL0, FeO_AuL30, FeO_AuL70, FeO_AuL130, and FeO_AuL170.





28

Figure S13. A structure evolution with time for short-DNA FeO-Au DH assemblies

(FeO_Au15_15 ).





29

Figure S14. A structure evolution with time for short-DNA FeO-Au DH assemblies

(FeO_Au35_35).





30

Figure S15. Characterization of QD-Au assemblies by SAXS, SEM and EDS. (a) The

effects of DNA-length on the structure of Q7_Au DH systems, including Q7_Au0_15,

Q7_Au3_15, Q7_Au15_15, Q7_Au35_35, and Q7_Au65_65, assembled by QD705 (CdTe@ZnS)

and 10 nm Au nanoparticles. (b1) Low- and (b2) high-magnification SEM images for dried

system Q7_AuL30C24 on Si wafer. Although the interparticle distances are reduced, lattice

fringe-like structures were clearly observed, which might be caused by their high ordered

superlattices in the solution and the rigid DNA design. (c) EDS analysis for system

Q7_AuL30C24. The EDS was taken from the purple rectangle region in SEM image (c1), the

spectrum (c2) with energy from 0 to 4.2 keV, and the EDS mapping for elements (c3) Cd

from Q7 and (c4) Au. The distribution of elements Cd and Au is spatial correlated in the

whole sample. The quantitative EDS analysis gives a value of ~ 8 for the atomic ratio of Au

to Cd, which corresponds to 1:1 for their particle ratio.





31

Figure S16. The fit of SAXS-obtained structure factors S(q) for QD-Au systems. The SAXS

fit of S(q) for Q7_Au DH systems, including Q7_Au0_15, Q7_Au35_35, and Q7_Au65_65, without

consideration of a compositional disorder..





32

Figure S17. The effect of DNA length on structure of Q6-Au systems. The effects of DNA-

length on the structure of Q6_Au DH systems, including Q6_Au0_15, Q6_Au15_15, Q6_Au35_35,

and Q6_Au65_65, assembled by QD605 (CdSe@ZnS) and 10 nm Au nanoparticles.





33

Figure S18. The effect of DNA length effects on structure of Q5-Au systems. The effects

of DNA-length on the structure of Q5_Au DH systems, including Q5_Au0_15, Q5_Au15_15,

and Q5_Au35_35, assembled by QD525 (CdSe@ZnS) and 10 nm Au nanoparticles.





34

Figure S19. Structure of QD-QD systems. The structure factor S(q) QD-QD DH systems,

including Q7_Q70_15, Q7_Q715_15, Q7_Q50_15, and Q7_Q515_15. The Q7_Q7 and Q7_Q5

systems were assembled by QD705 with QD705 and QD705 with QD525, respectively.





35

Figure S20. Structure of Pd-Pd systems. The structure factor S(q) of Pd DH systems,

including PC_PC15_15, PD_PD15_15, and PC_PD15_15. The PC_PC, PD_PD and PC_PD systems

were assembled by PC with PC, PD with PD, and PC with PD, respectively.





36

Figure S21. Structure of QD-Pd systems. The structure factor of QD_Pd DH systems,

including Q7_PC15_15 and Q7_PD15_15. The Q7_PC and Q7_PD systems were assembled by

Q7 with PC and Q7 with PD, respectively.





37

Figure S22. Time-resolved photoluminescence (PL) spectra, collected from Q7_Q53_3

DH system assembled with QD705 and QD525.





38

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9 Xiong, H. M., van der Lelie, D. & Gang, O. Phase Behavior of Nanoparticles Assembled by DNA Linkers. Phys. Rev. Lett. 102, 015504 (2009).

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