supplementary information - nature · © 200 9 macmillan publishers limited. ... 10.1038/nchem.290...

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nature chemistry | www.nature.com/naturechemistry

Supplementary informationdoi: 10.1038/nchem.290

Metal-Nucleic Acid Cages

Hua Yang, Christopher K. Mclaughlin, Faisal A. Aldaye, Graham D. Hamblin, Andrzej Z. Rys, Isabelle Rouiller, Hanadi F. Sleiman*

Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal,

QC H3A-2K6,Canada

Supplementary Information

Table of Contents

I General 1

II Instrumentation 1

III Synthesis of dpp-phosphoramidite 2

IV Oligonucleotides Prepared for 2D and 3D Object Construction 3

V Enzymatic Optimization for T1 and T2 5

VI Metal Coordination of Triangles and Characterization Procedures 6

VII Enzymatic Optimization for the Characterization of Triangular Prism (TP) 10

VIII Metal Coordination of DNA Prism and Characterization Procedures 11

IX Further Design Strategies Developed for TP Assembly 14

X Dimensions of TP 16

XI Analysis of TP by Electron Microscopy (EM) 17

XII References 18

Metal-Nucleic Acid Cages

Hua Yang, Christopher K. Mclaughlin, Faisal A. Aldaye, Graham D. Hamblin, Andrzej Z. Rys, Isabelle Rouiller, Hanadi F. Sleiman*

Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal,

QC H3A-2K6,Canada

Supplementary Information

Table of Contents

I General 1

II Instrumentation 1

III Synthesis of dpp-phosphoramidite 2

IV Oligonucleotides Prepared for 2D and 3D Object Construction 3

V Enzymatic Optimization for T1 and T2 5

VI Metal Coordination of Triangles and Characterization Procedures 6

VII Enzymatic Optimization for the Characterization of Triangular Prism (TP) 10

VIII Metal Coordination of DNA Prism and Characterization Procedures 11

IX Further Design Strategies Developed for TP Assembly 14

X Dimensions of TP 16

XI Analysis of TP by Electron Microscopy (EM) 17

XII References 18


nature chemistry | www.nature.com/naturechemistry 1


1

I. General Toluene and ether were dried by refluxing over Na and dichloromethane was dried by

refluxing over CaH2. 1,10-N,N-phenanthroline, p-bromoanisole, tert-BuLi, MnO2, 4-

methoxyltritylchloride, chlorodiethyleneglycol, anhydrous pyridine, HCl, triethylamine,

diisopropylethylamine, dimethylaminopyridine, ethylenediaminetetracetic acid (EDTA),

trichloroacetic acide (TCA), StainsAll®, acetic acid, tris(hydroxymethyl)-aminomethane (Tris),

formamide, amyl amine and urea were used as purchased from Aldrich. Acetic acid, boric acid,

and MgCl2·6H2O were purchased from Fisher Scientific and used without further purification. 2-

cyanoethyl diisopropylchloro-phosphoramidite, nucleoside (dA,T,dC,dG) derivatized 500 Å and

1000Å LCAA-CPG supports with loading densities between 25-40 µmol/g, 5-ethylthiotetrazole,

1,6-hexanediol phosphoramidite and reagents used for automated DNA synthesis were purchased

from ChemGenes Incorporated. Sephadex G-25 (super fine, DNA grade) was purchased from

Amersham Biosciences. Mung Bean Nuclease (MBN, source: Mung Bean Sprouts) and

Exonuclease VII (ExoVII, source: recombinant) were purchased from BioLynx Incorporated.

Carbon coated 400 mesh copper EM grids were purchased from SPI.

II. Instrumentation 1H-NMR spectra were obtained using a Mercury 400 MHz NMR spectrometer. 13C-NMR

spectra were obtained using a Mercury 300 MHz NMR spectrometer. 31P-NMR spectra were

obtained using a Gemini 200 MHz NMR spectrometer. Standard automated oligonucleotide solid-

phase synthesis was performed on a Perspective Biosystems Expedite 8900 DNA synthesizer.

UV/Vis experiments and thermal denaturing experiments were conducted on a Varian Cary 300

biospectrophotometer. Gel electrophoresis experiments were carried out on an acrylamide 20 X

20 cm vertical Hoefer 600 electrophoresis unit. Fluorescence experiments were carried out on a

PTI (Photon Technology International) TimeMaster Model C-720F spectrofluorimeter. Circular

dichroism experiments were collected on a JASCO J-810 or JASCO J-815 spectropolarimeter at

20 oC. Enzymatic digestions were conducted using a Flexigene Techne 60 well thermocycler.

EM measurements were performed on a Technai G2 F20 microscope operating at 200 keV and

equipped with a Gatan Ultrascan 4k x 4k CCD camera. All measurements were performed under

low dose conditions.




2

III. Synthesis of dpp-phosphoramidite

The dpp-phosphoramidte (3) is synthesized according to a previously reported procedure.S1 31PNMR: 149.7(s), HR-ESI: 1013.4613 (target MS: 1013.4597)

A 1,6-hexanediol hd-phosphoramidite (4) was used as received from ChemGenes

Incorporated, and introduced into LSa-c via standard automated solid-phase DNA synthesis

protocols.

dpp-phosphoramidite (3)

hd-phosphoramidite (4)




3

IV. Oligonucleotides Prepared for 2D and 3D DNA Constructs

Name Sequence (5 3 ) 1a TCTAGGAGAC 3 ACATTAGGTA 3 CTTTCAACTT

1b AAGTTGAAAG 3 GTTTGCTGGG 3 GTGATGTCAT

1c ATGACATCAC 3 CCGCCGATTA 3 GTCTCCTAGA

2a TCTGGTAGAT 3 AACTCTTGAA 3 CTTTCAACTT

2b AAGTTGAAAG 3 CCTGCTCATA 3 GTGGTGTCAT

2c ATGACACCAC 3 GAAACGACAA 3 ATCTACCAGA

LSa TAATCGGCGG 4 TTTATTAAAGTCTCAGT 4 TTGTCGTTTC

LSb CCCAGCAAAC 4 TTTATTAAAGTCTCAGT 4 TTCAAGAGTT

LSc TACCTAATGT 4 TCACAGAATACCTCTCT 4 TATGAGCAGG

RSa CTGAGACTTTAATAA

RSb GAGAGGTATTCTGTG

General Procedure for Solid-Phase DNA Synthesis

DNA synthesis was performed on a 0.5 mol scale, starting from the required nucleotide

modified 500Å or 1000 Å LCAA-CPG solid-support. The phosphoramidte derivative of dpp (3)

was coupled on the growing chain of oligonucleotide as an artificial base with a prolonged

coupling time of 5min. The coupling efficiency was monitored after trityl removal. All sequences

were fully deprotected in concentrated ammonium hydroxide (55 oC, 16 hours).

Purification

Crude products were purified on 24% polyacrylamide/8M urea polyacrylamide gels (PAGE;

up to 20 OD260 of crude DNA per gel) at constant current of 15 mA for 7 hours, using 0.09M

Tris-Boric acid (TB) buffer (pH 8.3). Following electrophoresis, the plates are wrapped in plastic




4

and placed on a fluorescent TLC plate and illuminated with a UV lamp (254nm). The bands were

quickly excised, and the gel pieces were crushed and incubated in 10 mL of sterile water at 55 oC

for 16 hours. Samples were then dried to 1.5 mL, desalted using size exclusion chromatography

(Sephadex G-25), and quantified (OD260) using UV-vis spectroscopy.

After quantification, a denaturing PAGE was performed to analyze the purity of the modified

DNA strands site-specifically modified with 3. As is seen in Figure S1a, the 6 strands doubly

modified with 3 (1a-c and 2a-c) appear as single bands with no byproducts. Similar analysis was

performed on the linking strands (LSa-c) and rigidifying strands (RSa and RSb), as seen in

Figure S1b.

1 2 3 4 5 6a

1 2 3 4 5b

Figure S1 24% denaturing PAGE characterization of the purified oligonucleotides required for T1 and T2 assembly and for 3D assembly of TP a, lane 1-1a, lane 2-1b, lane 3-1c, lane 4-2a, lane 5-2b, and lane 6-2c. b, lane 1-LSa, lane 2-LSb, lane 3-LSc, lane 4-RSa, and lane 5-RSb




5

V. Enzymatic Optimization for T1 and T2

To ensure that the connectivity of T1 and T2 is indeed

cyclic, 2D starting materials were subjected to

Exonuclease VII (ExoVII) digestion. ExoVII is selective

for the digestion of single-stranded open DNA, over that of

cyclic closed DNA.S2 In a typical experiment 0.05 nmoles

of DNA (total), whether linear, 2D or 3D, was placed in 10

uL of TAMg buffer. According to the ExoVII optimization

experiments performed on linear single-stranded open-

form DNA shown in Figure S2, 5 U of ExoVII is required

to completely digest this mixture at 15 °C for 2 hrs.

Using these above outlined conditions, T1 was

subjected to ExoVII digestion. Figure S3 indicates that T1

(lane 1) is not digested by ExoVII (lane 2) while an open-

form single-stranded analogue of triangle T1 (lane 3) is

indeed almost completely digested (lane 4). Similar results

were obtained for T2 and revealed that the connectivity of

the triangles was indeed closed and cyclic.

1 2 3 4

Figure S2 8% non-denaturing PAGE characterization of 0.05 nmole of linear DNA in TAMg buffer after digestion with various units (U) of ExoVII. Lane 1-0 U, lane 2-1U, lane 3-3 U and lane 4-5 U.

1 2 3 4

T1

Figure S3 8% non-denaturing PAGE characterization of 0.05 nmole of T1 (lanes 1 and 2) and a single-stranded open-form intermediate of T1 (lanes 3-4). Lanes 2 and 4 are after digestion with 5U of ExoVII, 2hr, 15 °C.




6

VI. Metal Coordination and Characterization of Triangles T1 and T2

Preparation of T1.AgI3 and T2.AgI

3

0.342nmol of T1 or T2 were made in phosphate buffer (10mM NaH2PO4-Na2HPO4, pH 7.2)

or TAmg buffer (Tris-Acetic acid, 12mM MgCl2, pH 8). After incubation at room temperature for

15 min, 1.03 µl of 1 mM silver nitrate solution was added. Incubation was conducted at room

temperature, for 15 minutes.

Preparation of T1.CuI3 and T2.CuI

3

0.342nmol of T1 or T2 were made in phosphate buffer (10mM NaH2PO4-Na2HPO4, pH 7.2)

or TAMg buffer (Tris-Acetic acid, 12mM MgCl2, pH 8). After incubation at room temperature

for 15 min, 1.03µl of 1mM Cu(CH3CN)4PF6 acetonitrile solution (or CuSO4 and TCEP·HCl

(Tris[2-carboxyethyl]phosphine hydrochloride 1:2 mixture, water solution, final CuI

concentration 1mM) was added. At high concentrations a red color was observed due to CuI(dpp)2

complex.

Scheme S1 Site-specific metalation of triangles T1 or T2 with a transition metal M.

T1 or T2

M ( )




7

Preparation of T1.ZnII3 and T2.ZnII

3

Zn(NO3)2 (5eq.) as an aqueous 1 mM solution was added to 0.342nmol of T1 or T2 in

TAMg buffer and incubated at room temperature for 3 hr.

Preparation of T1.CoII3 and T2.CoII

3

CoCl2 (20eq.) as an aqueous 1 mM solution was added to 0.342nmol of T1 or T2 in TAMg

buffer and incubated at room temperature for 3 hr.

Preparation of T1.CdII3 and T2.CdII

3

CdCl2 (10eq.) as an aqueous 1 mM solution was added to 0.342nmol of T1 or T2 in TAMg


Preparation of T1.EuII3 and T2.EuII

3

EuCl2 was freshly prepared as an aqueous 1 mM solution and mixed with 2 equivalents

(2mM) of TCEP in TAMg buffer. 10eq. of EuCl2 was added to 0.342nmol of T1 or T2 in TAMg


Preparation of T1.AuI3 and T2.AuI

3

AuCN was freshly prepared as an aqueous 1 mM solution and mixed with 2x equivalents

(2mM) of TCEP in TAMg buffer. 20eq. of this AuCN solution was added to 0.342nmol of T1 or

T2 in TAMg buffer and incubated at room temperature for 3 hours.

In order to characterize the efficiency of the above metalation protocols for T1 and T2,

denaturing PAGE analysis (12 %, TB, 15 mA, 250 V, 4 °C) was performed. An example of this

characterization is shown in Figure S4 for T1 which utilized the above outlined metalation

protocols for each of the individual transition metals assayed. Upon addition of 4M urea to a

sample of T1, this system is denatured into component strands 1a-c (Figure S4 A, lane 1). After

the addition of various transition metals (Figure S4 a, lanes 2-8) a new band of reduced mobility

is observed. This band is evidence that after site-specific metalation T1 has resisted denaturation

and remains held in a cyclic structure due to metal-dpp ligand interactions. It is also noteworthy

that a variety of transition metals which do not usually bind in this environment appear to be

coordinated by this DNA- templated junction. In addition, metal binding to T1 does not affect the

apparent structure as revealed by non-denaturing PAGE (Figure S4 b).




8

UV-Vis Spectroscopy

Spectra were recorded for the non-metalated and

metalated triangles T1.M3 and T1.M3. As an

example, the spectra recorded for T2 is shown in

Figure S5. Absorbance due to the dpp ligands at ca.

350 nm is partially obscurred due to the large peak

observed for DNA at 260 nm. Peaks can be seen,

though, in the cases of metalated T1.M3, especially

for T1.CuI3 (_), that are indicative of Metal to

Figure S5 UV/Vis spectrum recorded in TAMg buffer for non-metallated T1 ( - ), T1.CuI

3 ( - ), and T1.AgI

3 ( - ).

a

b

T1 CuI AgI ZnII CoII CdII AuI EuII

1 2 3 4 5 6 7 8

1 2 3 4 5 6

1a-c

T1

Figure S4 Metalation of T1 and analysis by PAGE a, 12% non-denaturing PAGE characterization of T1 before and after site-specific metalation with a variety of transition metals as indicated in the top of the gel. b, 8% non-denaturing PAGE characterization of T1.M3.




9

Ligand Charge Transfer (MLCT) (ca. 470 nm and 600 nm). Similar results were obtained for

T2.

Thermal Denaturation Experiments

T1.CuI3 or T1.AgI

3 (0.342 nmol each, respectively) were prepared in TAMg buffer (Tris-Acetic

acid, 12 mM MgCl2, PH 8). The change in absorbance at 260 nm was monitored after heating the

systems from 15 oC to 90 oC at a rate of 0.5oC/min. As shown in Figure S6a, the denaturation

curves are shifted to higher temperatures upon complexation with either silver or copper. Using

these denaturation curves the melting temperatures were calculated from the first derivative of

absorbance over temperature. The following Tm values were calculated: T1, Tm=49oC;

T1.AgI3, Tm=56oC; T1CuI

3, Tm=76oC. In addition, a control experiment was performed

whereby Cu(I) (Cu(MeCN)4.PF6) was added to a 10 base duplex (5 -CCAGCGACAC +

complement) in the same ratio (1.2:1, Cu:DNA) as metalation of T1 or TP. It is clear from the

denaturation curves presented in Figure S6b that the addition of metal has minimal effects on

duplex stability. This experiment helps to confirm that the increased stabilization observed for the

modified DNA structures (T1, T2, and TP) is a result of site-specific binding at the dpp-dpp

junction and not due to non-specific interactions.

Figure S6 a) Thermal denaturation curves obtained for non-metalated T1 (-),T1.CuI3

(-), and T1.AgI3 (-). b) Control experiment for the addition of copper to a

unfunctionalized duplex DNA (10 bases in length)

a b




10

Circular Dichroism (CD) of T1.CuI3 or T1.AgI

3

In a typical CD experiment, 0.684nmol Triangle T1 or T2 was prepared in 100ul TAMg

buffer (Tris-Acetic acid, 12mM MgCl2, PH=8), and various molar equivalents of a Cu+ solution

(CuSO4 and TCEP·HCl (Tris[2-carboxyethyl]phosphine hydrochloride 1:2 mixture, water

solution, final CuI concentration 1mM solution) were added. After 2 min, a CD spectrum was

recorded at room temperature. Similarly, a 1 mM solution of silver nitrate was used to look at AgI

binding. Each of the obtained CD spectra were then analyzed at the absorbance maximum

corresponding to the dpp-dpp ligand system (ca. 345 nm) to obtain the molar equivalents of

metal required to reach binding saturation. As an example, the obtained titration curves for

T1.AgI3

and T1.CuI3 are shown in Figure S7 a and b. The saturation of the CD signal in both

cases occurs near the addition of exactly equivalents of silver or copper, indicating that site-

specific metalation takes place at the DNA-templated dpp-dpp junction.

Figure S7 CD titration curves obtained for a) T1.AgI

3 and b) T1.CuI3 . The peak where spectral data was

collected is shown on the y-axis.

VII. Enzymatic Optimization for TP In a similar fashion as was done for T1 and T2, the connectivity of TP was examined using

enzymatic digestion protocols. The protocol outlined in Section V for ExoVII was again

employed without further optimization. In order to obtain more information about the

connectivity of TP, a second enzyme was used, mung bean nuclease (MBN). MBN is selective




11

for the digestion of single-stranded DNA over double-stranded DNA by a factor of 30,000.S3,S4

Again, prior to MBN digestions of the 3D cage and various intermediates, experiments were

performed using ssDNA and dsDNA systems to optimize conditions. MBN digestion conditions

were again optimized at 15 °C for 2 hr in a 1xTAMg buffer system. The single stranded DNA is

almost completely degraded upon addition of 20U of the MBN enzyme (Figure S8 a, lane 5)

while the dsDNA control is not degraded at this enzyme concentration (Figure S8 b, lane 5).

VIII. Metal Coordination of DNA Prisms

a 1 2 3 4 5 6 7 8 9 10

Figure S8 Optimization of MBN enzymatic assay conditions. a, 8% non-denaturing PAGE characterization of 0.05 nmole of linear open form single-stranded DNA in TAMg buffer after digestion with increasing units (U) of MBN b, A similar analysis done for double stranded DNA. The lane assignments in both both a and b are the same: lane 1-0 U, lane 2- 5 U, lane 4-10 U, lane 5- 15 U, lane 6-20 U, lane 7- 25 U, lane 8- 30 U, lane 9- 35 U, lane 10- 40 U.

1 2 3 4 5 6 7 8 9 10 b

Scheme S2 Site-specific metalation of TP

TP. M6

M ( )




12

The 3D architecture TP was prepared as described in the

text of the paper and as shown in Scheme S2 found above.

After 3D construction the metalation protocols described in

Section VI of this document were employed to site-specifically

metalate TP. The main difference here is that the number of

dpp-dpp ligand junctions is doubled after TP preparation and

was taken into account when adding the desired molar

equivalents of transition metal salts. All other characterization

methods and protocols described in Section VI were also used

to analyze the metalated TP system. As was shown for

triangles T1 and T2, metalation also does not perturb the final TP structure as evidenced by the

uniformity observed in the PAGE results found in Figure S9.

Circular Dichroism (CD) of TP.AgI6

Similar to the measurements made for

TP.CuI6, CD titrations for TP.AgI

6 also

produced a saturation point for metal

binding that indicated the site-specific

binding of 6 silver atoms (Figure S10).

Intermediate ratios of metal addition to TP

We also performed a gel titration experiment where we added 0, 1, 2, and 3 equiv. of

Cu(I) to the triangle (Figure S11a), and 0, 1, 2, 3, 4, 5 and 6 equiv. (Figure S11b) of Cu(I)

to the cage. As all bis-dpp binding sites are equivalent in these structures, addition of

intermediate amounts of metal should give a distribution of fully, partially and non-

Figure S10 CD titration data compiled for TP after various additions of silver nitrate (TP.AgI

6).

EuIZnIAgI CuI No

Metal1 2 3 4 5 6

Figure S9 7% non-denaturing PAGE characterization of TP after the addition of various transition metals (TP.M6).




13

metalated species. Figures S11a and S11b indeed show the presence of the tris-, bis-,

mono and non-metalated triangles at intermediate ratios, with the proportion of tris-

metalated triangle increasing and that of the non-metalated triangle decreasing as more

copper is added.

Figure S11 Analysis of 2D and 3D metalation products under various equivalents of added transition metal. a, T1 before metal addition (lane 1) and after the addition of 1, 2, and 3 equiv. Cu(I) (lanes 2-4, respectively). Proposed intermediates are represented to the right of the gel. b, TP before metal addition (lane 1) and after the addition of 1-6 equiv. Cu(I) (lanes 2-7, respectively). Intermediates are again shown schematically to the right of gel.

T1.CuI3 TP.CuI

6

CuI: 0eq. 1eq. 2eq. 3eq. 4eq. 5eq. 6eq.

LS

RS

T1 and T2 Metalated

T1 and T2 Denatured

CuI: 0eq. 1eq. 2eq. 3eq.

Denatured T1

T1.CuI3

a b

1 2 3 4 1 2 3 4 5 6 7




14

IX. Further Design Strategies Developed for TP Assembly As outlined in the text of the paper, multiple iterations on the development of an appropriate

LS set was required to achieve a stable TP structure that would site-specifically bind transition

metals. Two such modifications that were made to the LS set of sequences are shown in Scheme

S3.

The first LS set was designed to contain non base-pairing thymidine (T) residues (LSTa-

c) on either side of the region that would hybridize to and ultimately connect triangles T1 and T2.

Assembly of this construct TPT occurred in good yield at room temperature as shown in Figure

S12a. Unfortunately, the final product was not stable under the optimized enzymatic conditions

(MBN and ExoVII) required to confirm the desired connectivity (Figure S12b).

O

O

O N

NH

O

OSpacers:

OO

O

OO

LST

LSEG

LS

O

Scheme S3. Modifications performed on LSa-c in order to obtain a stable TP system




15

In order to address this problem, a commercially available triethylene glycol (EG)

derivative was inserted in place of the T residues (shown in Scheme S3). As is observed in Figure

S13a, the sequential assembly of T1 and T2 using the EG modified linking strands LSEGa-c leads

to the quantitative formation of a 3D product TPEG which was indeed stable under both ExoVII

and MBN digestion conditions (data not shown). Although the LS modification led to the desired

product, problems were encountered upon metalation. As evidenced by the CD data shown in

Figure S13b, a large excess of copper was required to promote saturation of the signal. This large

molar excess was indeed rectified upon insertion of the C6 1,6-hexanediol derivative which led to

both excellent assembly, stability, and transition metal binding properties of TP.

a b 1 2 3 4 5 1 2 3

Figure S12 PAGE analysis of the 3D construct TPT a, 7% non-denaturing PAGE characterization of 3D structure TPT prepared by starting from T1 (lane 1) and sequentially adding LSTa (lane 2), LSTb (lane 3), LSTc (lane 4) and finally RSa and RSb (lane 5). b, 7% non-denaturing PAGE analysis of TPT (lane 1) and the results of digestion with MBN (lane 2) and ExoVII (lane 3).




16

X. TP Dimensions

Figure S14 Approximate dimensions of TP based on modeling. a, A top-view of TP with the triangular face labeled with height (h 5 nm) and base (a 5 nm ) markers. b, Side-view of TP showing one of the rectangular sides labeled with height (c 3 nm ) and width (b 4 nm) markers.

a b

a b

Figure S13 PAGE analysis of the 3D construct TPEG a, 7% non-denaturing PAGE characterization of 3D structure TPEG prepared by starting from T1 (lane 1) and sequentially adding LSEGa (lane 2), LSEGb (lane 3), LSEGc (lane 4) and finally RSa and RSb (lane 5). b, CD titration experiment for TPEG which reveals a disruption of site-specific metal binding for this 3D architecture.




17

Molecular mechanics modeling of the TP structure using the AMBER force field were

performed using the HyperChem software suite in order to ascertain approximate DNA-cage

dimensions. Shown in Figure S14 are both a top-view (Figure S14a) and side-view (Figure 14Sb)

of the modeled TP structure. The values in Figure S14 outline the approximate dimensions of

both the triangular and rectangular geometries that comprise the prismatic structure. An

approximate range for the inner volume of TP is calculated to be 25-30 nm3.

XI. Analysis of TP by Electron Microscopy (EM) We used TEM to image the DNA cage TP under negative staining conditions. Best

imaging results for stained particles were obtained when a 40 nM concentration of the structure

was deposited onto grids that had been glow discharged in the presence of amyl amine. A typical

TEM field of view is shown in Figures S15a where a number of single particles with dimensions

in agreement with that of the TP cage can be observed. Images selected from the negative stained

data, shown here in Figure S15b, reveal a number of projections that are in agreement with the

size determined from modeling TP. Some of the particles observed did appear to be broken or

distorted which is likely do to denaturation caused by the low pH of uranyl acetate. EM imaging

under negative staining conditions did however provide direct visual evidence of the structural

dimensions of TP which agree with the in silico generated model.




18

Figure S15 TEM images of negatively stained TP cages. a, A typical field of view obtained for TP (40 nM) deposited onto a 400 mesh carbon coated copper grid subsequently stained with a 2% solution of uranyl acetate. Imaging was performed at a nominal magnification of 50K, on a Tecnai G2 F20 microscope operating in low dose conditions at an accelerating voltage of 200 keV. Images were recorded on a Gatan Ultrascan 4k x 4k CCD camera. Scale bar shown is 100 nm. b, Representative particles obtained from the negative-staining TEM data for TP. Dimensions of the box used to select each particle are ca. 22 x 22 nm.

XII. References S1. Yang, H. & Sleiman, H.F. Templated synthesis of highly stable, electroactive, and

dynamic metal-DNA branched junctions. Angew. Chem. Int. Ed. 47, 2443-2446 (2008).

S2. Aldaye, F.A. & Sleiman, H.F. Modular access to structurally switchable 3D discrete

DNA assemblies. J. Am. Chem. Soc. 129, 13376-13377 (2007).

S3. Kroeker, W. D.; Kowalski, D.; Laskowski, M. Sr. Mung bean nuclease I. Terminally

directed hydrolysis of native DNA. Biochemistry 15, 4463-4467 (1976).

S4. Johnson, P. H.; & Laskowski, M. Sr. Mung Bean Nuclease I. II. Resistance of double

stranded deoxyribonucleic acid and susceptibility of regions rich in adenosine and

thymidine to enzymatic hydrolysis. J. Biol. Chem., 245, 891 – 898 (1970).

a b

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