Supporting Information. Copyright Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 2007

Transcription

1 Supporting Information Copyright Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 2007

2 DNA based control of interparticle interactions for regulated micro- and nano-particle assembly** Mathew M. Maye, 1 Dmytro Nykypanchuk, 1 Daniel van der Lelie, 2 and Oleg Gang 1 * 1 Brookhaven National Laboratory, Center for Functional Nanomaterials, Upton, NY Brookhaven National Laboratory, Biology Department, Upton, NY 1973 *ogang@bnl.gov These authors contributed equally Supporting Information Experimental Details: Surface modification of polystyrene particles: Single-stranded 3 -primary amine modified ssdna (Invitrogen Co.), Table S1, was grafted on to carboxylated polystyrene colloidal spheres, 1.9 µm, (Invitrogen Co.), following the procedure outlined in ref. S1. Typically, 0.15 wt. % of the particle suspension was incubated with 15 µm DNA (L DNA + N DNA) solution in 100mM Imidazole buffer ph 7.0 for three hours at 50ºC in the presence of 100mM EDAC. The modified particles were cleaned 3x in 0.5% SDS solution by successive centrifugation (at 800g, 6 min) and supernatant exchange. Then, similarly, they were washed three times in hot (60ºC) deionized water and re-dispersed in 10mM phosphate buffer, ph 7.7, for storage at 4ºC. The fraction of N DNA on the surface, f N, was controlled by changing the ratio of DNA concentrations [L] and [N] used in the grafting procedure, f N = [N]/([N]+[L]). The DNA surface density was quantified by fluorescence measurements. [S2] Nanoparticle Synthesis: Gold nanoparticles (Au, 9.6 ±0.8 nm) were synthesized by a slightly modified citrate (Cit) reduction procedure. [S3] Briefly, an aged 1 mm HAuCl 4 solution was heated to ~95 o C for 30 minutes. To this solution, a warm (~40 o C) 10 ml aliquot of 38 mm trisodium citrate solution was added. Upon initial color change to red, the solution was immediately cooled to ~80 o C and annealed for 2 hrs. The sample was left to cool to room temperature and allowed to stand overnight. The solution was then purified via centrifugation (30

3 min, 4,500g) and stored at the desired concentrations in the dark. The Au concentrations were calculated via a measured extinction coefficients of 1.0 x 10 8 L mole -1 cm -1. Nanoparticle Modification: Thiol-functionalized single stranded oligonucleotides were purchased from IDT (Integrated DNA Technologies, Coralville, IA, U.S.A) as disulfides, Table S1. Before functionalizing the particles, the oligonucleotides were first reduced by dissolving the lyophilized samples (100~300 nmoles) for 30 minutes with 0.3 ml of a 100 mm dithiolthreitol (DTT) solution in purified water or buffer. The reduced DNA was loaded onto a freshly purified sephadex column (G-25, Amersham Bioscience) and eluted with 2.5 ml 10 mm phosphate buffer (ph = 7.0). The DNA was quantified using UV-Vis analysis with the specific DNA extinctioncoefficient. The synthesized Au were functionalized with a ratio of L and N following methods for high DNA coverage. [S4] In a typical experiment, an aliquot (1-50 µl) of a purified DNA µm solution was added to a 1 ml solution of Au ([Au] = nm). In a typical procedure, the L A or L B -type ssdna were first added to the Au solution, stirred for 5 min, and left to anneal at room temperature for 1 hr. Then, the N-type ssdna was added, stirred for 5 min, and then left for 3 hr. The total ssdna ([L] + [N]) to Au ratio ([L] + [N])/[Au] was kept constant at ~150X. The surface coverage fraction of N, f N =[N]/([N]+[L]) was tailored by their respective concentrations. The ssdna + Au solutions incubated at room temperature in a nonbuffered solution for at least 3 hr before adding phosphate buffer to bring its concentration to 10mM (ph = 7.1); the solution then was left to anneal for 4 hr. The salt concentration then was increased gradually from to 0.1 M NaCl over 6 hrs, and finally to a 0.3 M NaCl concentration for an additional 12 hr; L+N modified Au were stable indefinitely at these high salt concentrations. The excess DNA next was removed from the solutions by centrifuging them at least three times for 30 minutes at 4,500g. Fluorescence- and UV-Vis analyses showed that the total number (n) of L + N ssdna bound to each Au at each f N at this feed ratio (150X) was ~60 (±5) (~31.7 pmol/cm 2 ). [S4]

4 Melting Analysis: Analysis of the melting profile was carried out by fitting the melting curves to eq S1, following the methods described in Ref. S5. f melted 1 = H TOT exp R T TM S1 where f melted is the fraction of melted Au compared to assembled Au, and H tot is the total enthalpy change due to the melting process, R is the gas constant (8.31 J mole -1 K -1 ), T is temperature (K), and T m is the melting temperature. The value of H tot is the sum of multiple individual melting steps ( H i ), and is dominated by the melting of dsdna-linkages between particles; however, the unfolding of N ssdna at higher temperatures also contributes to H tot. Interaction Energy Dependence on Particle Size: Interactions between particles, covered with DNA at the surface densities and lengths used, and the separations between particle surfaces of ~ 8 nm or larger are due to interactions between the DNA molecules. [S2] Attraction, in this case, is caused by DNA hybridization, while repulsion reflects DNA steric interactions. Parameters affecting the interactions include DNA surface density, DNA length and structure, particle size, shape, and separation between particles. For two different sized particles with a DNA layer of constant structure, e.g., identical radial segmental density distribution, the DNA-mediated interaction between particles is determined by geometrical factors, i.e., the distance between the [S2, S6] particles, d p, and the particle s radius, R. The former determines the degree of interpenetration of the two DNA layers, and accordingly, both the number of interacting DNA molecules, m, and the average energy per molecule, E m, in penetrating regions. Particle radius, at constant distances between particles, determines only the area, A, of the largest cross-section of interpenetrating layers; hence, it affects only the number of interacting molecules, m~a, with interaction energy per particle s contact, E, changing as E = me m ~A. From geometrical considerations, the largest cross-section for repulsion, Figure S5, can be approximated as A~(R+d r /2) 2 -(R+d p /2) 2 S2

5 where d r is the repulsion range and usually equals to twice the DNA layer s thickness. The attraction cross-section is defined as (see ref. S2 for details) A~R 2 -(R-d a /2+d p /2) 2 S3 where d a is the maximum distance between particles at which hybridization between DNAs on surfaces is possible, and d a may or may not be equal to twice the DNA layer s thickness and is determined by the particularities of the DNA structure. Hence, for constant d p, d r, and d a, E ~ A ~ R. Instrumentation: UV-Visible Spectrophotometry (UV-Vis): UV-Vis spectra were collected on a Perkin-Elmer Lambda 35 spectrometer ( nm). Melting analysis was performed in conjunction with a Perkin-Elmer PTP-1 Peltier Temperature Programmer and was performed between o C with a temperature ramp of 1 o C/min while stirring, in a 10 mm phosphate buffer, 0.21 M NaCl, ph=7.1, buffer solution. Fluorometry: Fluorescence was measured with PTI fluorescent spectrometer or on a Tecan Ultra384 microplate reader. Transmission Electron Microscopy (TEM): TEM micrographs were collected on a JEOL-1200 microscope operated at 120 kv. The samples were prepared by dropcasting an aqueous nanoparticle or assembly solution onto a carboncoated copper grid, followed by the slow removal of excess solution with filter paper after 5 minutes. Dynamic Light Scattering (DLS): The DLS measurements were obtained with a Malvern Zetasizer ZS instrument. The instrument is equipped with a 633 nm laser source, and a backscattering detector at 173 o. The intensity correlation function was analyzed by the constrained regularized CONTIN method. In the DLS experiments, assembly was prepared with a 1:1 ratio of particles A and B ([Au] = 7.5 nm, 10 mm phosphate buffer, 0.30M NaCl, ph=7.1, T=25 o C).

6 Small Angle X-ray Scattering (SAXS): SAXS experiments [S7, 23] were performed in-situ at the National Synchrotron Light Source s (NSLS s) X-21A beamline. The scattering data were collected with a CCD area detector. The data is presented as the structure factor S(q) vs scattering vector, q = (4π/λ)sin(θ/2), where λ, and θ, respectively, are the wavelength of incident X-ray, and the scattering angle. S(q) was calculated as I a (q)/i p (q), where I a (q) and I p (q) are scattering intensities for Au aggregates and un-aggregated Au, respectively. The spacing, d, that correlates to average closest center to center interparticle distance, was calculated by, d=2π/q, where q is the position of the first peak in S(q). The values of q were calibrated versus silver behenate (q = A -1 ). The SAXS data were collected for assembled aggregates after their full precipitation and dispersion in 10 mm phosphate buffer, 0.20 M NaCl, ph = 7.1, T=30 o C. The diameter of the Au used in SAXS was 9.6 ± 0.8 nm. SAXS samples at f N of contained high concentrations of large aggregates of a few hundred nm and larger, allowing for measurement of a structure factor, and accurate d determination. However, for the small aggregate sizes at f N >0.75 (<100 nm), due the limited interference of scattered intensities from the small number of particles per aggregate, the accurate d measurement becomes problematic. The assembled aggregates were analyzed in quartz capillary (1.0 mm diameter) in a custom-made sample holder under temperature control. Details of the SAXS experiments will be described elsewhere.

7 Supporting Tables: Table S1. The ssdna used for particle functionalization DNA Sequence (5 to 3 ) Comment Microsystem L A TAC TTC CAA TCC AAT TTT TTT TTT TTT TTT-C 6 H 12 -NH 2 Complementary to L B L B ATT GGA TTG GAA GTA TTT TTT TTT TTT TTT-C 6 H 12 -NH 2 Complementary to L A N TTC TCT ACA CTC TCT TTT TTT TTT TTT TTT-C 6 H 12 -NH 2 non-complementary to L A, L B Nanosystem L A TAC TTC CAA TCC AAT GAT AGG TCG GTT GCT-C 3 H 6 -SH Complementary to L B L B ATT GGA TTG GAA GTA GAT AGG TCG GTT GCT-C 3 H 6 -SH Complementary to L A N TTC TCT ACA CTC TCT TTT TTT TTT TTT TTT-C 3 H 6 -SH non-complementary to L A,L B Table S2: Results of melting curve analysis (Figure S3) and curve fitting by equation S1. [S5] Melting Analysis f N T m ( o C) FWHM ( o C) H tot (kj/mole) ~2, ~2, ~2, ~1, ~ a a a a Insufficient aggregation for Tm measurement.

8 Supporting Figures: Figure S1: A representative set of TEM images of Au-assembled aggregates at fn of 0.25(a), and 0.50 (b), and a series of TEM images at fn of 0.75 (c), 0.85 (d), and 0.95 (e), each sampled after assembly for 2 h.

9 e Abs (525 nm) a b c d t (min) Figure S2: A set of UV-vis kinetic profiles monitoring the Au surface plasmon resonance band (SP-band) during assembly at f N of 0.05 (a), 0.25 (b), 0.50 (c), 0.75 (d), and 0.85 (e). ([A]=[B]=7.5 nm, 10 mm phosphate buffer, 0.3 M NaCl, ph = Norm. Abs (525 nm) e d c b a T ( o C) Figure S3: A set of melting profiles for the assembled aggregates at f N of 0.05 (a), 0.10 (b), 0.25 (c), 0.50 (d), and 0.75 (e). The melting curves are offset in Abs. for clarity. (10 mm phosphate buffer, ph = 7.1, 0.21 M NaCl, 1 o C/min)

10 S(q) a b c d e q (A -1 ) Figure S4: A set of results for in-situ SAXS structure factor (S(q)) for the assembled aggregates at f N of 0.00 (a), 0.25 (b), 0.50 (c), 0.60 (d), and 0.75 (e). The SAXS profiles are offset for clarity. Interparticle spacing, d, can be determined via d=2π/q. (Au = 9.9 ±0.8 nm, 10 mm phosphate buffer, ph = 7.1, 0.20 M NaCl, 30 o C) Figure S5. Geometry of the particles interactions. d p is the distance between particles, d r is the repulsion range due to the DNA layers, R is a particle s radius, and A is the linear dimension of the largest crosssection of interpenetrating DNA layers. Supporting References: S1. H. Kolarova, B. Hengerer BioTechniques 1996, 20, S2. D. Nykypanchuk, M.M. Maye, D. van der Lelie, O. Gang, Langmuir 2007, 23, S3. R. G. Freeman, et al. J. Phys. Chem. 1996, 100, S4. (a) A. K. R. Lytton-Jean, C. A. Mirkin, J. Am. Chem. Soc. 2005, 127, (b) L. M. Demers Anal. Chem. 2000, 72, (c) S. J. Hurst, A. K. R. Lytton-Jean, C. A. Mirkin, Anal. Chem. 2006, 78, S5. R. Jin, G. Wu, Z. Li, C. A. Mirkin, G. C. Schatz, G. C., J. Am. Chem. Soc. 2003, 125, S6. S. T. Milner Europhys. Lett. 1988, 7, S7. (a) S. J., Park, A. A., Lazarides, C. A. Mirkin, R. L. Letsinger, Angew. Chem. Int. Ed. 2001, 40, (b) S. J. Park, et al. J. Phys. Chem. B 2004, 108,