Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticle probes

Dynamic imaging of molecular assemblies in live cells based on nanoparticle plasmon resonance coupling

We used molecular-specific gold nanoparticles to monitor epidermal growth factor receptors (EGFR) in live A431 cells over time. Dark-field hyperspectral imaging, electron microscopy, and electrodynamic modeling were used to correlate optical properties of EGFR-bound plasmonic nanoparticles with receptor regulation state. We showed that receptor trafficking resulted in a progressive red shift of greater than 100 nm in the nanoparticle plasmon resonance wavelength over a time period of 60 min. Furthermore, we demonstrated that changes in peak scattering wavelengths of gold nanoparticles from 546 +/- 15 to 574 +/- 20, and to 597 +/- 44 nm are associated with EGFR trafficking from the cell membrane, to early endosomes, and to late endosomes/multivesicular bodies, respectively. Finally, we used the changes in scattering spectra of EGFR-bound nanoparticles and a straightforward statistical analysis of RGB-channel color images of labeled cells to create near real-time maps of EGFR regulatory states in living cells.

Nucleic acid conjugated nanomaterials for enhanced molecular recognition

Nucleic acids, whether designed or selected in vitro, play important roles in biosensing, medical diagnostics, and therapy. Specifically, the conjugation of functional nucleic acid based probe molecules and nanomaterials has resulted in an unprecedented improvement in the field of molecular recognition. With their unique physical and chemical properties, nanomaterials facilitate the sensing process and amplify the signal of recognition events. Thus, the coupling of nucleic acids with various nanomaterials opens up a promising future for molecular recognition. The literature offers a broad spectrum of recent advances in biosensing by employing different nanoplatforms with designed nucleic acids, especially gold nanoparticles, carbon nanotubes, silica nanoparticles, and quantum dots. The advantages of these novel combinations are discussed from the perspective of molecular recognition in chemistry, biology, and medicine, along with the problems confronting future applications.

Gold nanoparticles for molecular diagnostics

Gold nanoparticles (AuNPs) exhibit a unique phenomenon, known as surface plasmon resonance, which is responsible for their large absorption and scattering cross-sections, which are four to five orders of magnitude larger than those of conventional dyes. In addition, their optical properties can be controlled by varying their sizes, shapes and compositions. AuNPs can be easily synthesized and functionalized with different biomolecules including oligonucleotides. Numerous methods have been utilized for detecting AuNPs such as colorimetric, scanometric, fluorescence, surface-enhanced Raman scattering and electrochemical techniques. These unique aspects have permitted the development of novel AuNP-based assays for molecular diagnostics which promise increased sensitivity and specificity, multiplexing capability, and short turnaround times. AuNP-based colorimetric assays in particular show great potential in point-of-care testing assays. This review discusses properties of AuNPs and their utilization for the development of novel molecular assays.

Direct detection of unamplified DNA from pathogenic mycobacteria using DNA-derivatized gold nanoparticles

Mycobacterial infections have a high economic, human and animal health impact. Herein, we present the development of a colorimetric method that relies on the use of gold nanoparticles for fast and specific detection of Mycobacterium spp. dispensing with the need for DNA amplification. The result can be recorded by visual and/or spectrophotometric comparison of solutions before and after acid induced AuNP-probe aggregation. The presence of a complementary target prevents aggregation and the solution remains pink, whereas in the opposite event it turns to purple. The application of the proposed method on isolated bacteria produced positive results with the mycobacterial isolates and negative with the controls. The minimum detection limit of the assay was defined at 18.75 ng of mycobacterial DNA diluted in a sample-volume of 10 microl. In order to obtain an indication of the method's performance on clinical samples we applied the optimized assay to the detection of Mycobacterium avium subsp. paratuberculosis DNA in faeces, in comparison with real-time PCR. The concordance of the two methods with connection to real-time PCR positive and negative sample was defined respectively as 87.5% and 100%. The proposed method could be used as a highly specific and sensitive screening tool for the detection of mycobacteria directly from clinical samples in a very simple manner, without the need of high-cost dedicated equipment. The technology described here, may develop into a platform that could accommodate detection of many bacterial species and could be easily adapted for high throughput and expedite screening of samples.

Label-free DNA detection on nanostructured Ag surfaces

The dramatic local electric-field enhancement property of Ag nanoparticles was used as the basis to significantly increase the signal output of a novel label-free (or "self-labeled") fluorescence-based DNA detection system. In response to identical amounts of analyte, nanostructured Ag substrates provided a posthybridization fluorescent sensor response over 10-fold larger than the response from planar Au substrates. Detection performance strongly depended upon the Ag substrate roughness. Consistent with work by others on metal-enhanced fluorescence, fluorescence intensity also depended strongly on the distance between the fluorophore and the Ag substrate surface. Adjusting the surface roughness, amount of the Ag deposited on the surface, and the DNA probe length allowed for production of an optimized response. In addition to constituting a novel label-free DNA sensor, we anticipate that these structures will provide a unique platform for testing concepts in plasmonics.

Plasma polymerized non-fouling thin films for DNA immobilization

Development of DNA sensors has been an issue of great interest, owing to their potential applications in different fields, such as the diagnosis of infectious diseases, food quality control, or for environmental monitoring. Most DNA sensors involved the immobilization of single-stranded oligonucleotides, so-called DNA probes, onto the sensor surfaces. Here we report on a new approach for DNA probe immobilization using the streptavidin-biotin assembly coupled with a non-fouling thin film. Pulsed plasma polymerization of di(ethylene glycol) monovinyl ether (ppEO2) will result in non-fouling thin films, which are employed to immobilize streptavidin. By careful control of the thickness and the chemistry of ppEO2 films, the embedded streptavidin are able to bind the biotinylated oligonucleotides. The resulting DNA sensors show good resistance towards adsorption of both BSA and fibrinogen, and are employed to discriminate different DNA sequences from protein-containing sample solutions, as seen by surface plasmon enhanced fluorescence spectroscopy (SPFS). This result suggests that the present sensor is very promising for the detection of a DNA sequence from a complex solution.

A simple, universal colorimetric assay for endonuclease/methyltransferase activity and inhibition based on an enzyme-responsive nanoparticle system

An enzyme responsive nanoparticle system that uses a DNA-gold nanoparticle (AuNP) assembly as the substrate has been developed for the simple, sensitive, and universal monitoring of restriction endonucleases in real time. This new assay takes advantage of the palindromic recognition sequence of the restriction nucleases and the unique optical properties of AuNPs and is simpler than the procedure previously described by by Xu et al. (Angew. Chem. Int. Ed. Engl. 2007, 46, 3468-3470). Because it involves only one type of ssDNA modified AuNPs, this assay can be directed toward most of the endonucleases by simply changing the recognition sequence found within the linker DNA. In addition, the endonuclease activity could be quantitatively analyzed by the value of the reciprocal of hydrolysis half time (t(1/2)(-1)). Furthermore, our new design could also be applied to the assay of methyltransferase activity since the methylation of DNA inhibits its cleavage by the corresponding restriction endonuclease, and thus, this new methodology can be easily adapted to high-throughput screening of methyltransferase inhibitors.

Typing Chlamydia trachomatis: from egg yolk to nanotechnology

A historical review is provided of the various methods used for half a century to differentiate and type Chlamydia trachomatis strains. Typing of C. trachomatis is an important tool for revealing transmission patterns in sexual networks, and enabling association with clinical manifestations and pathogenicity. Serotyping using the major outer membrane protein (MOMP) has been the mainstay of epidemiological work for several decades. However, the development of nucleic acid amplification techniques (NAAT) and easy access to sequencing have shifted the focus from MOMP serotypes to omp1 genotypes. However, insufficient epidemiological resolution is achieved by characterization of both MOMP and omp1. This calls for new high-resolution genotyping methods applying for example a multilocus variable number tandem repeat assay (MLVA) or multilocus sequence typing (MLST). The futuristic nanotechnology already seems at hand to further simplify and automate the high-resolution genotyping method based on NAAT and sequencing of various targets in the C. trachomatis genome. Thereby, a high throughput can be achieved and more epidemiological information can be obtained. However, it is important to realize that culture of C. trachomatis may still be needed to detect and characterize new variants of C. trachomatis.

Single-molecule immunosorbent assay as a tool for human immunodeficiency virus-1 antigen detection

Ultrasensitive detection and quantification of viral antigen with a novel single-molecule immunosorbent assay (SMISA) was achieved. Antigen from human immunodeficiency virus type 1 (HIV-1), the major etiological agent of acquired immune deficiency syndrome, served as the screening target in this study. The target molecule was sandwiched between a polyclonal capture antibody and a monoclonal detector antibody. The capture antibody was covalently immobilized on (3-glycidoxypropyl) trimethoxy silane-modified glass slides. The detector antibody was conjugated with fluorescent Alexa Fluor 532 labeled secondary antibody prior to being used as a probe for the antigen. Imaging was performed with a total internal reflection fluorescence single-molecule detection system. This technique is demonstrated for detecting HIV-1 p24 antigen down to 0.1 pg/mL with a dynamic range of over four orders of magnitude. A Langmuir isotherm fits the molecule count dependence on the target concentration. The target antigen was further tested in 20% human serum, and the results showed that neither sensitivity nor dynamic range was affected by the biological matrix. SMISA is therefore a promising approach for the early diagnosis of viral induced diseases.

Synthesis and characterization of functionalized ionic liquid-stabilized metal (gold and platinum) nanoparticles and metal nanoparticle/carbon nanotube hybrids

Carboxylic acid- and amino-functionalized ionic liquids were used as the stabilizer for the systhesis of metal nanoparticles in aqueous solution. Smaller gold nanoparticles (3.5 nm) and platinum nanoparticles (2.5 nm) were prepared with NaBH4 as the reductant. Larger gold nanospheres (23, 42, and 98 nm) were synthesized using different quantities of trisodiumcitrate reductant. The morphology and the surface state of the metal nanoparticles were characterized by high-resolution transmission electron microscopy, UV-visible spectroscopy, and X-ray photoelectron spectroscopy. X-ray photoelectron spectroscopy spectra indicated that binding energies of C 1s and N 1s from ionic liquids on the surface of metal nanoparticles shifted negatively compared with that from pure ionic liquids. The mechanism of stabilization is proposed to be due to the interactions between imidazolium ions/functional groups in ionic liquids and metal atoms. Resonance Rayleigh scattering property of the functionalized ionic liquid-stabilized metal nanoparticles was also explored. It was found that amino-functionalized ionic liquid-stabilized gold nanoparticles exhibited lower resonance Rayleigh scattering intensity than trisodiumcitrate stabilized gold nanoparticles, which is expected to decrease the background of the resonance Rayleigh scattering intensity in the determination of various analytes. Moreover, it was found that all the as-prepared metal nanoparticles could be easily assembled on the multiwalled carbon nanotubes, which was confirmed by high-resolution transmission electron microscopy and energy dispersive X-ray spectroscopy. In this case, ionic liquids acted as a linker to connect metal nanoparticles with carbon nanotubes. The imidazolium ring moiety of ionic liquids might interact with the pi-electronic nanotube surface by virtue of cation-pi and/or pi-pi interactions, and the functionalized group moiety of ionic liquids might interact with the metal NPs surface. Finally, it was observed that plantinum nanoparticle/multiwalled carbon nanotube hybrids could be well dispersed in water, which may find future applications in fields such as catalysis, nanoscale electronics, as well as sensors.

Curvature-induced base pair "slipping" effects in DNA-nanoparticle hybridization

Experiments are presented that suggest DNA strands chemically immobilized on gold nanoparticle surfaces can engage in two types of hybridization: one that involves complementary strands and normal base pairing interactions and a second one assigned as a "slipping" interaction, which can additionally stabilize the aggregate structures through non-Watson-Crick type base pairing or interactions less complementary than the primary interaction. The curvature of the particles appears to be a major factor that contributes to the formation of these slipping interactions as evidenced by the observation that flat gold triangular nanoprism conjugates of the same sequence do not support them. Finally, these slipping interactions significantly stabilize nanoparticle aggregate structures, leading to large increases in T(m)'s and effective association constants as compared with free DNA and particles that do not have the appropriate sequence to maximize their contribution.

A gold-nanoparticle-enhanced immune sensor based on fiber optic interferometry

A method using gold nanoparticles (GNPs) to enhance fiber optic interferometry (GNPFOI) for immune-sensing is reported in this paper. It is suggested that an enlarged index mismatch and an elongated optical path by GNPs conjugated on recognition proteins will contribute most to signal enhancement in the interference fringe shift. Theoretical and experimental results show that the interference fringe shift is linearly related to both the amount and size of the GNPs binding on the sensor surface. The detected signal for 30 nm GNPs can reach a lowest detection limit of 18 pM (10(10) particles ml(-1)). Immune-sensing for rabbit IgG as the antigen to anti-rabbit IgG has been demonstrated and a detection cycle has been completed by elution buffer for surface regeneration. The repeatability of the immune-sensing on one GNPFOI sensor has also been verified by three identical cycles, and the detection limit for 13 nm GNPs conjugated anti-rabbit IgG reaches 0.17 nM (∼25.5 ng ml(-1)). The sensory mechanism has the potential to be engineered on the tip of a needle-type micro-device, which would allow it to monitor immune recognition signals in the future.

Depolarization of surface-enhanced fluorescence: an approach to fluorescence polarization assays

Localized surface plasmons of metallic particles of subwavelength sizes strongly modify the spectral properties of nearby fluorophores. The enhanced radiative decay rate leads to high fluorescence efficiencies and decreased fluorescence lifetimes. In this report we show that metal-enhanced fluorescence generated by the presence of the silver islands on the glass substrate displays high depolarization. Intensities, lifetimes, and emission anisotropies of several fluorophore protein conjugates have been studied in the absence and presence of metallic nanostructures. Despite highly decreased lifetimes of about 10-fold and immobilization of conjugates on the solid substrate, the observed emission anisotropies for all fluorophores on the metal-enhanced substrate decreased 300-500% compared to that in solution. This observation implies a new generation of fluorescence polarization immunoassays with broad applications because of no restrictions to the lifetime of the probe and the size of labeled biomolecules. The changes in polarization are due to binding that occur on the bioactive surface localized near the metal particles.

A novel method for monitoring monoclonal antibody production during cell culture

We describe a new format for surface-based fluoroimmunoassays that allows detection of biomolecule interactions without separation steps. The bioactive layer was immobilized on the surface of a glass substrate covered with silver islands that provide optical amplification of the distinctive fluorescence signal from bound probes when compared to unbound probes. The technique used was phase-modulation fluorometry that allows sensitive detection of bound probes with a very short lifetime in the presence of excess free probes in solution. The new method was applied to assay monoclonal antibody production during cell culture. Excellent agreement was found between the new method and ELISA analysis of hybridoma cell culture samples. It is predicted that the near real time monitoring of protein products during bioprocessing will be possible with the described technology.

Luminescent lanthanide nanoparticles as labels in DNA microarrays for quantification of methyl tertiary butyl ether degrading bacteria

We report application of lanthanide nanoparticles for DNA quantification in a microarray platform as a substitute for conventional organic fluorophores. A non-PCR based DNA microarray assay for quantifying bacteria capable of biodegrading methyl tertiary-butyl ether (MTBE) was demonstrated. Probe DNA was immobilized on a glass surface, hybridized with biotinylated target DNA and subsequently incubated with Neutravidin-biofunctionalized nanoparticles. The fluorescence spot intensities, measured by a commercial laser scanner, show a linear relationship (R2 = 0.98) with bacterial 16S rDNA over a range of target DNA concentrations, while the background fluorescence remained low. In addition, nanoparticles fluorescence shows a stronger intensity than Quasar570 (Cy3). Present sensitivity of the assay is 10 pM of target DNA. The selectivity of the DNA-nanoparticle-probes to discriminate a non-target DNA with two base pairs mismatch in the 16S rDNA gene sequence was shown. The use of Eu:Gd2O3 nanoparticles as biolabels provides a relatively non-toxic, inexpensive, rapid and sensitive alternative to the materials currently used in DNA microarrays.

Ultrasensitive optical biodiagnostic methods using metallic nanoparticles

Dramatic progress has been made over the recent decade in the applications of metallic nanoparticles in the field of biomolecule detection. The useful physical and chemical properties (e.g., availability of various synthetic methods of size- and shape-controlled nanoparticles, size- and shape-dependent optical properties, availability of various surface chemistries and biocompatibility) of metallic nanoparticles have brought development to the ultrasensitive detection of biomolecules at the attomolar level and this sensitivity enables the diagnosis of otherwise undetectable biomarkers of many fatal diseases, including Alzheimer’s disease. Furthermore, coupled with the strong physical properties and biocompatible nature of gold nanoparticles in in vivo conditions, the scope of applications for these particles have been broadened into the field of in vivo imaging, such as X-ray contrasting agents, and also cellular tracking. Here, we review synthetic methods and optical properties of metallic nanoparticles and their use in ultrasensitive, in vitro and in vivo biodiagnostic methods.

Facile synthesis of gold nanoparticles with narrow size distribution by using AuCl or AuBr as the precursor

Gold(I) halides, including AuCl and AuBr, were employed for the first time as precursors in the synthesis of Au nanoparticles. The synthesis was accomplished by dissolving Au(I) halides in chloroform in the presence of alkylamines, followed by decomposition at 60 degrees C. The relative low stability of the Au(I) halides and there derivatives eliminated the need for a reducing agent, which is usually required for Au(III)-based precursors to generate Au nanoparticles. Controlled growth of Au nanoparticles with a narrow size distribution was achieved when AuCl and oleylamine were used for the synthesis. FTIR and mass spectra revealed that a complex, [AuCl(oleylamine)], was formed through coordination between oleylamine and AuCl. Thermolysis of the complex in chloroform led to the formation of dioleylamine and Au nanoparticles. When oleylamine was replaced with octadecylamine, much larger nanoparticles were obtained due to the lower stability of [AuCl(octadecylamine)] complex relative to [AuCl(oleylamine)]. Au nanoparticles can also be prepared from AuBr through thermolysis of the [AuBr(oleylamine)] complex. Due to the oxidative etching effect caused by Br(-), the nanoparticles obtained from AuBr exhibited an aspect ratio of 1.28, in contrast to 1.0 for the particles made from AuCl. Compared to the existing methods for preparing Au nanoparticles through the reduction of Au(III) compounds, this new approach based on Au(I) halides offers great flexibility in terms of size control.

Gold nanoparticles for the development of clinical diagnosis methods

The impact of advances in nanotechnology is particularly relevant in biodiagnostics, where nanoparticle-based assays have been developed for specific detection of bioanalytes of clinical interest. Gold nanoparticles show easily tuned physical properties, including unique optical properties, robustness, and high surface areas, making them ideal candidates for developing biomarker platforms. Modulation of these physicochemical properties can be easily achieved by adequate synthetic strategies and give gold nanoparticles advantages over conventional detection methods currently used in clinical diagnostics. The surface of gold nanoparticles can be tailored by ligand functionalization to selectively bind biomarkers. Thiol-linking of DNA and chemical functionalization of gold nanoparticles for specific protein/antibody binding are the most common approaches. Simple and inexpensive methods based on these bio-nanoprobes were initially applied for detection of specific DNA sequences and are presently being expanded to clinical diagnosis. Figure Colorimetric DNA/RNA detection using salt induced aggregation of AuNP-DNA nanoprobes.

Use of the interparticle i-motif for the controlled assembly of gold nanoparticles

In this letter, we present a new design that uses single-stranded (ss) DNAs containing two stretches of cytosine (C)-rich domains for the controlled assembly of gold nanoparticles (Au NPs). We show that this assembly is driven by the formation of interparticle i-motif (four-stranded C-quadruplex) structures formed between the C-rich domains of the ssDNAs on neighboring Au NPs. The assembly happens only at slightly acidic pH conditions (pHs below the pKa of the i-motif). The assembly is reversible and can be switched by changing the solution pH. The assembly and disassembly process is accompanied by distinct color changes that are clearly visible to the naked eye. This development may have applications in the controlled assembly of reversible pH-sensitive nanostructures and/or devices.

Quantitative enhanced Raman scattering of labeled DNA from gold and silver nanoparticles

Surface-enhanced resonance Raman scattering (SERRS) from silver nanoparticles using 514.5-nm excitation has been shown to offer huge potential for applications in highly sensitive multiplexed DNA assays. If the technique is to be applied to real biological samples and integrated with other methods, then the use of gold nanoparticles and longer wavelengths of excitation are desirable. The data presented here demonstrate that dye-labeled oligonucleotide sequences can be directly detected by SERRS using gold nanoparticles in a quantitative manner for the first time. The performance of gold and silver nanoparticles as SERRS substrates was assessed using 514.5-, 632.8-, and 785-nm excitation and a range of 13 commercially available dye-labeled oligonucleotides. The quantitative response allowed the limit of detection to be determined for each case and demonstrates that the technique is highly effective, sensitive, and versatile. The possibility of excitation at multiple wavelengths further enhances the multiplexing potential of the technique. The importance of effectively combining the optical properties of the nanoparticle and the dye label is demonstrated. For example, at 632.8-nm excitation, the dye BODIPY TR-X and gold nanoparticles make a strong SERRS combination with very little background fluorescence. This study allows the choice of nanoparticle and dye label for particular experimental setups, and significantly expands the applicability of enhanced Raman scattering for use in many disciplines.

Homogeneous Detection of Nucleic Acids Based upon the Light Scattering Properties of Silver-Coated Nanoparticle Probes

Herein we report the development of a simple, rapid, homogeneous, and sensitive detection system for DNA based on the scattering properties of silver-amplified gold nanoparticle probes. The assay uses DNA-functionalized magnetic particle probes that act as scavengers for target DNA, which can be collected via a magnetic field. Once the DNA targets are isolated from the initial sample, they are sandwiched via hybridization by a second set of probes. The latter probes are 13-nm gold nanoparticles modified with a different target complementary DNA. Excess probes are removed through repetitive washing steps. The gold particles are dispersed in solution by dehybridization, corresponding to an assumed 1:1 ratio with the target DNA. Electroless deposition of silver on the surface of the gold probes results in particle growth, which increases their scattering efficiency with time. The scattering efficiency and the extinction signatures of the particle sizes are monitored as a function of time and correlated with target concentration. The limit of detection for this novel assay was determined to be 10 fM.

Nanoparticle-based detection and quantification of DNA with single nucleotide polymorphism (SNP) discrimination selectivity

Sequence-specific DNA detection is important in various biomedical applications such as gene expression profiling, disease diagnosis and treatment, drug discovery and forensic analysis. Here we report a gold nanoparticle-based method that allows DNA detection and quantification and is capable of single nucleotide polymorphism (SNP) discrimination. The precise quantification of single-stranded DNA is due to the formation of defined nanoparticle-DNA conjugate groupings in the presence of target/linker DNA. Conjugate groupings were characterized and quantified by gel electrophoresis. A linear correlation between the amount of target DNA and conjugate groupings was found. For SNP detection, single base mismatch discrimination was achieved for both the end- and center-base mismatch. The method described here may be useful for the development of a simple and quantitative DNA detection assay.

Gold nanoparticle aggregation-based highly sensitive DNA detection using atomic force microscopy

The potential ability of atomic force microscopy (AFM) as a quantitative bioanalysis tool is demonstrated by using gold nanoparticles as a size enhancer in a DNA hybridization reaction. Two sets of probe DNA were functionalized on gold nanoparticles and sandwich hybridization occurred between two probe DNAs and target DNA, resulting in aggregation of the nanoparticles. At high concentrations of target DNA in the range from 100 nM to 10 microM, the aggregation of gold nanoparticles was determined by monitoring the color change with UV-vis spectroscopy. The absorption spectra broadened after the exposure of DNA-gold nanoparticles to target DNA and a new absorption band at wavelengths >600 nm was observed. However, no differences were observed in the absorption spectra of the gold nanoparticles at low concentrations of target DNA (10 pM to 10 nM) due to insufficient aggregation. AFM was used as a biosensing tool over this range of target DNA concentrations in order to monitor the aggregation of gold nanoparticles and to quantify the concentration of target DNA. Based on the AFM images, we successfully evaluated particle number and size at low concentrations of target DNA. The calibration curve obtained when mean particle aggregate diameter was plotted against concentration of target DNA showed good linearity over the range 10 pM to 10 nM, the working range for quantitative target DNA analysis. This AFM-based DNA detection technique was three orders of magnitude more sensitive than a DNA detection method based on UV-vis spectroscopy.