ARTICLE pubs.acs.org/bc
Self-Assembled G4-DNA-Silver Nanoparticle Structures Irit Lubitz and Alexander Kotlyar* Department of Biochemistry, George S. Wise Faculty of Life Sciences and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
bS Supporting Information ABSTRACT: Here, we describe the preparation and properties of discrete conjugates between silver nanoparticles and G-quadruplex DNA. The 20 nm silver nanoparticles (AgNPs) were connected by G-quadruplexes containing phosphorothioate anchor residues at both ends of the DNA, and the resulting conjugates were separated on the basis of the number of nanoparticles by gel electrophoresis. The molecular morphology of discrete conjugates was confirmed by TEM analysis. We have shown that the absorption spectrum of the conjugates is broader than that of AgNPs not connected to each other, indicating the presence of plasmon-mediated interparticle interactions. We discuss possible application of the conjugates in nanoelectronics.
’ INTRODUCTION Since its discovery by Alivisatos and Mirkin in 1996,1,2 DNAdirected assembly of nanoparticles has become a subject of extensive investigation by chemists, biologists, and physicists. Nanoparticle-DNA conjugates (NP-DNA) exhibit unique physical, chemical, and optical properties and proved to be useful in many different areas of nanoscience including nanoassembly,3,4 bio nano technologies, 5-7 and nanoelectronics.8,9The vast majority of studies in this field to date have been conducted on gold nanoparticles functionalized with thiol-modified singlestranded (ss) DNA. Only a few studies have focused on DNAdirected assembly of silver particles (Ag-NP).10,11 This was mainly due to the instability of the particles and DNA-NP systems. A new method for the covalent functionalization with single-stranded phosphorothioate oligonucleotides enables the preparation of relatively stable Ag-NPs which are suitable for selfassembly.12 In a classical approach, the self-assembly is guided by bimolecular recognition of complementary oligonucleotide strands attached to different particle. Annealing of the strands leads to the formation of multiparticle structures.2,13,14 It is known that, besides the classical double-helical, certain sequences can adopt triple-helical and four-stranded conformations. This is especially true for relatively short15-19 (16-32 bases) and long20,21 (thousands of bases) G-rich sequences, that can form noncanonical G-quadruplex structures. These structures (termed G4DNA) are composed of stacked tetrads; each of the tetrads arises from the planar association of four guanines by Hoogsteen hydrogen bonding (see Scheme 1A). G-quadruplex structures are very polymorphic and are characterized by various molecularity, topology, and strand orientation.22 They may be formed from one, two, and four separate DNA strands, thus termed r 2011 American Chemical Society
mono-, bi-, and tetramolecular G4-DNA, correspondingly.23-28 The short G4-DNA structures composed of a small (3-5) number of tetrads are stable only in the presence of stabilizing cations (Kþ or Naþ);15-19 removal of the cations results in unfolding of these structures. It has been shown that gold nanoparticles functionalized with either G-rich sequences29,30 or derivatives of G-monomers31 aggregate in the presence of Na and K ions. This indicates that the aggregation process is driven by the formation of multiple G-quadruplex links between the particles in the presence of the above cations. Here, we report the preparation of discrete conjugates between silver nanoparticles and 30 tetrad G-quadruplexes and characterize their morphology and optical properties.
’ EXPERIMENTAL PROCEDURES Unless otherwise stated, reagents were obtained from SigmaAldrich (USA) and were used without further purification. DNA Samples. The deoxyoligonucleotides, a5G30a5, A5G30A5, a10A5 were purchased from Alpha DNA (Montreal, Canada). The latter oligonucleotide (∼1 mg) was dissolved in 200 μL of double distillate water and was used in a capping procedure (see below). The two former G-rich oligonucleotides were dissolved in 200 μL of 0.1 M LiOH and incubated for 30 min at room temperature. The oligonucleotide samples were subsequently passed at room temperature through a prepacked Sephadex G-25 DNA-Grade column (Amersham Biosciences) equilibrated with 2 mM Tris-Ac (pH 8.5). The oligonucleotide eluted in the void volume was collected in 0.4-0.5 mL. The Received: November 8, 2010 Revised: January 11, 2011 Published: February 14, 2011 482
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Scheme 1. Schematic Drawing of (A) G-Tetrad, (B) Tetra-, and (C) Monomolecular G-Quadruplexes Containing Phosphorothioate Residues (Marked in Red)
eluate (OD at 260 nm of ∼100) was either incubated at room temperature for 30 min and then diluted 100 times with 100 mM Tris buffer (concentrated sample) or diluted approximately 100 times with 100 mM Tris-Ac (pH 8.5) and then incubated for 30 min at room temperature (dilute sample). Concentrations of a5G30a5, A5G30A5, a10A5 oligonucleotides were calculated using extinction coefficients at 260 nm of 1080, 1080, and 142 mM-1 cm-1, respectively. Synthesis of Ag-NPs. Ag-NPs with 20 nm diameter were prepared by 0.1 M AgNO3 reduction in the presence of borohydride (NaBH4) as follows: 0.45 mL of freshly prepared AgNO3 was added into 180 mL of precooled to 4 °C deionized/ filtered water. Then, 0.90 mL of 50 mM sodium citrate solution and 0.75 mL of 0.6 M NaBH4 were added to the reaction mixture under vigorous stirring in the melting ice bath. The solution developed a clear yellow color. The solution was kept at 4 °C overnight; the mixture turned dark yellow. 0.72 mL of 2.5 M LiCl was added to the mixture solution under vigorous stirring at ambient temperature. The mixture was incubated for 15 min and centrifuged at 11 000 rpm for 1.2 h at 20 °C in a Sorval SS-34 Rotor. A clear supernatant was carefully discarded, and the pellet was suspended in 4-5 mL of residual supernatant; OD of the particle suspension should be approximately equal to 100 at 400 nm. 40 μL of 1 mM a10A5 solution in deionized water was added to 4 mL of the above particle suspension followed by the addition of 100 μL of 1 M NaCl. The mixture was incubated for 1 h at 50 °C and was subsequently loaded onto a Sepharose 6B-CL 16/ 40 column equilibrated with 10 mM Na-Pi buffer (pH 7.4) at a flow rate of 0.6 mL/min. The particles were isocratically eluted with 40-50 mL of the buffer after a dark blue fraction containing nanopatricle aggregates. The particles completely separated from non-covalently bound a10A5 (eluted 20 mL after the particle fraction) and the particle aggregates were collected from the column and concentrated by centrifugation at 14 000 rpm for 25 min on Eppendorf Table 5424 centrifuge. The resulting nanoparticles were screened for their size and uniformity by TEM, revealing an average diameter of 20 ( 3 nm. The UV-vis spectra showed a characteristic absorption peak at 397 nm. The particles were stable and did not precipitate at high (up to 0.3 M) salt concentrations. Concentration of the particles was calculated
Figure 1. CD spectra of G4-quadruplexes formed in concentrated and dilute a5G30a5 solutions. (A) Tris-Ac (pH 8.5) was added to a5G30a5 eluted from a Sephadex G-25 column to a final concentration of 100 mM. The sample (OD at 260 nm ∼100) was incubated at room temperature for 30 min and was then diluted 100 times with 100 mM Tris-Ac (pH 8.5). (B) a5G30a5 eluted from a Sephadex G-25 column was further diluted approximately 100 times with 100 mM Tris-Ac (pH 8.5) and incubated for 30 min at room temperature. The CD spectra were recorded at 25 °C. Each spectrum is an average of three scans. KCl was added to the samples (dashed curve on A and B) to give a final concentration of 10 mM.
using an extinction coefficient (ε) of 3 109 M-1 cm-1 at 390 nm.42 Gel Electrophoresis. The DNA-NP samples were loaded onto 2% agarose gel 7 7 cm2, and then electrophoresed at 4 °C at 130 V for 40 min. Tris-Acetate-EDTA (TAE) buffer, containing 40 mM Tris-Acetate and 1 mM EDTA, in addition to being used to prepare the agarose, also served as the running buffer. HPLC Separation. The chromatography of G-quadruplexes and DNA-Ag-NPs conjugates was achieved with a TSK-gel G-5000-PW HPLC column (7.8 300 mm) from TosoHaas (Japan) by isocratic elution with 20 mM Tris-Ac (pH 8.5), for 30 min at a flow rate of 0.5 mL/min. HPLC was conducted on an Agilent 1100 HPLC system with a photodiode array detector. Peaks were identified from their retention times obtained from the absorbance at 260 and 400 nm for DNA and DNA-AgNP conjugates, respectively. TEM Measurement. TEM samples were prepared by dropping 2.5 μL of a sample solution in 20 mM Tris-Ac (pH 8.5) onto 483
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Figure 2. Size-dependent HPLC of G4-quadruplexes formed in concentrated (solid curve) and dilute (dashed curve) a5G30a5 solutions. The DNA samples were prepared as described in Figure 1. 0.5 mL of a DNA solution was loaded onto a size-exclusion G-5000 (Toso-Hass, Japan) column and chromatographed in 20 mM Tris-Ac (pH 8.5) at a flow rate of 0.5 mL/min. The elution was followed at 260 nm.
a carbon-coated grid (400 mesh). The grids (before depositing) were negatively glow discharged using Emitech K100X glow discharger. After incubating for 5 min at ambient temperature, the excess solution was removed by blotting with filter paper. TEM imaging was performed on a TEM JEM model 1200 EX instrument operated at an accelerating voltage of 120 kV.
Figure 3. Electrophoretic separation of G4-DNA-AgNP conjugates. Lane 1: AgNPs (OD at 400 nm is equal to 200). Lane 2: AgNPs were incubated with G4-structures (OD at 260 nm is equal to 0.1) formed in a concentrated a5G30a5 solution (see Figure 1) in 10 mM Na-Pi buffer (pH = 7.4) containing 250 mM NaCl for 2 h at 50 °C. 20 μL aliquots of each sample were loaded onto a 2% agarose gel and electrophoresed at 130 V for 40 min at 4 °C.
’ RESULTS Short G-rich oligonucleotides are known to assemble into high-molecular-weight multistrand aggregates.23,32,33 These aggregates formed spontaneously upon the dissolution of commercial preparations of G-rich oligonucleotide. They, however, can be disassembled at pH higher than 12; addition of 0.1 M LiOH to the oligonucleotide solution leads to dissociation of the aggregates into single oligonucleotide strands. The dissociation is driven by deprotonation of G-bases at the N1-site at pH higher than pKa (9.4) and is caused by strong electrostatic repulsion of the deprotonated strands. We dissolved a5G30a5, an oligonucleotide containing 30 central G-base fragment (G30) flanked by two runs of phosphorothioated adenines (a5) on either side, in 0.1 M LiOH. The pH was subsequently reduced during chromatography of the alkaline oligonucleotide solution on a Sephadex G-25 column equilibrated with 2 mM Tris-Ac (pH 8.5). The oligonucleotide eluted from the column is characterized by a weak CD signal (data not presented), indicating that the strands do not fold into a quadruple helix during the chromatography stage. The increase of the ionic strength in the eluate results in the appearance of CD signals corresponding to G4-DNA. Addition of Tris-Ac buffer (100 mM final concentration) to the eluate containing oligonucleotide (OD >100 at 260 nm) followed by incubation for 30 min at room temperature and ∼100-times dilution of the sample with 100 mM Tris-Ac (pH 8.5) induces a strong positive CD band at 258 nm in the spectrum (see Figure 1A, solid curve). The addition of Tris-Ac (100 mM final concentration) to the eluate diluted 100-fold with 2 mM Tris-Ac buffer results in the appearance of a positive CD band at 255 and a negative one at 275 nm (see Figure 1B, solid curve) in the CD spectrum of the oligonucleotide. The CD spectrum is affected by
K-ions; addition of 10 mM KCl results in a strong reduction of a negative signal at 275 nm and a shift of the positive signal maximum to 260 nm (Figure 1B, compare solid and dashed curves). The effect of the cation on the CD spectrum of structures formed at high concentrations of the oligonucleotide is less pronounced. Similar effects of K-ions (see Figure 1A,B) were reported for monomolecular34 and tetramolecular20 G4wires. The G-strand folding mechanisms are mainly governed by G-strand concentration.20,34 Self-folding is a major (if not the only) G-quadruplex formation pathway at low concentrations of G-strands. On the contrary, high strand concentrations favor formation of bi- and tetramolecular G4-structures. Indeed, the shape of the CD spectrum shown in Figure 1B resembles that of a self-folded G-strand20,26,27,34 suggesting the monomolecular mechanism of a5G30a5 folding (see Scheme 1C) at low concentration in the presence of 100 mM buffer. The CD spectrum of the oligonucleotide assembled at high concentrations (see Figure 1A) corresponds nicely to that of four parallel-stranded G-quadruplexes.34,35 We thus suggest that the association of four strands takes place upon formation of G-quadruplexes.20,35,36 This suggestion was supported by the size-exclusion HPLC analysis of the structures. The molecules formed in the concentrated solution elute from the column earlier (see Figure 2) than those formed in the dilute solution in the presence of 100 mM Tris-Ac. This shows that the former structures are bigger (longer) compared to the latter ones, which is consistent with the proposed mechanisms of the strand folding. 484
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Figure 4. TEM images of G4-DNA-AgNP conjugates. Molecules were electroeluted from gel slices corresponding to bands 1 (A), 2 (B), and 3 (C) of the gel (Figure 3), deposited on 400 mesh copper carbon grids and visualized by TEM.
Scheme 1B), for 2 h in 10 mM Na-Pi buffer (pH 7.4) containing 250 mM NaCl yielded a mixture of conjugates containing a discrete number of nanoparticles. The conjugates can be efficiently separated by electrophoresis in a 2% agarose gel (see Figure 3). The yellow bands indicated by arrows and marked by numbers in Figure 3 (lane 2) correspond to conjugates comprising one, two, and three particles, respectively. In the conjugates, each pair of AgNPs is bridged by G4-DNA. Incubation of AgNPs with G4-structures formed in concentrated solutions of a non-phosphorothioated A5G30A5, or in a dilute solution of a5G30a5 (see Figure 1B and Scheme 1C) did not yield conjugates comprising two or more particles (Supporting Information, Figure S2). This observation is consistent with spatial orientation of phosphorotioate residues in mono- and tetramolecular G-quadruplexes and supports the suggested mechanism of the strand folding at high and low concentrations of the oligonucleotide. In a monomolecular G-quadruplex, the phosphorothioated 50 - and 30 -ends of a5G30a5 are situated close together on one side of the molecule (see Scheme 1C). In contrast, association of the four strands yields the quadruplex containing phosphorothioate residues, capable of covalent bonding to metal particles, at both ends of the structure (see Scheme 1B). The tetramolecular G-quadruplex can thus bind a pair of particles bridging them into a dimer. In contrast, the monomolecular structures, containing phosphorothioate residues only at one end, cannot connect the particles. To obtain individual conjugates, each band was cut out of the gel with a razor blade. The yellow gel slices were placed in dialysis bags containing TEA buffer; each sample was then electroeluted into a bag and collected. The molecules extracted from each band were characterized by TEM. As seen in Figure 4, conjugates extracted from gel slices corresponding to bands 1, 2, and 3 composed of 1, 2, and 3 nanoparticles, respectively. We have shown (see Figure 5) that the absorption spectrum of the DNA-AgNP dimer is broader than that of the particles not connected to each other (compare solid and dashed curves in Figure 5). These changes in the shape of the absorption spectrum indicate for the plasmon-mediated interparticle interaction in the dimer. The plasmonic coupling between the particles is, however, not strong enough to produce very strong effect on the spectrum. The plasmonic properties are strongly dependent on interparticle distance.42 In the dimer, the particles are separated from each other by about 7 nm, which corresponds to the length of a 30 tetrad G-quadruplex.27 The effect on the spectrum is expected to be more pronounced if shorter G-quadruplex linkers will be used. This work is underway in our laboratory.
Figure 5. Absorption spectra of AgNPs (dashed curve) and G4-DNAAgNPs dimers (solid curve). The dimers were electroeluted from the gel slice corresponding to band 2 (see Figure 3).
We have shown that the structures formed in the presence of 100 mM buffer interact with high affinity with Thiazole orange (TO); binding to the oligonucleotide results in the tremendous increase of the dye fluorescence. No such fluorescence enhancement was observed in 2 mM Tris-Ac (Supporting Information, Figure S1). We have recently demonstrated that TO at low concentrations binds preferentially to G4-DNA, as compared to single- and double-stranded DNA forms.37 Efficient and selective fluorescent staining of the above structures indicates that the oligonucleotide folds into G-quadruplex structures in the presence of 100 mM Tris-Ac. Folding of the oligonucleotide into G-quadruplexes is in a good agreement with earlier studies on folding of T4GnT4 oligonucleotides.35,38 To prepare G4-DNA-AgNP conjugates, we used 20 nm silver particles. The citrate-capped nanoparticles formed during the reduction of silver ions in the presence of citrate are unstable and tend to agglomerate at salt concentrations higher than 20 mM. In addition, the particles interact with phosphate groups of the DNA backbone. In order to increase the stability and to avoid the backbone-mediated interactions, we have coated the particles with a 15-mer oligonucleotide, a10A5. This oligonucleotide is composed of ten phosphorothioate adenine (a) residues that can tightly and covalently anchor the strand to the surface of a silver nanoparticle12,39 and five regular adenine (A) bases that form a protective coating layer on the particle surface. We have shown that incubation of the particles with phosphorothioate-functionalized G4-DNA structures, formed at a high concentration of the oligonucleotide (see Figure 1A and 485
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’ DISCUSSION G4-quadruplexes were proposed as building blocks for molecular electronics.21 These structures, composed of stacked Gtetrad plains, provide better conditions for π overlap compared to the base pairs of the canonical double-stranded DNA. Guanine base composing the G-quadruplexes is characterized by the lowest ionization potential among the DNA bases, which also increases the probability of charge migration through G4DNA structures.40,41 We have recently demonstrated that G-quadruplexes are characterized by a clear electrical polarizability,20 which is indicative of possible electrical conductivity. In order to directly measure the electrical conductivity, one should depose the DNA molecule between the electrodes. The deposition of single DNA molecules is very challenging due to their small size (several nanometers) and poor electrical connection to metal surfaces. Attachment of metal particles to the ends of the G-quadruplex may provide good electric communication via metal/metal contact interactions, thus promoting charge migration though the DNA. In addition, attachment of 20 nm particles to both ends of the 30 tetrad G-quadruplex makes it possible to depose the conjugate in between electrodes separated by 30-40 nm.
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’ ASSOCIATED CONTENT
bS
Supporting Information. Additional information as described in the text. This material is available free of charge via the Internet at http://pubs.acs.org.
’ AUTHOR INFORMATION Corresponding Author
*To whom correspondence should be addressed. E-mail:
[email protected].
’ ACKNOWLEDGMENT This work was supported by European Commission FP6 Information Society Technologies program, grant “DNA- Based Nanodevices’’, and by the ISF Converging Technologies program, grant 1714/0. ’ REFERENCES (1) Alivisatos, A. P., Johnsson, K. P., Peng, X., Wilson, T. E., Loweth, C. J., Bruchez, M. P., Jr., and Schultz, P. G. (1996) Organization of ’nanocrystal molecules’ using DNA. Nature 382, 609–11. (2) Braun, E., Eichen, Y., Sivan, U., and Ben-Yoseph, G. (1998) DNA-templated assembly and electrode attachment of a conducting silver wire. Nature 391, 775–8. (3) Fu, A., Micheel, C. M., Cha, J., Chang, H., Yang, H., and Alivisatos, A. P. (2004) Discrete nanostructures of quantum dots/Au with DNA. J. Am. Chem. Soc. 126, 10832–3. (4) Goluch, E. D., Nam, J. M., Georganopoulou, D. G., Chiesl, T. N., Shaikh, K. A., Ryu, K. S., Barron, A. E., Mirkin, C. A., and Liu, C. (2006) A bio-barcode assay for on-chip attomolar-sensitivity protein detection. Lab Chip 6, 1293–9. (5) Mirkin, C. A., Letsinger, R. L., Mucic, R. C., and Storhoff, J. J. (1996) A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382, 607–9. (6) Mitchell, G. P., Mirkin, C. A., and Letsinger, R. L. (1999) Programmed assembly of DNA functionalized quantum dots. J. Am. Chem. Soc. 121, 8122–8123. 486
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