S1

Supporting Information

Electrostatic Nucleic Acid Nanoassembly Enables Hybridization

Chain Reaction in Living Cells for Ultrasensitive mRNA Imaging

Zhan Wu, Gao-Qin Liu, Xiao-Li Yang, Jian-Hui Jiang*

State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering,

Hunan University, Changsha, 410082, P. R. China

Email: jianhuijiang@hnu.edu.cn

S2

ADDTIONAL EXPERIMENTAL DETAILS

Synthesis of CTAB-modified Gold Nanoparticles (AuNPs). AuNPs of diameter ~17 nm were

synthesized through a two-step seeding growth approach.S1

Briefly, seed nanoparticles were obtained by

adding 0.6 mL of ice-cold, freshly prepared 0.1 M NaBH4 into 20 mL aqueous solution containing 0.25

mM HAuCl4 and 2.5 mM trisodiun citrate under vigorous stirring. The growth solution was prepared by

adding 6 g of solid cetyltrimethylammonium bromide into 200 mL aqueous solution of 0.25 mM

HAuCl4 under heating. The first step of seeding growth yielded AuNPs with a diameter ~8 nm by add-

ing 1.0 mL of seed solution under stirring into a mixture of 9 mL of growth solution with 0.05 mL of

freshly prepared 0.1 M ascorbic acid solution followed by 10 min reaction. In the second step, AuNPs

with a diameter ~16 nm were obtained by adding 1.0 mL of AuNPs with a diameter ~8 nm under stirring

into a mixure of 9.0 mL of growth solution with 0.05 mL of freshly prepared 0.1 M ascorbic acid solu-

tion followed by 10 min reaction. The resuling CTAB-modified AuNPs were stored at 4 oC for 24 h and

then centrifuged at 3000 rpm for 5 min to remove CTAB sediments. Furthermore, the suspension of

AuNPs was centrifuged twice at 15000×g for 10 min. The sediments were re-dispersed in sterile ul-

trapure water. The concentration of the as-prepared CTAB-modified AuNPs was determined to be ~3

nM using its absorbance at 524 nm according to its molar extinction coefficient 2.7 × 108 M

-1 cm

-1.

Characterization of DNA Nanoassembly. TEM was performed with a Hitachi H-7000 electron

microscope (Tokyo, Japan) at an accelerating voltage of 200 kV. The TEM samples were prepared by

dropping 10 µL of 0.5 nM CTAB-modified AuNPs, 0.5 nM peptide-coated AuNPs and 0.5 nM DNA

nanoassembly, respectively, on carbon-coated grids and dried for 5 min. With the residual solution blot-

ted off using filter paper, the grids were washed four times by floating in 200 µL double-distilled water.

Then, the prepared samples were stained with 2% phosphotungstic acid (pH 6.5) for 5 min in light-

shielding conditions. The stained samples were washed again before TEM measuerments.

Zeta potential and dynamic light scattering (DLS) measuments of CTAB-modified AuNPs, peptide-

coated AuNPs and DNA nanoassembly were performed at 25 °C on a Zetasizer Nano ZS90 Analyzer

(Malvern Instruments, UK). The samples were 0.1 nM CTAB-modified AuNPs, 0.1 nM peptide-coated

AuNPs and 0.1 nM DNA nanoassembly dispersed in ultrapure water and the pH value of the solution

was adjusted to 7.2 with 1 M NaOH before the analysis.

Surface coverage analysis for peptide and DNA on nanoassembly. The coverage for peptides on

the nanoassembly was determined according to a previously reported protocol.S2

Briefly, 100 µL of 3

nM peptide-modified AuNPs were centrifuged at 10,000 rpm for 30 min, and the sediments were dis-

S3

solved using a mixture of 50 µL KCN (25 mM) and 75 µL sodium bicarbonate (10 mM). The solutions

were shaken gently and placed in dark at room temperature until it turned colorless. A 10 µL aliquot the

released peptide solution was directly subjected to electrospray ionization (ESI) mass spectrometric

analysis on a linear trap quadropole (LTQ) orbitrap Velos mass spectrometry equipped with a nanoelec-

trospray source (Thermo Fisher Scientific, Bremen, Germany). The concentration of the released peptide

was determined to be ~2.38 µM according to its intensity of the parent ion peak with reference to three

standard solutions of the peptide. The surface coverage of peptide on AuNPs was then estimated to be

~796 molecules per particle.

The analysis of DNA coverage on probe H1-carrying nanoassembly was performed with 100 µL of

3 nM DNA nanoassembly followed by centrifugation and dissolution using 50 µL KCN (25 mM) and 75

µL sodium bicarbonate (10 mM). The concentration of DNA probe H1 was then determined via fluores-

cence measures with reference to a set of standard solutions for probe H1 to be ~101 nM. The surface

coverage of probe H1 on H1-carrying nanoassembly was then estimated to be ~42 molecules per particle.

Assuming that the total loading amount for probe H1 on probe H1-carrying nanoassembly was the same

as that for nanoassembly carrying probe H1 and H2, we inferred that there was ~21 H1 and ~21 H2 mol-

ecules on the nanoassembly carrying probe H1 and H2.

Estimation of distance of FAM label from AuNP surface. The fluorescence quenching efficien-

cies for FAM and TMR and AuNPs in DNA nanoassembly was calculated according to the fluorescence

intensity of the nanoassembly divided by the fluorescence intensity for probe H1 released from the

nanoassembly (Figure S3). The distance between FAM and AuNP surface was estimated according to

the SET model in which the quenching efficiency was given as follows:

4

0 )/(1

1

rr+=Φ

For AuNPs with a diameter < 20 nm, r0 for FAM fluorophore was reported to be round 6-8 nm.17c

Taking an average value of 7 nm, we calculated the distance from FAM labeled in probe H1 in the

nanoassembly to AuNP surface was ~3.6 nm.

Cellular toxicity assay for DNA nanoassembly. HeLa cells were seeded into a 96-well microplate

at 10,000 cells per well and 5 wells for each concentration. The cells were incubated at 37 °C for 24 h in

200 µL RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U mL-1

penicillin and 100

U mL-1

streptomycin. Subsequently, cells were treated with DNA nanoassembly of a given concentra-

tion (0 µg mL-1

, 25 µg mL-1

, 50 µg µL-1

, 100 µg mL-1

, 200 µg mL-1

) in 200 µL RPMI 1640 medium at

S4

37 °C for 8 h. The medium was removed, and the mixture of 20 µl of Cell Proliferation Assay reagent

and 100 µL of fresh medium was added to each well followed by absorbance measurements at 490 nm

using a VersaMax Tunable Microplate Reader (VWR International, USA).

Fluorescence assay for stability of DNA probes against DNase I. The nuclease digestion assay

for DNA nanoassembly was performed as follows: 16 µL of probe H1 carrying DNA nanoassembly (3

nM) was mixed with 74 µL water and 10 µL 10× assay buffer containing 100 mM Tris-HCl (pH 7.5), 25

mM MgCl2, and 5 mM CaCL2. Note: The concentration of H1 in the mixture was ~20 nM. A 10 µL ali-

quote of DNase I (2.5 U L-1

) in 1× assay buffer was then added. The mixture was incubation at 37 oC for

2 h, and real-time monitoring of the fluorescence signal was measured at a time interval of 30 s with 488

nm excitation and 525 nm emission.

The nuclease digestion assay for hairpin probe H6 was performed as follows: 20 µL of probe H6

(100 nM) was mixed with 70 µL water and 10 µL 10× assay buffer containing 100 mM Tris-HCl (pH

7.5), 25 mM MgCl2, and 5 mM CaCl2 and the final concentration of H6 was 20 nM. The mixture was

also incubation at 37 oC for 2 h under real-time fluorescence measurements.

The nuclease digestion assay was also performed using DNA nanoassembly and probe H6 with dif-

ferent concentrations (10 nM, 25 nM, 50 nM, 100 nM and 200 nM) for probes H1 and H6 to calculate

the enzyme-substrate association constants Km and the maximum reaction velocity Vmax. The initial reac-

tion rates were determined from the slope of the progress curve from the first 10 date points (300 s) on

the addition of DNase I.

Gel electrophoresis analysis of cytoplasm extract from Hela cells. HeLa cells were seeded in a

square culture dish (224 mm × 224 mm) at 105 cells/cm

2 and incubated for 24 h. The cells were then in-

cubated for 3 h with 50 ml fresh culture medium containing 0.3 nM nanoassembly carrying H1 and H5,

0.3 nM nanoassembly carrying H1 and 0.3 nM nanoassembly carrying H7, respectively. The cytoplasm

extract (1 mL) was collected using a cytoplasmic extraction kit (Beyotime, China) followed by concen-

trated to 125 µL using a vacuum centrifugal concentrator. The concentrated extracts (10 µL) were direct-

ly analyzed by electrophoresis on a 4% agarose gel. To avoid staining RNA in the cytoplasm extracts,

only DNA size marker was stained with SYBR Green I (1:10000 dilution) before electrophesis, while

the extracts were not stained. The probes and HCR products were visualized using their FAM labels us-

ing a Tocan 240 gel imaging system (Tocan Biotech. Co., Shanghai).

Flow cytometry assay of mRNA expression using DNA nanoassembly. HeLa or C166 cells (105

cells) were incubated with 0.3 nM nanoassembly in 2 mL fresh medium at 37 oC for 3 h and washed

S5

three times with cold PBS. Then, the cells was detached with 50 µL of 0.25 % trypsin for 5 min and cen-

trifuged for 5 min at 300 g followed by two washes with 500 µL PBS and re-suspension in 1 mL PBS

for flow cytometry assay on a FACSVerseTM

flow cytometer (BD Biosciences, USA).

TEM analysis of microtomed cross-sections of cells. HeLa cells seeded in 6-well plate were

grown to at least 70% confluency followed by treatment with 0.3 nM nanoassembly in fresh medium.

The cells were washed three times for at least 5 min each time with cold PBS to remove excess nanoas-

sembly. Then, the cells were digested with 50 µL of 0.25% trypsin and then centrifuged in capsules for 5

min at 300 g at room temperature to form a pellet at the bottom. The cells were fixed by adding ~1 ml of

fresh 2.5% glutaraldehyde in PBS at room temperature for 2 h. After fixation was complete, the cells

were thoroughly rinsed with PBS, three times for 10 min each. For the purpose of straining, ~1 ml of 1%

osmium tetroxide in PBS was added to the cell pellet for 1 h and the cell pellet were rinsed using PBS

five times for 10 min each and then double-distilled water twice for 10 min each. After the staining,

cells were dehydrated at room temperature in a graded ethanol series of 30%, 50%, 70% and 95% twice

(5 min for each grade), followed by three rinses of 100% ethanol for ten min each. After dehydration,

resin embedding was performed by adding a mixture of resin and ethanol (in a ratio 50:50) for 40 min

followed by replacing the diluted resin mixture with 100% resin to infiltrate into the cell pellet overnight

(~15 h). The cell pellet was then infiltered with 100% epon-araldite and stored at 55 °C for 48 h to allow

resin polymerization. The embedded samples were sliced with a thickness of 75 nm, producing a suffi-

cient number of sections which were collected on carbon-coated grids. After allowed to dry for a few

min, the cell sections on grids were stained first with 1% uranyl acetate solution for 30 min. Then, the

grids were washed floating in 200 µL double-distilled water followed by blotting dry on filter paper.

Further staining was performed by placing the grid face down a drop of lead citrate solution containing

80.3 mM lead nitrate and 143 mM sodium citrate for 10 min followed by quickly dipping of each grid in

a drop of 0.1 M NaOH. TEM imaging was performed with a Hitachi H-7000 electron microscope (To-

kyo, Japan) at an accelerating voltage of 75 kV.

Quantification of cellular uptake of DNA nanoassembly using single-particle inductively

coupled plasma mass spectrometry (ICP-MS). HeLa cells were seeded in 6-well plates at 105 cells per

well and incubated for ~24 h. Cellular uptake at 37 oC was performed as follows: The cells were incu-

bated with 2 mL fresh medium containing 0.3 nM nanoassembly for 1 h. For cellular uptake at 4 oC,

cells were first incubated at 4 oC for 0.5 h and then grown in 1 mL culture medium containing 0.3 nM

nanoassembly at 4 oC for 1 h. For cellular uptake in the presence of NaN3, cells were first pretreated at

37 oC for 1 h with 1 mL culture medium containing 1% NaN3 and then incubated with 1 mL culture me-

S6

dium containing 0.3 nM nanoassembly and 1% NaN3 at 37 oC for 1 h. For single-particle ICP-MS assay,

the cells were sufficiently rinsed five times with 700 µl of cold PBS for 5 min each. All washing buffer

solutions (5.5 mL in total) were collected and diluted by 2,500 times using ultrapure water before single-

particle ICP-MS detection.

Single-particle ICP-MS detection was performed via recording the signal of 197

Au+ ions with a

sampling interval of 0.2 ms. In total 40,000 data points were acquired in 10 s for ~350 µL of sample

solution. All assays were done in triplicate.

Single-particle ICP-MS detection was also measured on a set of standard solutions and a calibration

curve was obtained by plotting the concentrations of nanoassembly versus the total counts in 10 s. The

concentrations of DNA nanoassembly were then calculated using the corresponding counts in single-

particle ICP-MS detection with reference to the calibration curve, which was used for the estimation of

the concentrations of DNA in a single cell.

Quantitative Reverse transcription-PCR (qRT-PCR) analysis of mRNA in cells. Total cellular

RNA was extracted from different cells such as HeLa, MCF-7, MCF-10A and SKBR-3 cells using the

RNeasy Mini Kit (Qiagen, USA) according to the indicated protocol. The cDNA samples were prepared

by using reverse transcription (RT) reaction with an iScript kit (Bio-Rad, USA) according to its manual.

The cDNA samples were store at -20 °C for future use. qPCR analysis of cDNA was performed with

SybrGreen PCR Master Mix (ABI, USA) on an ABI StepOnePlus qPCR instrument. The 20 µL reaction

solution contained 2 µL cDNA sample, 10 µL SybrGreen qPCR Master Mix, 2 µL primer mixture and 6

µL nuclease-free waster. The PCR conditions were as follows: an initial 94 oC for 2 min followed by 40

cycles of 94 oC for 10 s and 62

oC for 40 s. Relative level of survivin mRNA was quantified via normal-

ization to an endogenous control of β-actin RNA. The primers used in this experiment were: survivin

forward, 5’- TCC ACT GCC CCA CTG AGA AC-3’; survivin reverse, 5’-TGG CTC CCA GCC TTC

CA-3’; actin forward, 5’-AAA GAC CTG TAC GCC AAC ACA GTG CTG TCT GG-3’; actin reverse,

5’- CGT CAT ACT CCT GCT TGC TGA TCC ACA TCT GC-3’. We evaluated all the data with re-

spect to the mRNA expression by normalizing to the expression of actin and using the 2–∆∆Ct

method.S2

References:

(S1) Jana, N. R.; Gearheart, L.; Murphy, C. J. Langmuir. 2001, 17, 6782-6786.

(S2) Wen, Q.; Gu, Y.; Tang, L.J.; Yu, R. Q.; Jiang, J.H. Anal. Chem. 2013, 85, 11681-11685.

S7

Table S1. Sequences of synthesized oligonucleotides.a

Probe RNA or DNA sequence (5’-3’)

RNA Target UCU CAA GGA CCA CCG CAU CUC UAC

Non-homologous RNA GGU GAA ACC GCA UCU CUA CUA AAG AUA

Hairpin probe H1 GTA GAG ATG CGG TGG TCC TTG AGA CT(-FAM)A AGT TCT

CAA GGA CCA CCG CAT

Hairpin probe H2 TMR-TCT CAA GGA CCA CCG CAT CTC TAC ATG CGG TGG

TCC TTG AGA ACT TAG

Linear probe L1 GTA GAG ATG CGG TGG TCC TTG AGA-FAM

Control probe H3 TTA ACC CAC GCC GAA TCC TAG ACT(-FAM) CAA AGT AGT

CTA GGA TTC GGC GTG

Control probe H4 TMR-AGT CTA GGA TTC GGC GTG GGT TAA CAC GCC GAA

TCC TAG ACT ACT TTG

Hairpin probe H5 TCT CAA GGA CCA CCG CAT CTC TAC ATG CGG TGG TCC

TTG AGA ACTTAG

Hairpin probe H6 FAM-ATG CGG TGG TCC TTG AGA CTA AGT TCT CAA GGA

CCA CCG CAT-DABCYL

Hairpin probe H7 FAM-TCT CAA GGA CCA CCG CAT CTC TAC ATG CGG TGG

TCC TTG AGA ACTTAG

a RNA target is the initiator for HCR reaction between probes H1 and H2. L1 is a linear truncated probe

of H1 that, after hybridizing with target RNA, has no single-strand tail to hybridize with H2. Control

probes H3 and H4 are two hairpin probes not complementary to target RNA. H5 is a non-labeled version

of probe H2, which is used for validating the signal amplification in intracellular HCR. H6 is a self-

quenched hairpin probe with the first 6 nucleotides removed from probe H1, which is used for testing

the nuclease resistance of the nanoassembly. H7 was FAM labeled version of probe H2 with TMR tag

replaced by FAM.

S8

Figure S1. (a) Photographs for DNA nanoassembly in 10 mM pH 7.4 PB (left), 10 mM PB with 0.5 M

NaCl (middle), and phenol red-free RPMI-1640 medium (right). (b) Fluorescence spectra for nanoas-

sembly in 10 mM PB with 0.5 M NaCl (blue line), 10 mM PB with 1.0 M NaCl (black line) and 10 mM

PB containing 2.7 mM KCl, 137 mM NaCl and 5 mM MgCl2 (pink line). Fluorescence spectrum for 3

nM nanoassembly after dissolved by KCN solution (brown line) is shown as the reference. It is observed

that there is no dissociation of DNA probes from the nanoassembly in 10 mM PB with 0.5 M NaCl and

10 mM PB containing 2.7 mM KCl, 137 mM NaCl and 5 mM MgCl2, but slight desorption appears for

the nanoassembly in 10 mM PB with 1.0 M NaCl.

1 2 3

a)

b)

S9

Figure S2. TEM images at low magnification for different nanoparticles. (a) CTAB-coated AuNPs, (b)

peptide-modified AuNPs, (c) DNA nanoassembly.

a)

b)

c)

S10

Figure S3. Fluorescence spectra for nanoassembly before (pink) and after (blue) dissolved by KCN so-

lution. (a) H1-carrying DNA nanoassembly, (b) H2-carrying DNA nanoassembly.

Wavelength (nm)

500 520 540 560 580 600 620 640

F (x105)

0

5

10

15

20

25a)

Wavelength (nm)

580 600 620 640 660 680 700

F (x105)

0

10

20

30

40

50b)

S11

Figure S4. Agarose gel (4%) electrophoresis image for HCR-based assay. Lane 1, DNA size marker;

Lane 2, 1 µM probe H1; Lane 3, 1 µM probe H2; Lane 4, 1 µM H1 and 1 µM H2 probes; Lane 5, 10 nM

RNA target plus 1 µM H1 and 1 µM H2 probes incubated for 3 h at 37 oC; Lane 6, 10 nM non-

homologous RNA plus 1 µM H1 and 1 µM H2 probes incubated for 3 h at 37 oC; Lane 7, supernatant

obtained from centrifuge of 100 µL of 9 nM H1-carrying nanoassembly; Lane 8, supernatant obtained

from centrifuge of 100 µL of 9 nM H2-carrying nanoassembly; Lane 9, supernatant obtained from cen-

trifuge of 100 µL of 9 nM H1- and H2-carrying nanoassembly; Lane 10, supernatant obtained from cen-

trifuge for 100 µL mixture after incubating 9 nM H1- and H2-carrying nanoassembly with 10 nM non-

homologous RNA for 3 h at 37 oC; Lane 11, supernatant obtained from centrifuge for 100 µL mixture

after incubating 3 nM H1- and H2-carrying nanoassembly with 10 nM target RNA for 3 h at 37 oC.

S12

Figure S5. (a) Fluorescence spectra for nanoassembly carrying H1 and H2 in assay buffer (pink) and in

response to 1 nM RNA target (black) as well as 100 nM target (brown), nanoassembly carrying L1 in

assay buffer (red) and in response to 1 nM RNA target (blue) as well as 100 nM target (cyan); (b) Fluo-

rescence spectra for nanoassembly carrying H1 in assay buffer (red) and in response to 100 nM RNA

target (black), nanoassembly carrying H2 in assay buffer (pink) and in response to 100 nM RNA target

(blue). Both plots are shown in the same scale for comparison. One observes that the fluorescence re-

sponse to 100 nM RNA target is appreciably higher for the nanoassembly carrying L1 than the nanoas-

sembly carrying H1, which is attributed to partial adsorption of RNA-H1 duplex through its single-

strand tail.

a)

b)

S13

Figure S6. (a) Plot of fluorescence peak intensities (at 575 nm) versus RNA target concentrations, (b)

Fluorescence peak intensities versus RNA target concentrations in logarithmic scale. Error bars indicat-

ed SDs across four repetitive assays. The excitation wavelength used in the assay 488 nm.

CmRNA

(nM)0 10 20 30 40 50 60 70 80 90 100

Flurescence

0

200

400

600

800

1000

1200

1400

1600a)

b)

CmRNA

(nM)

0.0001 0.001 0.01 0.1 1 10

Fluoresennce

100

1000

S14

Figure S7. Real-time fluorescence signals for 6 nM nanoassembly in response to 20 nM RNA target

(pink), nanoassembly in response to 20 nM non-homologous RNA (blue), and HCR reaction of H1 and

H2 with 20 nM RNA target (green).

Time (s)

0 4000 8000 12000 16000

Fluorescence

0

2000

4000

6000

S15

Figure S8. Cell proliferation assay for cytotoxicity of DNA nanoassembly. The cell viability values (%)

are determined by incubated HeLa cells with DNA nanoassembly of varying concentrations (0, 25, 50,

200 µg mL-1

) for 8 h.

CNanoassembly

(µµµµg mL-1)

Cell Viability (%)

0

20

40

60

80

100

120

0 25 50 100 200

S16

Figure S9. Fluorescence assay for stability of DNA probes against DNase I. (a) time-dependent fluores-

cence peak intensities (at 520 nm) for DNase I-mediated digestion reaction for H1-carrying nanoassem-

bly (black) and fluorescence-quenched probe H6, (b) Double reciprocal (Lineweaver-Burk) plot of ini-

tial degradation rates as a function of DNA concentrations for calculating reaction kinetic parameters.

Time (sceond)

0 2000 4000 6000

Fluorescence (Norm

alized)

0.2

0.4

0.6

0.8

1.0a)

1/[DNA] (nM-1)

0.00 0.02 0.04 0.06 0.08 0.10 0.12

1/V(nM-1 sec)

0

100

200

300

400

500b)

S17

Figure S10. Dark-field resonant light scattering images for HeLa cells incubated with DNA nanoassem-

bly. (a) Cells incubated at 37 oC, (b) cells incubated at 4

oC, (c) cells pretreated using NaN3 followed by

incubated at 37 oC.

a)

b)

c)

S18

Figure S11. Single-particle ICP-MS detection for AuNPs concentrations in cell growth media. (a) be-

fore 1 h incubation of HeLa cells with DNA nanoassembly at 37 oC, (b) after 1 h incubation of HeLa

cells with DNA nanoassembly at 37 oC, (c) after 1 h incubation of HeLa cells with DNA nanoassembly

at 4 oC, (d) after HeLa cells pretreated using NaN3 followed by 1 h incubation with DNA nanoassembly

37 oC. The values given on the left top of each plot are the average counts with the standard deviations

for three repetitive experiments. The concentrations of AuNPs in a single cell are calculated to be ~4.2

×105, ~4.8 ×10

5, ~4.3 ×10

5 particles per cell, respectively, for HeLa cells incubated at 37

oC, 4

oC and 37

oC with a pretreatment using NaN3.

Time (s)0 2 4 6 8 10

Intersity

(counts per 0.2 m

s)

0

20

40

60

Time (s)0 2 4 6 8 10

Internsity

(Counts per 0.2 m

s)

0

20

40

60

Time (s)0 2 4 6 8 10

Intersity

(Counts per 0.2 m

s)

0

20

40

60

Time (s)0 2 4 6 8 10

Intensity

(counts per 0.2ms)

0

20

40

60

a)

b)

c)

d)

879±±±±38

459±±±±23

413±±±±20

442±±±±26

S19

Figure S12. TEM images of microtomed cross-sections (~75 nm thickness) of HeLa cells for precise

localization of DNA nanoassembly. (a) HeLa cells incubated with DNA nanoassembly at 37 oC, (b)

HeLa cells incubated with DNA nanoassembly at 4 oC, (c) HeLa cells pretreated using NaN3 followed

by incubation with DNA nanoassembly 37 oC.

a)

b)

c)

S20

Figure S13. Flow cytometric assay for cells incubated with nanoassembly. The black curve is obtained

for cells incubated with nanoassemnly carrying H3 and H4. The red curve is the response for the cells of

interest. (a) Hela cells incubated with nanoassembly carrying H1 and H2, (b) C166 cells incubated with

nanoassembly carrying H1 and H2, (c) Hela cells incubated with nanoassembly carrying L1, (d) Hela

cells incubated with nanoassembly carrying H1 and H5.

Count

Cy3

a)

Cy3

Count

b)

FAM

Count

c)Count

FAM

d)

S21

Figure S14. Fluorescence imaging for Hela cells. (a) Hela cells incubated with nanoassembly carrying

H1, (b) Hela cells incubated with nanoassembly carrying H2, (c) Hela cells incubated with nanoassem-

bly carrying H1 and H2.

1

2

2

3

3

1 2 3

1 2 3

FAM FRET to TAM Merge

a)

b)

c)

S22

Figure S15. Fluorescence imaging of Hela cells incubated with nanoassembly carrying H1 and H2 for 3

h followed by 25 nM LysoTracker Green DND-26 for 15 min.

Lyso@tracker Nanoassembly Merge

S23

Figure S16. Agarose gel electrophoresis image for cytoplasm extracts form Hela cells. Lane 1, DNA

size marker; Lane 2, cytoplasm extract from Hela cells incubated with DNA nanoassembly only carrying

H1; Lane 3, cytoplasm extract from Hela cells incubated with DNA nanoassembly only carrying H7;

Lane 4, cytoplasm extract from Hela cells incubated with DNA nanoassembly carrying H1 and H5.

S24

Figure S17. (a) Fluorescence images for Hela cells treated with varying concentrations of a survivin ex-

pression repressor YM155 followed by incubation with the nanoassembly. Orange fluorescence image

(top), differential interference contrast image (bottom). (b) Fluorescence intensity analysis of the images.

Each data point is the average of the ROIs from 30 different Hela cells. The error bars are the standard

deviations.

a) 0 nM YM155 1.2 nM YM155 2.5 nM YM155

CYM155

Fluorescence

0

400

800

1200

1600

0 nM 1.2 nM 2.5 nM

b)

S25

Figure S18. Expression analysis of survivin mRNA in Hela cells treated with a survivin expression re-

pressor YM155 of varying concentrations. (a) Real-time fluorescence curves in qRT-PCR analysis, (b)

relative expression levels for survivin mRNA. The error bars are the standard deviations across three

repetitive assays.

Cycle5 10 15 20 25 30 35

∆ ∆ ∆ ∆Rn

0

20000

40000

60000

7434.38

a)

b)

Relative Level of Survivin m

RNA

0

2

4

6

8

10

12

14

0 nM YM155 1.2 nM YM155 2.5 nM YM155

S26

Figure S19. (a) Flow cytometric assay for of Hela cells treated with varying concentration YM155 fol-

lowed by incubation with nanoassembly. The red curve is obtained for cells incubated with nanoassemn-

ly carrying H3 and H4. The pink, blue and black curves are the response for cells treated with 0, 1.2, 2.5

nM YM155, respectively. (b) Fluorescence intensity analysis of the curves. Geometric mean values of

integral fluorescence intensities with standard deviations were obtained across three repetitive assays.

Cy3

Count

a)

Geom. Mean

0

10

20

30

40 Background

2.5 nM YM155

1.2 nM YM155

0 nM YM155

b)

S27

Figure S20. Expression analysis of survivin mRNA in SKBR-3 (red), MCF-7 (blue) and MCF-10A

(pink) cells. (a) Real-time fluorescence curves in qRT-PCR analysis, (b) Relative expression levels for

survivin mRNA.

Cycle5 10 15 20 25 30 35

∆∆ ∆∆Rn

0

20000

40000

60000

80000

9497.18

Relative Level of Survivin m

RNA

0

2

4

6

8

10

12

MCF-10A MCF-7 SKBr-3

a)

b)