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Gold nanorods 3D-supercrystals as surface enhanced Raman scattering spectroscopy substrates for the rapid detection of scrambled prions Ramón A. Alvarez-Puebla a,1 , Ashish Agarwal b , Pramit Manna c , Bishnu P. Khanal c , Paula Aldeanueva-Potel a , Enrique Carbó-Argibay a , Nicolas Pazos-Pérez a , Leonid Vigderman c , Eugene R. Zubarev c,1 , Nicholas A. Kotov a,b,1 , and Luis M. Liz-Marzán a,1 a Departamento de Química-Física and Unidad Asociada Consejo Superior de Investigaciones CientificasUniversidade de Vigo, 36310 Vigo, Spain; b Departments of Chemical Engineering, Materials Science and Engineering, and Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109; and c Department of Chemistry, Rice University, Houston, TX 77005 Edited by Nicholas J. Turro, Columbia University, New York, NY, and approved March 28, 2011 (received for review November 4, 2010) Highly organized supercrystals of Au nanorods with plasmonic antennae enhancement of electrical field have made possible fast direct detection of prions in complex biological media such as serum and blood. The nearly perfect three-dimensional organiza- tion of nanorods render these systems excellent surface enhanced Raman scattering spectroscopy substrates with uniform electric field enhancement, leading to reproducibly high enhancement fac- tor in the desirable spectral range. S urface enhanced Raman scattering (SERS) spectroscopy is not only one of the most sensitive analytical techniques but also can be used under biological conditions. Additionally, SERS signals are strongly dependent on conformational changes in macromolecules such as proteins (1). Unfortunately, although SERS of proteins has been consistently investigated during the last decade (26), enhancement factors (EFs) obtained for most conventional (nonfluorescent) proteins are still insufficient for their direct detection in complex biological media (7). There are two additional very serious challenges as well. Both quanti- tative detection by SERS and reproducible geometry of the hot spotsnecessary for SERS are difficult to achieve. The way to solve these challenges is to design and fabricate a highly orga- nized photonic structure (8) that provides a high electromagnetic field enhancement in a reproducible geometry (9, 10). Recent de- monstration of near-field focalization by nanoantennas (11, 12) has paved the way for development of ultrasensitive SERS sub- strates that can concentrate the near field within certain confined regions, allowing one to obtain extremely high EFs (1315). Such a nanoantenna effect was predicted and found for nanorod (NR) dimers, where the maximum focalization is present at the NR tips (16, 17). One can hypothesize, therefore, that a highly organized system of NRs (1821) acting as an extended nanoantenna may provide resolution for the SERS challenges of proteins or their segments. In turn, this hypothesis can lead to significant techno- logical development for relevant biomedical problems. One example of those problems is the presymptomatic detection of scrambled prions directly in biological fluids. Prions are hard-to-detect infectious agents that cause a num- ber of fatal neurodegenerative diseases in mammalians such as bovine spongiform encephalopathy (BSE), scrapie of sheep, and CreutzfeldtJakob disease (CJD) of humans (22), and recently traced as well to other neurodegenerative syndromes as Alzheimers (23) and Parkinson (24). Invariably, all of these dis- eases involve the modification of the endogenous and functional prion protein (PrP C ) into a nonfunctional but much more stable form (PrP SC ) giving rise to the so-called amyloid plaques in the brain and other nervous tissues (25). Detection of its presence for contention in cattle or diagnosis in humans or blood transfusion banks (26) is very difficult even by state-of-the-art immunological methods such as fluorescence immunoassay, RIA, or ELISA (27) or protein misfolding cyclic amplification (PMCA), which can be used for presyntomatic prion detection. However, it is complex and requires more than 525 h per sample (7 cycles of 75 h each) (27, 28). Thus the confirmation of BSE, scrapie, or CJD still relies on the postmortem imaging analysis of the degenerated tissues of the suspected individuals, usually resulting in late response, implying risk of pandemic outbreak with additional important economic consequences. The development of unique detection techniques capable of accurately detecting/diagnosing the pre- sence of prions in the blood or serum of infected but not clinically sick animals to avoid the dissemination of the disease is therefore much needed. Results and Discussion Gold NRs (75 × 25 nm; aspect ratio 3) were made using the seed- mediated method (9, 29). Modifications of the synthetic protocol described in Materials and Methods resulted in improvements of the resulting NRs, which are quite significant: (i) a 1,000-fold increase in the amount of NRs synthesized in one batch and (ii) very narrow size distributions (σ 3%). Consequently, NRs were able to spontaneously and reproducibly crystallize into 3D colloidal crystals (supercrystals) arranged as individual islands of fairly uniform dimensions (Fig. 1A) when the aqueous NR disper- sions were slowly dried in humid atmosphere (Fig. 1). Both the diameter (Fig. 1B) and height of individual NR islands were in the range of 1 μm, which corresponds to approximately 15 layers of NRs perpendicular to the substrate. SEM examination re- vealed that the crystalline assemblies do not contain any grain boundaries and the orientational and positional order of indivi- dual NRs is the same throughout the entire structure and from island to island. The separation between the adjacent NRs is approximately 3 nm, which corresponds to a bilayer of the catio- nic surfactant cetyltrimethyl-ammonium bromide (CTAB), and has been described as the optimal separation between particles for the generation of hot spots (3032). The optical response of the supercrystals (Fig. 2D) was char- acterized using an inverted dark-field microscope. The localized surface plasmon resonance was found to be very homogeneous throughout the entire surface and exhibits a maximum at 696 nm. Electric near-field enhancement simulations of different NR supercrystals support the hypothesis of the nanoantenna effect. Comparison of the simulations for a three-layer rod-stacked Author contributions: R.A.A.-P., E.R.Z., N.A.K., and L.M.L.-M. designed research; R.A.A.-P., A.A., P.M., B.P.K., P.A.-P., E.C.-A., N.P.-P., and L.V. performed research; R.A.A.-P. analyzed data; and R.A.A.-P., E.R.Z., N.A.K., and L.M.L.-M. wrote the paper. The authors declare no conflict of interest. This article is a PNAS Direct Submission. 1 To whom correspondence may be addressed. E-mail: [email protected], lmarzan@ uvigo.es, [email protected], or [email protected]. This article contains supporting information online at www.pnas.org/lookup/suppl/ doi:10.1073/pnas.1016530108/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1016530108 PNAS May 17, 2011 vol. 108 no. 20 81578161 CHEMISTRY

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Gold nanorods 3D-supercrystals as surface enhancedRaman scattering spectroscopy substrates for therapid detection of scrambled prionsRamón A. Alvarez-Pueblaa,1, Ashish Agarwalb, Pramit Mannac, Bishnu P. Khanalc, Paula Aldeanueva-Potela,Enrique Carbó-Argibaya, Nicolas Pazos-Péreza, Leonid Vigdermanc, Eugene R. Zubarevc,1,Nicholas A. Kotova,b,1, and Luis M. Liz-Marzána,1

aDepartamento de Química-Física and Unidad Asociada Consejo Superior de Investigaciones Cientificas–Universidade de Vigo, 36310 Vigo, Spain;bDepartments of Chemical Engineering, Materials Science and Engineering, and Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109;and cDepartment of Chemistry, Rice University, Houston, TX 77005

Edited by Nicholas J. Turro, Columbia University, New York, NY, and approved March 28, 2011 (received for review November 4, 2010)

Highly organized supercrystals of Au nanorods with plasmonicantennae enhancement of electrical field have made possible fastdirect detection of prions in complex biological media such asserum and blood. The nearly perfect three-dimensional organiza-tion of nanorods render these systems excellent surface enhancedRaman scattering spectroscopy substrates with uniform electricfield enhancement, leading to reproducibly high enhancement fac-tor in the desirable spectral range.

Surface enhanced Raman scattering (SERS) spectroscopy isnot only one of the most sensitive analytical techniques but

also can be used under biological conditions. Additionally, SERSsignals are strongly dependent on conformational changes inmacromolecules such as proteins (1). Unfortunately, althoughSERS of proteins has been consistently investigated during thelast decade (2–6), enhancement factors (EFs) obtained for mostconventional (nonfluorescent) proteins are still insufficient fortheir direct detection in complex biological media (7). Thereare two additional very serious challenges as well. Both quanti-tative detection by SERS and reproducible geometry of the “hotspots” necessary for SERS are difficult to achieve. The way tosolve these challenges is to design and fabricate a highly orga-nized photonic structure (8) that provides a high electromagneticfield enhancement in a reproducible geometry (9, 10). Recent de-monstration of near-field focalization by nanoantennas (11, 12)has paved the way for development of ultrasensitive SERS sub-strates that can concentrate the near field within certain confinedregions, allowing one to obtain extremely high EFs (13–15). Sucha nanoantenna effect was predicted and found for nanorod (NR)dimers, where the maximum focalization is present at the NR tips(16, 17). One can hypothesize, therefore, that a highly organizedsystem of NRs (18–21) acting as an extended nanoantenna mayprovide resolution for the SERS challenges of proteins or theirsegments. In turn, this hypothesis can lead to significant techno-logical development for relevant biomedical problems. Oneexample of those problems is the presymptomatic detection ofscrambled prions directly in biological fluids.

Prions are hard-to-detect infectious agents that cause a num-ber of fatal neurodegenerative diseases in mammalians such asbovine spongiform encephalopathy (BSE), scrapie of sheep,and Creutzfeldt–Jakob disease (CJD) of humans (22), andrecently traced as well to other neurodegenerative syndromes asAlzheimer’s (23) and Parkinson (24). Invariably, all of these dis-eases involve the modification of the endogenous and functionalprion protein (PrPC) into a nonfunctional but much more stableform (PrPSC) giving rise to the so-called amyloid plaques in thebrain and other nervous tissues (25). Detection of its presence forcontention in cattle or diagnosis in humans or blood transfusionbanks (26) is very difficult even by state-of-the-art immunologicalmethods such as fluorescence immunoassay, RIA, or ELISA (27)or protein misfolding cyclic amplification (PMCA), which can be

used for presyntomatic prion detection. However, it is complexand requires more than 525 h per sample (7 cycles of 75 h each)(27, 28). Thus the confirmation of BSE, scrapie, or CJD still relieson the postmortem imaging analysis of the degenerated tissuesof the suspected individuals, usually resulting in late response,implying risk of pandemic outbreak with additional importanteconomic consequences. The development of unique detectiontechniques capable of accurately detecting/diagnosing the pre-sence of prions in the blood or serum of infected but not clinicallysick animals to avoid the dissemination of the disease is thereforemuch needed.

Results and DiscussionGold NRs (75 × 25 nm; aspect ratio 3) were made using the seed-mediated method (9, 29). Modifications of the synthetic protocoldescribed in Materials and Methods resulted in improvements ofthe resulting NRs, which are quite significant: (i) a 1,000-foldincrease in the amount of NRs synthesized in one batch and(ii) very narrow size distributions (σ ∼ 3%). Consequently, NRswere able to spontaneously and reproducibly crystallize into 3Dcolloidal crystals (supercrystals) arranged as individual islands offairly uniform dimensions (Fig. 1A) when the aqueous NR disper-sions were slowly dried in humid atmosphere (Fig. 1). Both thediameter (Fig. 1B) and height of individual NR islands were inthe range of 1 μm, which corresponds to approximately 15 layersof NRs perpendicular to the substrate. SEM examination re-vealed that the crystalline assemblies do not contain any grainboundaries and the orientational and positional order of indivi-dual NRs is the same throughout the entire structure and fromisland to island. The separation between the adjacent NRs isapproximately 3 nm, which corresponds to a bilayer of the catio-nic surfactant cetyltrimethyl-ammonium bromide (CTAB), andhas been described as the optimal separation between particlesfor the generation of hot spots (30–32).

The optical response of the supercrystals (Fig. 2D) was char-acterized using an inverted dark-field microscope. The localizedsurface plasmon resonance was found to be very homogeneousthroughout the entire surface and exhibits a maximum at 696 nm.Electric near-field enhancement simulations of different NRsupercrystals support the hypothesis of the nanoantenna effect.Comparison of the simulations for a three-layer rod-stacked

Author contributions: R.A.A.-P., E.R.Z., N.A.K., and L.M.L.-M. designed research;R.A.A.-P., A.A., P.M., B.P.K., P.A.-P., E.C.-A., N.P.-P., and L.V. performed research; R.A.A.-P.analyzed data; and R.A.A.-P., E.R.Z., N.A.K., and L.M.L.-M. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.1To whom correspondence may be addressed. E-mail: [email protected], [email protected], [email protected], or [email protected].

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1016530108/-/DCSupplemental.

www.pnas.org/cgi/doi/10.1073/pnas.1016530108 PNAS ∣ May 17, 2011 ∣ vol. 108 ∣ no. 20 ∣ 8157–8161

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supercrystal (Fig. 2E) and a single rod monolayer (Fig. 2F) indi-cate increased plasmon concentration on the top surface as layersof rods are added. Note that the field intensity between the rodsin the middle of the stack is also very high (see SupportingInformation). The island morphology of the NR film with tall col-umns of supercrystals (Fig. 1 A and B) helps taking advantage ofthe interstitial hot spots accessible for analytes from the solution

as well. Characterization of the SERS enhancing efficiency of NRsupercrystals was carried out in the same area, using benzenethiol(BT). A highly homogeneous intensity was registered for threedifferent laser lines with an extremely high intensity for all ofthem, which is again consistent with the electric field calculationsas shown in the Supporting Information. Extensive comparativetesting revealed that NR supercrystals as SERS substrates werelargely superior to previously used arrangements of nanoparticlesand NRs, including single particle and fractally aggregated or par-allel NRs (33) (Fig. 2K and Supporting Information). Islands ofNR supercrystals offer additional advantages for bioanalysis suchas chemical stability, reproducibility, and highly homogeneousdistribution of field intensity making possible quantitative SERSdetection of complex biomolecules. Mechanical robustness of theNR supercrystal islands, which allows multiple use of the sub-strates upon plasma etching of the previous analyte, is also a plus.It can be exemplified by SERS analysis of BT and a secondmolecular probe (1-naphthalenethiol, 1NAT) on the same NRsupercrystal upon plasma etching of BT (Fig. 3). Notably, aftercleaning, no signal of BT was registered (see SupportingInformation) even when mapping a large area (30 × 30 μm) whilethe morphology of the supercrystal remained unaltered and theSERS intensity was still extremely high.

The unique potential of these SERS substrates was thusexploited for the ultrasensitive detection of scrambled prionswithin complex biological media such as serum. Due to the highrequirement of a biosecurity lab level 3 for manipulation of realprions, we selected a model peptide (106–126, Fig. 4A), widelyused to investigate prion diseases (34) as it forms fibrils in vitroand causes apoptotic cell death in neuron culture. First, we inves-tigated the SERS spectra of the biologically active and thescrambled prion in PBS. Then we studied the lower proportionof PrPSC in PrPC that can be unambiguously determined. Because

Fig. 1. Nanorod supercrystals morphology. (A–C) SEM images correspondingto different magnifications of a typical nanorod supercrystal island film.(D) View from the edge of the supercrystal.

Fig. 2. Optical properties of the nanorod supercrystals. (A–C) Optical, SEM, and dark-field images of an NR supercrystal, respectively, after plasma-etchingremoval of surfactant coating of the NRs. (D) Localized surface plasmon resonance bands of the rods in solution (gray) and within a supercrystal, either at thecenter or at the edges (red and black boxes of Fig. 2C, respectively) . Dotted arrows indicate the excitation laser lines used for SERS. (E and F) Electric fieldenhancement maps calculated for the top part of a three layer rod-stacked supercrystal (E) and for the same location in a single monolayer (F). (G–J) SERSintensity maps at 1;072 cm−1 (BT ring breathing) corresponding to the supercrystal in A, for BT as excited with a 633 (G), 785 (H), and 830 nm (I) laser lines,representative SERS spectra for each laser being presented in J. (K) Comparison of the SERS intensities at 1;072 cm−1 provided by a gold rod supercrystal(Au-RSC) film with common SERS substrates, including aggregated ultralong nanowires (Au-NW), single rods, parallel and fractally aggregated gold NRs (SingleAu-NR, Parallel Au-NR, and Fractal Au-NR, respectively). The intensity is the result of averaging over 50 different randomly distributed spots in the supercrystaland those corresponding to maximum intensity for the rest of substrates. More information about the different substrates can be found in the SupportingInformation.

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the primary chemical structure of both prions is very similar,so are their respective vibrational patterns (see SupportingInformation). SERS is dominated by a band at 762 cm−1 assignedto the interaction of Au-S-C, and a triplet in PrPC (1,390; 1,416;and 1;446 cm−1) which becomes a singlet (1;448 cm−1) in thescrambled version. These bands are related to the side-chainbands together with the amide II′ and III modes, especially inthe -Met-Lys-His-Met- fragment, responsible for the binding ofthe peptide to the gold surface. It is important to bear in mindthat, when prions are mixed, spectral patterns from the misfoldedprions are fully identifiable even when their relative concentra-tion is as low as 1% that of the normal prion. This fact is probablydue to induction of the misfolding of the α-helix structure of theendogenous PrPC into the β-sheet of the scrambled version. Infact, it is this behavior that has been previously exploited forthe detection of prions by PMCA (35). On the other hand, bysystematically diluting the mixture containing 1% PrPSC and99% PrPC, we were able to detect scrambled prion signal for atotal prion concentration of as low as 10−10 M, which is equiva-lent to 10 molecules per area sampled (i.e., zeptomol regime)(see Supporting Information). Such high sensitivity may make pos-sible direct and fast detection of prions in real complex biologicalfluids, such as blood or serum, which was never possible before(36). To demonstrate this statement, detection of a mixture con-taining 1% of scrambled prions in the functional protein wascarried out within a complex matrix, such as bovine serum. SERSspectrum of PrPSC∶PrPC in serum (Fig. 4E) is dominated bybands corresponding to the C-N stretching (1;118 cm−1), Phe(1,003 and 1;033 cm−1), Trp (1,011 and 1;560 cm−1), Tyr(845 cm−1), and Cys (720 cm−1). Upon sequential dilution of theprion mixture (1% of PrPSC in 99% of PrPC) in serum, thecharacteristic prion bands can still be clearly recognized downto concentrations as low as 10−10 M. For all the analyzed samples,no evidence of biologically functional prion was found, implyingits conversion into the scrambled version, which is consistent withthe results obtained in PBS. The fact that the prion proteins canbe clearly identified in serum, e.g., a complex solution containinghigh concentrations of electrolytes and proteins, such as albuminsglobins, hormones, antibodies, and many other exogenous sub-stances (drugs and microorganisms), is likely to indicate the highaffinity of prions for gold, which is in agreement with the capacity

of -Met-Lys-His-Met- groups present in prions to efficientlychelate Au atoms (37). When greater surface area is available,bigger components can interact as well.

Further, to test the viability of this technique to discern con-taminated blood samples in, for example, transfusion blood banks(26), and demonstrate validity of a SERS-based protocol for suchanalysis, an experiment was designed to detect low concentrationof prions in human blood. Samples of blood spiked with prionswere centrifuged to obtain plasma (serum plus coagulation fac-tors). Fig. 5 shows SERS spectra of blood and plasma before andafter addition of prions. Direct analysis of blood (Fig. 5 A and B)does not offer any insights about the presence of infection.Notwithstanding, after centrifugation of the sample to obtainplasma, scrambled prions are clearly identified at the attomolregime (Fig. 5 C and D). The identification becomes even more

Fig. 3. Reusability of supercrystals after plasma cleaning. SEM images andSERS spectra andmapping of a supercrystal before and after cleaning the firstanalyte (1;072 cm−1, BT) and adding a different one (1;351 cm−1, 1NAT).

Fig. 4. Scheme showing the prion mutation and detection limits for thescrambled version in bovine serum. (A) Biologically active (PrPC α-helix)and (B) scrambled (PrPSC β-sheet) prions; the fragment corresponding to106–126 peptide is highlighted in green. SERS spectra of (C) PrPC α -helixand (D) PrPSC(scrambled). (E–I) Detection limits of PrPSC∶PrPC (1∶99) in bovineserum at 10−6, 10−7, 10−8, 10−9, and 10−10 M in total prion, respectively; and(J) bovine serum.

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Fig. 5. Prion ultradetection in human blood. SERS spectra of (A) natural and(B) spiked human blood; (C) natural and (D) spiked human plasma. (E) SERSspectra spiked human plasma after spectral subtraction of the matrix (humanplasma). (F) SERS spectra of the scrambled prion (equivalent to that ofFig. 4B).

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obvious after spectral subtraction (Fig. 5E) of the plasma vibra-tional signature (Fig. 5 C and D).

In summary, highly organized supercrystals of Au NRs withplasmonic antennae enhancement of electrical field have madepossible direct detection of prions in complex biological mediasuch as serum or blood. Three-dimensional organization ofNRs into supercrystals render these systems excellent SERS sub-strates with uniform electric field enhancement, high intensity ofthe hot spots, and reproducible EFs in the desirable spectralrange. From the practical perspective, these substrates show greatpromise for the fast online presymptomatic detection of prions inbiological fluids such as blood or urine. This approach also avoidsincreased risk of infection or additional digestion stages, whichfurther increase the time for detection and uncertainty of thefinal results.

Materials and MethodsMaterials. Tetrachloroauric acid, silver nitrate, sodium borohydride, ascorbicacid, trisodium citrate, hydrochloric acid, CTAB, oleylamine (OA, technicalgrade, 70%), chloroform (99%), ethanol (EtOH), BT, serum albumin, PBSsolution, prion protein fragment 106–126 (PrPc), prion protein fragment106–126 scrambled (PrPSC), BSA, bovine serum, and human blood were pur-chased from Sigma-Aldrich. Naphthalene-1-thiol (1NAT) was obtained fromAcros Organics. All chemicals were used as received. All glassware waswashed with aqua regia prior to the experiments. Milli-Q deionized water(resistivity > 18 MΩ cm−1) was used for all preparations.

Synthesis of Monodisperse NRs and Supercrystals. Au NRs were prepared by amodification of the usual seeded-growth method (38). Specifically, thegrowth solution was prepared by a twofold increase in the concentrationof Au (III) ions, AgNO3, and ascorbic acid, whereas the amount of seedparticles solution was increased from 12 μL to 9.6 mL as compared withthe conventional method (see below). The presence of a slight excess ofascorbic acid (0.1 mol equiv with respect to gold) promotes the growth ofNRs as soon as the seed solution is added. The NRs reach the size of45 nm in length and 10 nm in width within 2 h, at which point the growthstops, although there is still nearly 80% of the initial gold chloride presentin solution. All these ions can be reduced and deposited onto the surface ofthe NRs if an additional amount of ascorbic acid (1.1 mol equiv) is introducedat a very slow rate. This process leads to an amplification of the NRs dimen-sions, which reach 75 nm in length and 25 nm in diameter. Most importantly,the size distribution of NRs becomes much narrower (σ ∼ 3%) as shown inthe Supporting Information. Because of their narrow size distribution, theNRs have sharp peaks in the UV-visible absorption spectrum and (seeSupporting Information) can crystallize into 3D colloidal crystals when a dropof their aqueous suspension is cast on a substrate and allowed to dry veryslowly (24 h) in a saturated moist atmosphere.

Preparation of Flexible Gold Ultralong Nanowire Films for Comparison of SERSEffects. In a typical synthesis, HAuCl4 (2.60 mg) was dissolved in OA (5 mL) byvortexing the mixture at room temperature until the solution turned frompale yellow, the characteristic color of OA, to an intense orange color, whichindicates complex formation between Au3þ and OA. Thereafter, the solutionwas left undisturbed for 24 h, during which time the solution color changedagain gradually from orange to pale yellow, indicating the reduction of Au3þ

to Auþ. Next, the gold solution was aged for 5 d in a thermostatic bath at35 °C. Then, to 1 mL of this solution, 3 mL of CHCl3 and 3 mL ethanol wereadded. The solution was centrifuged at 5,000 rpm for 20 min. The superna-tant was discarded and the precipitate redispersed in 3 mL CHCl3. A secondcentrifugation step (4,000 rpm, 60 min) was carried out after the addition ofethanol (3 mL), the supernatant was discarded, and the precipitate redis-persed in 3 mL CHCl3 (see Supporting Information). Films were preparedby drop-casting and air-drying 10 μL of the suspension on an indium tin oxide(ITO) slide.

Preparation of Gold Nanorod Films. A solution of gold seeds was prepared byborohydride reduction of HAuCl4 (0.25 mM, 5 mL) in aqueous CTAB solution(0.1 M). An aliquot of seed solution (24 μL) was added to a growth solution(10 mL) containing CTAB (0.1 M), HAuCl4 (0.5 mM), ascorbic acid (0.8 mM),silver nitrate (0.12 mM), and HCl (19 mM). For the deposition of the goldnanorods on silicon wafers, 2 mL of the as-prepared suspension was centri-fuged twice for 15 min, first at 6,500 rpm and then at 4,000 rpm. Afterdiscarding the supernatant, the precipitate was redispersed finally in 1 or0.25 mL of water, either to obtain nonaggregated particles (see

Supporting Information) or aggregated films made of rods with predomi-nantly parallel orientation, respectively, by spin-coating 10 μL of the suspen-sion on ITO slides. To prepare the fractal film of nanorods, the as-preparedsuspension was centrifuged five times (6,000 rpm, 15 min) and, after discard-ing the supernatant, 10 μL of the precipitate, redispersed in 0.25 mL of water,was drop-cast on a ITO slide.

Characterization. Transmission electron microscopy images were obtainedusing a transmission electron microscope (JEOL JEM-1010) operating at anacceleration voltage of 100 kV. Solid thin films were characterized usinga field emission SEM (JEOL JSM-6700f). Gold nanorod supercrystals wereimaged and their scattering spectra acquired using a 100-W halogen lampillumination source on a Nikon Eclipse TE-2000 inverted optical microscopecoupled to a Nikon Dark-Field Condenser (dry, 0.95–0.80 N.A.). The scatteredlight from selected supercrystal areas was collected with a Nikon Plan Fluor-ELWD 40× (0.60 N.A.) objective and focused onto the entrance slit of a Mi-croSpec 2150i imaging spectrometer coupled with a thermoelectric-cooledCCD camera (PIXIS 1024B ACTON Princeton Instruments). The light scatteredby the supercrystals was recorded in the dark-field microscope with collectiontimes of 20 s. SERS experiments were conducted with a micro-RamanRenishaw InVia Reflex system attached to a Leica microscope, a two-dimen-sional CCD camera, and an automated stage with 100-nm spatial resolution.The spectrograph used high-resolution gratings (1,200 or 1;800 gmm−1) withadditional bandpass-filter optics. Several laser excitation energies wereemployed, including laser lines at 633 (HeNe), 785 (diode), and 830 nm(diode). All measurements were made in confocal mode in backscatteringgeometry using a 100× (0.90 N.A.) objective, which provides a resolutionof 500 nm. SERS maps were collected by using the Renishaw StreamLineaccessory with a step size of 500 nm.

Plasma Cleaning of the Nanostructured Surfaces. Samples on ITO were cleanedwith plasma previously to SEM characterization and SERS analysis. In the caseof the supercrystals, samples were cleaned as well after the analyte exposureto check the efficiency in removing the organics and the possibility of reusingthe sample. Plasma was generated in a Solarus™ (Model 950) AdvancedPlasma Cleaning System under the following conditions: 27.5 sccm (standardcubic centimeters per minute) O2, 6.4 sccm H2, 70 mTorr and expositionof 2 min.

SERS Characterization. In order to characterize the gold crystal rods films, BTwas adsorbed in gas phase over the whole surface of the films by casting adrop of BT (0.1M in ethanol) in a Petri box where the film was also contained.Surfaces were then mapped using the Renishaw StreamLine accessory, takingmapping areas of 25 × 35 μm2, with a step size of 0.5 nm (1,440 spectraeach) upon excitation with three different laser lines: 633, 785, and 830 nm.Acquisition times were set to 200 ms with power at the sample of 1 mW. Forcomparison, the same experiments (following the same protocol) werecarried out on the rest of the films (i.e., noninteracting AuNRs, AuNRsaggregated parallel to each other, and fractally aggregated AuNRs).

Reusability of the Supercrystal films. Material recyclability was tested byexposing the substrate to BT in gas phase, registering (see above), cleaningthe sample with the H2-O2 plasma (see above), and casting a dilute solutionof 1NAT (10 μL, 10−4 M). After each exposure, the sample was mapped withthe Renishaw StreamLine accessory (55 × 67 μm2, 500-nm step size with atotal spectra collection of 14,310 points) with the 785-nm laser line in thesame conditions as described above. Mapping was carried out in two differ-ent spectral windows from 905 to 1;190 cm−1 characteristic of BT and from1,670 to 1;580 cm−1, characteristic of 1NAT. This procedure was repeated inseveral samples several times to ensure reproducibility.

Prion Detection. Stock solutions of PrPc and PrPsc 10−4 Mwere prepared in PBS(12 mM NaCl, 0.27 mM KCl, and 1 mM phosphate buffer salts). From these,PrPsc solution was consistently diluted in PrPc solution (100%, 50%, 25%,10%, 1%, and 0% in PrPsc). Then, 10-mL samples of each solution were casteach onto a different supercrystal film and studied with SERS (λex: 785 nm,10 s, 1 mW of power at the sample). Ten points were collected for each sam-ple to ensure reproducibility. This process was repeated as well on a singlecrystal film, cleaning it with the plasma after each analysis, with similarresults. After setting the detection limit of PrPsc in PrPc to 1%, absolutedetection limits of PrPsc were determined by diluting the stock solutioncontaining 1% of PrPsc in 99% of PrPsc until concentrations of 10−11 M. SERSspectra were acquired in the same conditions as described above. To probethe viability of this method to be implemented in real samples with no need

8160 ∣ www.pnas.org/cgi/doi/10.1073/pnas.1016530108 Alvarez-Puebla et al.

for any complicated separation protocol, the same experiment was repeatedusing bovine serum as solution.

For prion detection in human blood, PrPsc was spiked to reach a final con-centration of 10−10 M. After waiting 2 h to ensure mixing, the sample wascentrifuged (15 min, 4,000 rpm) to obtain blood plasma. Then, 10 μL ofthe sample, either blood or plasma, was cast and air-dried onto a supercrystalsurface and studied by Raman microspectroscopy as previously described.

ACKNOWLEDGMENTS.We thankW. Ni for carrying out the dark-field measure-ments. R.A.A.-P. acknowledges the RyC Program (Ministerio de Ciencia e

Innovación, Spain). N.A.K. acknowledges the Spanish Ministerio de Cienciae Innovación for a research fellowship. This work was funded by the SpanishMinisterio de Ciencia e Innovacion (MAT2010-15374 and MAT2008-05755)and the Xunta de Galicia (PGIDIT09TMT011314PR and 08TMT008314PR).N.A.K. is thankful for research grants from the National Science Foundation(NSF) (R8112-G1, ECS-0601345, 0932823), National Institutes of Health(1R21CA121841 and 5R01EB007350), and Defense Advanced Research Plan-ning Agency (W31P4Q-08-C-0426). Support for E.R.Z. was provided by TheRobert A. Welch Foundation (C-1703), NSF (DMR-0547399), and Alliancefor Nanohealth (W8XWH-07-2-0101).

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