Sensing Thermally Denatured DNA by Inhibiting the Growth of Au

ARTICLE pubs.acs.org/JPCC

Sensing Thermally Denatured DNA by Inhibiting the Growth of Au Nanoparticles: Spectral and Electrochemical Studies Hongcheng Pan,*,† Dunnan Li,† Jiangtao Liu,† Jianping Li,† Wenyuan Zhu,† and Yixin Zhao*,‡ † ‡

College of Chemistry and Bioengineering, Guilin University of Technology, 12 Jiangan Road, Guilin 541004, P. R. China Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States

bS Supporting Information ABSTRACT: The inhibition effect of DNA bases, guanine (G), adenine (A), cytosine (C), or thymine (T), on the growth of Au nanoparticles (NPs) was clarified by UVvis absorption spectra, resonance light scattering (RLS) spectra, transmission electron microscopy (TEM), differential pulse voltammetry (DPV), and theoretical calculations. It is found that the inhibition efficiency of the bases in the growth of Au NPs follows the order G > A > C > T, confirmed by the nucleobase concentration-dependent absorbance and RLS study. The DPV analysis reveals that observed base-dependent differences could be attributed to the varying ability of the bases to coordinate to the Au(III). The conditional stability constants of the complexes of Au(III)G, Au(III)A, Au(III)C, and Au(III)T are also in the order of G > A > C > T and were determined to be 5.66 105, 3.55 104, 1.15 104, and 4.61 103, respectively. Further theoretical calculations support that the DNA bases bind to Au(III) with relative affinity G > A > C > T. The thermally denatured salmon sperm DNA has the same inhibition effect on the growth of Au NPs as the individual DNA bases, while native salmon sperm DNA shows no significant effect on the growth of Au NPs. The observed difference results from the fact that the binding sites of bases are freely accessible for interaction with Au(III) species in the thermally denatured DNA, but double-helix structure of DNA in the native salmon sperm sterically inhibits the bases from adopting their most strongly bound orientation, resulting in a weak interaction with Au(III). The presented method could be a potential indirect monitoring method for DNA damage and DNA basepair mismatch.

’ INTRODUCTION Research of goldDNA interactions has attracted more and more attention in recent years. Exploring the goldDNA interactions could help to understand the mechanism of DNA bases adsorbing on the gold surface and is of particular importance in further biotechnology and medical applications.19 For instance, fabrication of the Au nanoparticle (NP) based DNA biosensor requires detailed knowledge regarding the capture of the DNA strand on the Au NP surface.3 In addition, DNA binding affinity studies on Au(III) dithiocarbamate derivatives suggested that they possess an appreciable affinity for the DNA double helix, enabling them to emerge as promising anticancer agents.10,11 The controlled assembly of Au NPs using DNA oligonucleotides has been one of the most popular research topics since Mirkin et al. developed an oligonucleotide-mediated Au NP aggregation process for DNA detection.12 The formation of a polymeric network of DNAAu NPs by mixing two oligonucleotide-functionalized Au NP probes with a solution of DNA target results in a concomitant red-to-purple color change. Furthermore, DNA-modified Au NPs have been used for the colorimetric detection of duplex and triplex DNA binding molecules.1315 r 2011 American Chemical Society

The plasmon absorbance position of Au NPs is correlated with their particle sizes and shapes,1621 and the absorbance of the Au NP solution is quantitatively correlated to the concentration of gold nanoparticles. As a result, both the growth and the inhibition of Au NP growth can be monitored by absorbance intensity, which could be applied as a facile biosensing strategy. Recently, Willner et al. developed an approach to couple enzymes and Au NPs and then identify the substrate and the enzyme activity by comparing the growth process of Au NPs.2224 Inspired by these pioneering works, Li et al. reported a new design mode of electrochemical cholesterol biosensors by utilizing the enlargement of Au NPs.25 The phenolic acids were demonstrated as active reducing agents for the catalytic growth of Au NPs.26 Accordingly, a colorimetric method was developed for evaluating the antioxidant power of food-related phenolic acids. Zhu et al. developed a near-infrared sensing strategy for detection of glucose and xanthine based on biocatalytic growth of Au NPs.27 In their work, xanthine was found to inhibit the growth of Au NPs. Received: February 12, 2011 Revised: May 21, 2011 Published: June 21, 2011 14461

dx.doi.org/10.1021/jp201396j | J. Phys. Chem. C 2011, 115, 14461–14468

The Journal of Physical Chemistry C

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Figure 1. UVvis absorption spectra of Au NP growth solution in the presence of variable concentrations of (a) guanine, (b) adenine, (c) cytosine, and (d) thymine. Inset: the dependence of absorbance at 565 nm on the concentrations of G, A, C, and T.

Currently, there are two approaches for the inhibition of the Au NP growth: (1) in the enzyme/substrate-mediated growth of the Au NP system, the growth of Au NPs is inhibited by adding the enzyme inhibitors (paraxon) to decrease the enzyme (acetylcholine esterase) activity;28 (2) in the nonenzyme system, the inhibitors coordinate to Au(III) ions to decrease the reduction of Au(III). Some purine derivatives (pds) such as xanthine and uric acid were reported to block the growth of Au NPs, which may attribute to the formation of pdsAu(III) complexes.27 Different pds have different affinities to the Au(III) ion. However, it is still unclear how ligandAu(III) affinities affect the growth of Au NPs, although insight into this question would allow for a better understanding of the Au NPbiomolecule interactions and would inspire new ideas for the development of Au NP-based bioassays. Here, we report the use of DNA bases (guanine, adenine, cytosine, and thymine) as inhibitors for the growth of Au NPs. The inhibition mechanism of G, A, C, and T on the growth of Au NPs was studied by UVvis absorption spectra, resonance light scattering (RLS) spectra, and differential pulse voltammetry (DPV) and confirmed by theoretical calculations. These findings further provide a Au NP-based method for detecting denatured DNA.

’ EXPERIMENTAL SECTION Materials. HAuCl4 3 4H2O and salmon sperm DNA were purchased from sinopharm (Shanghai, China). Guanine (G),

Figure 2. Linear calibration plots of (A0 Ai)/A0 vs Ci for (1) guanine, (2) adenine, (3) cytosine, and (4) thymine.

adenine (A), and thymine (T) were supplied by Hualan Chemistry (Shanghai, China). Cytosine (C) was obtained from Bio Basic (Shanghai, China), and cetyltrimethylammonium chloride (CTAC) was from Zhongzi Chemical Technology (Jinzhong, China). Tannic acid (TA) was from Xilong Chemical Factory (Shantou, China). Other reagents were of analytical grade. Ultrapure water (>18 mω) was obtained from a wp-up-iv-30 purification system (Woter, China) and used in all experiments. 14462

dx.doi.org/10.1021/jp201396j |J. Phys. Chem. C 2011, 115, 14461–14468


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Thermal Denaturation of Thermally Denatured DNA. Thermally denatured DNA was produced by heating salmon sperm DNA solution in a boiling water bath (100 oC) for about 15 min, followed by rapid cooling in an ice bath.29,30 Inhibition of Au NPs Growth. A 10 mL graduated test tube was sequentially added with 0.25 mL of 0.2 M phosphate buffer solution (PBS, pH 7.4), 3 mL of ultrapure water, 0.05 mL of 1% (w/w) HAuCl4, 0.05 mL of 0.2 M CTAC, a certain amount of DNA base or thermally denatured DNA, and 0.5 mL of 1 mM TA. The mixture was diluted to 5 mL with ultrapure water, shaken for 15 s, and kept undisturbed for 30 min at room temperature. Spectral Measurements. UVvis absorption spectra were recorded on a tu-1901 double beam UVvis spectrophotometer (Purkinje General, China). Light-scattering studies were performed on a rf-5301pc (Shimadzu, Japan) spectrofluorophotometer at a 90° scattering angle. The RLS spectra were obtained

Table 1. UVvis Spectra Approach for the Detection of DNA Bases LOD KAbs (μM) (106)

DNA bases

regrssion equation

linear range (μM)

R

G

Ai = 1.6070.030 Ci

232

0.9993

0.52

A

Ai = 1.6220.021 Ci

448

0.9980

0.61

0.013

C

Ai = 1.6450.015 Ci

1260

0.9955

1.08

0.009

T

Ai = 1.5520.008 Ci

864

0.9979

1.98

0.005

0.019

by synchronously scanning the excitation and emission monochromators in the wavelength region from 500 to 850 nm (namely, λex = λem). All spectra were collected at room temperature. Electrochemical Measurements. Cyclic voltammetry (CV) and DPV measurements were carried out on a Chi 660b electrochemical workstation (Ch Instruments, China) with a conventional three-electrode system consisting of a glassy carbon electrode (GCE, 3 mm in diameter) as the working electrode, an Ag/AgCl (3 M KCl) electrode as the reference electrode, and a Pt column electrode as the counter electrode. The GCE, was polished sequentially with 0.5 and 0.03 μm alumina slurry to a mirror-like finish and cleaned ultrasonically in ethanol, followed by ultrapure water for 1 min each. The gce was further electrochemically cleaned in 0.1 M PBS (pH 7.4) and anodized at a potential of +1.70 V for 300 s, following by continuous scanning between +0.00 and +1.40 V with a scan rate of 100 mV/s until reproducible scans were recorded.31,32 CV experiments were carried out in a 0.1 M PBS solution at pH 7.4, containing a certain concentration of each base with or without a certain amount of 1% (w/w) HAuCl4 at different scan rates. DPV experiments were performed with a pulse amplitude of 50 mV, a pulse width of 50 ms, and a potential increment of 8 mV and carried out in a 0.01 M pbs solution at pH 7.4, containing a certain concentration of each base and varying concentration of HAuCl4. All potentials are reported versus the Ag/AgCl (3 M KCl) reference at room temperature.

Figure 3. RLS spectra of Au NP growth solution in the presence of variable concentrations of (a) guanine, (b) adenine, (c) cytosine, and (d) thymine. Inset: the dependence of RLS intensity at 654 nm on the concentrations of G, A, C, and T. 14463



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Morphology of the Au NPs. The morphology of the generated Au NPs was analyzed by transmission electron microscopy (TEM). The TEM images were obtained on a Jeol 2100 lab6 microscopy operated at an accelerating voltage of 200 kV. Computational Details. All electronic structure calculations were performed with the Gaussian 03 suite of programs. The geometry, energy, and harmonic vibrational frequencies of each stationary point considered here were determined initially using the B3LYP functional and the SDD basis set. Each reported minimum has no imaginary frequencies.

’ RESULTS AND DISCUSSION UVvis Absorption Spectra. Figure 1 shows the UVvis absorption spectra of Au NPs formed in the presence of the Au NP growth solutions consisting of HAuCl4 (243 μM), CTAC (2 mM), and tannic acid (0.1 mM) in phosphate buffer solution (0.01 M, pH 7.4) and variable concentrations of the DNA bases (G, A, C, or T). The generation of Au NPs proceeds without adding the Au NP seeds and involves the reduction of Au(III) to Au(0) by TA. In the absence of DNA bases, the resulting Au NPs exhibit characteristic absorbance maxima at 565 nm. The DNA bases (G, A, C, or T) are supposed to inhibit the growth of Au NPs. After adding the DNA bases, the plasmon absorbance bands turn broader, and the absorbance peaks become weaker and red-shifted, indicating inhibition of Au NP growth by these DNA bases. The intensity of the absorbance at 565 nm is found to decrease with the DNA base concentration. A pseudolinear dependence on the concentrations of inhibitors was found in proper concentration ranges (Figure 2), which allows quantitative optical detection of the inhibitors. Figure 2 and Table 1 show the results of linear regression analysis by using the equation

A0 Ai ¼ KAbs 3 Ci A0 Figure 4. Linear calibration plots of (Io Ii)/Io vs Ci for (1) guanine, (2) adenine, (3) cytosine, and (4) thymine.

Table 2. RLS Approach for the Detection of DNA Base DNA bases

regression equation

linear range (106 M)

R

LOD (106 M)

KRLS (106)

G

Ii = 394.616.3 Ci

216

0.99

0.25

0.042

A

Ii = 394.58.07 Ci

434

0.99

0.50

0.021

C

Ii = 394.04.84 Ci

1264

0.99

0.83

0.012

T

Ii = 410.53.05 Ci

1680

0.99

1.32

0.007

ð1Þ

where A0 and Ai denote the absorption intensities in the absence and presence of inhibitors, respectively; KAbs is the slope of the calibration curve; and Ci is the concentrations of inhibitors. The KAbs value provides a qualitative way of comparing different inhibitors for their efficiency in blocking the growth of Au NPs by G, A, C, and T and their different detection sensitivity. Figure 2 and Table 1 show that the KAbs value (i.e., sensitivity) follows the sequence G > A > C > T. RLS Spectra. Resonance light scattering (RLS) is based on the strong scattering enhancement when the frequency of the incident light is close to the intrinsic absorption band of the

Figure 5. TEM images and corresponding particle size distribution histograms of Au NPs obtained in presence of guanine (μM): (a) 0 and (b) 10. 14464



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Figure 6. Changes of oxidation peak current of DNA bases: (a) 30 μM guanine, (b) 30 μM adenine, (c) 200 μM cytosine, and (d) 200 μM thymine, in the presence of variable HAuCl4 concentrations at pH 7.4 (0.01 M PBS).

Figure 7. Dependence of log[(ΔIMAX ΔI)/ΔI] vs log[Au(III)]0: (a) 30 μM guanine, (b) 30 μM adenine, (c) 200 μM cytosine, and (d) 200 μM thymine in the solution including 0.01 M PBS (pH 7.4) and a variable concentration of HAuCl4.

nanoparticles.3335 Recently, RLS has been applied to the research of biological macromolecules, ion association complexes, trace amounts of metals, and nonmetals as a novel analytical technique.3638 The RLS spectra of Au NPs grown in variable concentrations of guanine, adenine, thymine, or cytosine are shown in Figure 3ad, respectively. The RLS spectra were first calibrated by measuring Rayleigh scattering of a 0.01 M PBS solution.39 The Au NPs display maxima RLS intensities at 654 nm and decrease with the presence of DNA bases. The RLS intensities at 654 nm are observed to linearly decrease with DNA base concentrations

up to 16 μM guanine, 34 μM adenine, 64 μM cytosine, and 80 μM thymine, respectively. Figure 4 and Table 2 show that the slope of the RLS calibration curve, KRLS, follows the sequence G > A > C > T. Morphology of the Generated Au NPs. Figure 5 presents the TEM images of the Au NPs grown in the absence and presence of guanine. Without guanine, the reduction of Au(III) to Au(0) by TA yields well-dispersed spherical Au NPs with an average diameter of 35 nm (Figure 5a). However, the Au NPs grown in the presence of guanine (105 M) have a larger average diameter of 73 nm (Figure 5b). The results of TEM analysis are 14465



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consistent with the observed red shift of the plasmon absorbance of Au NPs. DPV Investigations for the Interactions Between Au(III) and DNA Bases. The spectral evidence demonstrated that DNA bases have different inhibition efficiency on the growth of Au NPs. The trend of the inhibition efficiency follows the order G > A>C > T, as suggested by KAbs and KRLS. To elucidate the origin of the different inhibition efficiency, one key factor is thought to be the stability constant of Au(III)DNA complexes or the interactions between Au(III) and DNA bases. It is inconvenient to determine the stability constants by spectral methods because the Au(III)DNA base complexes have no characteristic peak in UVvisible range. In this work, we employed an electrochemical method to determinate the stability constants. In the cyclic voltammetry experiments, neither the reduction peaks of DNA bases nor redox peaks of Au(III)DNA base complexes are observed. The oxidation peak currents of DNA bases are proportional to the potential scan rate in the range from 100 to 400 mV/s (as shown in Figue S1, Supporting Information), indicative of a typical surface-controlled irreversible process. The relationship of Epa with log υ was further constructed for the calculation of the electrochemical parameters based on the Laviron equation40,41 0

Epa ¼ E0 þ

2:3RT ð1 RÞnFυ log ð1 RÞnF RTKs

ð2Þ

where R is the charge transfer coefficient; Ks is the surface electrochemical rate constants; n is the number of electrons 00 is the standard surface potential. The value of transferred; and E 0 E0 in eq 2 can be determined from the interception of the Epa versus υ plot on the ordinate by extrapolating the line to υ = 0,

and the n value can be calculated by the following equation40 nFQ υ ð3Þ 4RT The value of R, n, and Ks were calculated according to eq 2 and shown in Table S1 (Supporting Information). The results show that there are no significant differences in these parameters between DNA base solutions and Au(III)DNA complex solutions, indicating that Au(III) is coordinated to DNA bases to form electro-inactive complexes. To further understand the interaction between DNA bases and Au(III) ions, we determined the conditional stability constants and binding numbers of the baseAu(III) complexes by differential pulse voltammetry (DPV).4244 Figure 6 shows the oxidation peak currents of DNA bases in the absence and presence of HAuCl4. As the concentration of HAuCl4 increased, the oxidation peak currents of four DNA bases gradually decreased with slight changes in potential. The results further confirm that the baseAu(III) complexes are electrochemically inactive in the applied potential range. Assuming that DNA base and HAuCl4 only produce a single complex, BaseAu(III)m, the reaction scheme between DNA base and Au(III) ions is as follows ip ¼

base þ mAuðIIIÞ T baseAuðIIIÞm

ð4Þ

The chemical equilibrium between Au(III) and DNA base can be expressed in terms of the conditional stability constant K ¼

½baseAuðIIIÞm ½base½AuðIIIÞm

ð5Þ

where K is the conditional stability constant, [BaseAu(III)m] is the concentration of the complex; [Au(III)]m is the free Au(III) ion concentration; and [Base] is the total concentration of free ligand (charges omitted). Because increasing the DNA base concentration gave a linear increase in the oxidize currents (Figure S2, Supporting Information), we can write ΔIMAX ¼ k½base0

ð6Þ

ΔI ¼ k½base ¼ kð½base0 ½baseAuðIIIÞm Þ

ð7Þ

hence ΔIMAX ΔI ¼ k½baseAuðIIIÞm

ð8Þ

where ΔIMAX and ΔI are the peak currents of DNA bases in the absence and presence of HAuCl4. The following equation can be derived from eqs 5, 7, and 8 Figure 8. Dependence of KAbs and KRLS vs log K of DNA bases. Δ, 0, 3, and O are the KAbs values of guanine, adenine, cytosine, and thymine; 2, 9, 1, and b are the KRLS values of guanine, adenine, cytosine, and thymine, respectively.

log½ðΔIMAX ΔIÞ=ΔI ¼ log K þ m 3 log½AuðIIIÞ ð9Þ Because the concentration of HAuCl4 in the system is excessive, it is reasonable to replace [Au(III)] by [Au(III)]0.

Figure 9. Structure models of Au(III)base complexes: (a) Au(III)G, (b) Au(III)A, (c) Au(III)C, and (d) Au(III)T. 14466



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The plots of log[(ΔIMAX -ΔI)/ ΔI ] versus log[Au(III)]0 give straight lines with intercept of logK and slope of m (Figure 7). The values of m, obtained from the slope of the plots in Figure 7, range from 1.56 to 1.20, illustrating the formation of a 1:1 complex between Au(III) and DNA bases.45,46 The values of conditional stability constant, K, of Au(III)G, Au(III)A, Au(III)C, and Au(III)T are 5.66 105, 3.55 104, 1.15 104, and 4.61 103, respectively. Different slopes of the calibration curves obtained from the UVvis and RLS spectra are termed as KAbs and KRLS, respectively, which indicate different sensitivities for the detection of DNA bases. To obtain a further insight into the efficiency of DNA bases in blocking the growth of Au NPs, the KAbs and KRLS are compared with each other. The profound reasons for these differences in KAbs and KRLS could be related to the different affinities of DNA bases to Au(III). Figure 8 shows the plots of KAbs and KRLS against log(K). Both KAbs and KRLS demonstrate a strongly linear correlation with log(K) of Au(III)-DNA bases complexes. A close inspection of Figure 5 reveals that the values of KAbs and KRLS varies with K of the complexes in the same Table 3. Binding Energy and AuN Bond Length of [AuCl4] for the Different DNA Base Calculated by DFT complex

AuCl3G

AuCl3A

AuCl3C

AuCl3T

ΔE (kcal/mol)

51.23

49.96

46.14

20.55

2.07

2.08

2.09

2.10

AuN (Å)

Figure 10. Absorbance at 565 nm of the DNA with variable thermally denatured time: (a) 0, (b) 4, (c) 8, and (d) 12 min.

order: Au(III)-G > Au(III)-A > Au(III)-C > Au(III)-T. The origins of these base-dependent differences are likely due to that the larger the value of K, the tighter the binding of the bases to Au(III), the higher inhibition efficiency of the bases in the growth of Au NPs. A number of studies suggest that the most probable binding sites for Au(III) are N(7) of purines and N(3) of pyrimidines.4751 We performed the electronic structure calculations using the structure models listed in Figure 9. A previous report suggested that gold prefers to bind to the deprotonated N(3) of thymine,52 as listed in Figure 9d. The binding energy of [AuCl4] with different DNA bases is calculated by the following equation53 Eint ¼ EMA ðEM þ EA Þ

ð10Þ

where EMA, EM, and EA are sums of electronic and zero-point energies. From the calculation, the binding energy is G > A > C > T, and the bond length of the AuN bond in the AuCl3N (N = G, A, C, T) is T > C > A > G, which are consistent with each other. The binding energy and bond lengths of these complexes are listed in Table 3. Determination of Thermally Denatured DNA. The abovementioned results revealed that the binding energy between DNA bases and Au(III) leads to the inhibition effect on the growth of Au NPs, and the different inhibition effects can be observed through optical measurement. Furthermore, we compared the inhibition effect of native and denatured DNA on the growth of Au NPs. The thermally denatured DNA (tdDNA) exhibited an inhibition effect similar to the above results as shown in Figure 10; however, the native DNA (fs DNA) did not have any significant inhibition effect on the growth of Au NPs. The significant difference in the inhibition effect of the native and denatured DNA may result from the inaccessibility of the binding sites of base residues, which are hidden in the interior of the double-helical DNA molecule. In the thermally denatured DNA, these binding sites are freely accessible for interaction with Au(III) species because the hydrogen bonding between the bases is disrupted, and double-stranded DNA separates into singlestranded strands. This inhibition effect allows us to determine thermally denatured DNA concentration. As shown in the insets of Figure 11, the absorbance at 565 nm and RLS intensity at 654 nm follow a linear dependence on the thermally denatured DNA concentration up to 133 μM.

Figure 11. (a) UVvis absorption and (b) RLS spectra of Au NP growth solution in variable concentrations of thermally denatured DNA. Inset: the plots of the absorbance at 565 nm and RLS intensity at 654 nm vs thermally denatured DNA concentrations. 14467



’ CONCLUSIONS In this work, we report using DNA bases (G, A, C, and T) as active inhibitors for the growth of Au NPs. The optical properties of the generated Au NPs enable the quantitative analysis of the DNA bases by using UVvis and resonance light scattering (RLS) spectra. The sensitivity of detecting guanine (G), adenine (A), cytosine (C), and thymine (T) by two methods follows the same order: G > A > C > T. The differential pulse voltammetry reveals that the origin of difference in the sensitivity is dependent on the conditional stability constant of Au(III)DNA base complexes. The theoretical calculations confirmed that the trend of the tight binding of bases to Au(III) follows the order G > A > C > T, agreeing with the spectral and electrochemical analysis. The native DNA (fs DNA) has no significant effect on the growth of Au NPs, while the thermally denatured DNA inhibits the growth of Au NPs, which is due to the fact that binding sites in the thermally denatured DNA are freely accessible for interaction with Au(III) species. The results allow us to develop a AuNPbased method to detect denatured DNA, and further potential applications include the monitoring of DNA damage and DNA base-pair mismatch. ’ ASSOCIATED CONTENT

bS

Supporting Information. CV and DPV experiments and electrochemical parameters of DNA bases in the absence and presence of HAuCl4. This material is available free of charge via the Internet at http://pubs.acs.org.

’ AUTHOR INFORMATION Corresponding Author

*E-mail: [email protected] (H.P.); [email protected] (Y.Z).

’ ACKNOWLEDGMENT This work is supported by the National Natural Science Foundation of China (20905016), Guangxi Natural Science Foundation (0991082), and Innovation Project of Guangxi Graduate Education (2010105960703M13). ’ REFERENCES

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