Rapid aggregation of gold nanoparticles induced by non-cross-linking DNA hybridization

Colorimetric detection of DNA using unmodified metallic nanoparticles and peptide nucleic acid probes

We have developed a colorimetric assay for DNA detection based on the aggregation of unmodified metallic nanoparticles. Charge neutral peptide nucleic acids (PNA) are used as a "coagulant" of citrate anion-coated particles and as hybridization probe. In the absence of a complementary target DNA, free PNA molecules in solution induce aggressive particle aggregation because of the removal of charge repulsion as a result of PNA coating on nanoparticles. When a complementary DNA is present and PNA-DNA complexes are formed, the particles remain stable because the negative charges of the DNA strands in the complexes adsorbed on the particle surface ensure sufficient charge repulsions. In this method, no probe immobilization is needed and PNA-DNA hybridization occurs in a homogeneous phase. The assay results are displayed as rapidly as the changes in color and/or in UV-vis adsorption spectra of the colloidal solutions. We have validated the assay principle using gold- and silver-nanoparticles (AuNPs and AgNPs), with the involvement of a shorter (13 mer) and a longer (22 mer) probe sequences. A specific DNA can be detected in the presence of at least 10 times of interference DNA, and the detection limit is at a DNA/PNA ratio of 0.05. When NaCl is added to accelerate the particle aggregation, the selectivity is further improved, and single-base-mismatch discrimination is achieved. A two-component assay using a mixture of AuNPs and AgNPs has also been constituted, aiming to improve the result accuracy by making use of the multiple aggregation signatures from the two types of particles. For single-base-mismatch discrimination, the AgNPs offer a higher sensitivity than AuNPs by showing more obvious spectra and color alternation, and the two-component assay offers three parameters in the UV-vis adsorption spectra.

DNA-incorporating nanomaterials in biotechnological applications

The recently developed ability to controllably connect biological and inorganic objects on a molecular scale opens a new page in biomimetic methods with potential applications in biodetection, tissue engineering, targeted therapeutics and drug/gene delivery. Particularly in the biodetection arena, a rapid development of new platforms has largely been stimulated by a spectrum of novel nanomaterials with physical properties that offer efficient, sensitive and inexpensive molecular sensing. Recently, DNA-functionalized nano-objects have emerged as a new class of nanomaterials that can be controllably assembled in predesigned structures. Such DNA-based nanoscale structures might provide a new detection paradigm due to their regulated optical, electrical and magnetic responses, chemical heterogeneity and high local biomolecular concentration. The specific biorecognition DNA and its physical-chemical characteristics allows for an exploitation of DNA-functionalized nanomaterials for sensing of nucleic acids, while a broad tunability of DNA interactions permits extending their use for detection of proteins, small molecules and ions. We discuss the progress that was achieved in the last decade in the exploration of new detection methods based on DNA-incorporating nanomaterials as well as their applications to gene delivery. The comparison between various detection platforms, their sensitivity and selectivity, and specific applications are reviewed.

An optical biosensing platform for proteinase activity using gold nanoparticles

The surface plasmon resonance (SPR) wavelength of colloidal gold nanoparticles (AuNPs) can vary when the AuNPs aggregate, have different sizes or shapes, or are modified with chemical molecules. In this study, an optical biosensing platform for a proteinase activity assay was established based on the SPR property of AuNPs. The 13-nm AuNPs were modified with gelatin (AuNPs-gelatin) as a proteinase substrate and subsequently modified with 6-mercaptohexan-1-ol (MCH) (AuNPs/MCH-gelatin). After proteinase (trypsin or gelatinase) digestion, the AuNPs lose shelter, and MCH increases the attractive force between the modified AuNPs. Therefore, the AuNPs gradually move closer to each other, resulting in AuNPs aggregation. The AuNPs aggregation can be monitored by the red shift of surface plasmon absorption and a visible color change of the AuNPs is from red to blue. Such a color change can be observed with the naked eye. For detection, the absorption ratio, A(625)/A(525), of the reacted AuNPs solution can be used to estimate quantitatively the proteinase activity. A linear correlation has been established with trypsin activity at concentrations from 1.25 x 10(-1) to 1.25 x 10(2) U and matrix metalloproteinase-2 activity at concentrations from 50 ng/mL to 600 ng/mL.

Self-aggregation of oligonucleotide-functionalized gold nanoparticles and its applications for highly sensitive detection of DNA

A new self-aggregation phenomenon of single strand DNA-modified gold nanoparticles has been demonstrated and applied to highly sensitive DNA detection.

Colorimetric assay of glutathione based on the spontaneous disassembly of aggregated gold nanocomposites conjugated with water-soluble polymer

This article describes the glutathione-triggered disassembly of gold nanocomposites composed of gold cores and water-soluble copolymers [poly(N-n-isopropylacrylamide-co-acryloyldiethyletriamine)] attached to the surfaces of gold cores. The gold nanocomposites exhibit a bluish purple color because of the assembled gold cores that are conjugated with the diethylenetriamine groups incorporated into the copolymers. Glutathione added to the gold nanocomposite solution adsorbs onto the surface of the gold cores to liberate diethylenetriamine groups, resulting in spontaneous disassembly that changes the color of the solution to a reddish shade. Increasing the glutathione concentration facilitates the spontaneous disassembly of the gold nanocomposites. For the determination of glutathione, the colorimetric change of the gold nanoparticles is quantified with the a* value of the L*a*b* color coordinates defined by the CIE (Commission Internationale de l'Eclairage) chromaticity diagram. A linear relationship between the a* value and the glutathione concentration of up to 6 x 10(-6) mol/L is obtained 15 min after the addition of glutathione that has a detection limit (defined as 3sigma) of 2.9 x 10(-8) mol/L. The colorimetric assay is successfully applied to the determination of glutathione in eye drops and health supplements.

Simple synthesis of clay-gold nanocomposites with tunable color

Clay-based nanocomposites have been studied for several decades, mainly focusing on clay-polymer nanocomposites. Here, we report on a simple wet chemical method to synthesize clay-APTES-Au (CAAu) nanocomposites, where 3-aminopropyltriethoxysilane (APTES) acts as the linkage. The silane terminal of APTES formed bonds with the clay surface, while the other -NH(2) terminal bonds to gold nanoparticles. The color of clay changed when these CAAu nanocomposites were formed. By changing the size of the gold nanoparticles, the color of CAAu could be adjusted, simply by changing process parameters. TEM characterization of the synthesized nanocomposites showed an even distribution of gold nanoparticles on the clay surfaces. The nanocomposites were stable in strong acid and high concentration of salt conditions, while strong basic solution like NaOH could slightly influence the status of the gold nanoparticles due to the rupture of the Si-O-Si bonds between APTES and clay. To demonstrate the potential for label free sensing application of CAAu nanocomposites, we made hybrids of clay-APTES-Au-HD-Au (CAAuHAu), where hexamethylene diamine (HD) served as links between CAAu nanocomposites and the gold nanoparticles. The color of the composites changed from red to blue, when the hybrids were formed. Moreover, hemoglobin was loaded on the CAAu nanocomposites, which can potentially be used as a biosensor. These synthesized nanocomposites may combine the catalytic properties of clay and the well-known excellent properties of gold nanoparticles, such as the ability to anchor biological and chemical molecules. Furthermore, the color change of CAAu, when the CAAuHAu hybrids were observed, suggests the applications of these nanocomposites in biochemical and chemical sensing.

G-quadruplex signaling probe for highly sensitive DNA detection

Ferrocene-conjugated oligonucleotides that can form intermolecular guanine (G)-quadruplexes are prepared and used as signaling probes for detecting target DNA, improving substantially assay characteristics (e.g. a considerably wider linear dynamic range and lower detection limit).

Fluorescence-based detection of point mutation in DNA sequences by CdS quantum dot aggregation

We present a novel method for the detection of single base mismatch based on fluorescence quenching that unmodified CdS quantum dots exhibit upon aggregation. Target DNA sequences of interest are breast cancer 2 (BRCA2) and signal-induced proliferation-associated gene 1 (Sipa1) sequences. We monitor aggregation of CdS quantum dots upon addition of double-stranded DNAs at different salt concentration using quasi-elastic light scattering (QELS), transmission electron microscopy (TEM), photoluminescence spectroscopy, and zeta potential measurement. Our results indicate that the double-stranded DNA with a perfectly matched sequence can easily be discerned by naked eye from the single base mismatched one due to the fluorescence quenching phenomenon caused by selective aggregation of the CdS quantum dots.

Surface-enhanced Raman spectroscopy for facile DNA detection using gold nanoparticle aggregates formed via photoligation

We present a new type of nanoparticle-based DNA sensor using surface-enhanced Raman scattering (SERS) on gold nanoparticle (Au NP) aggregates formed by DNA photoligation. The DNA sensor exploits the photoligation reaction between oligodeoxynucleotides (ODNs) attached to the surfaces of Au NPs in the presence of target DNA (T-DNA). When hybridization takes place between the ODNs and T-DNA, Au NPs are covalently crosslinked to form aggregates via photoligation. Once the NP aggregates are formed, the interspace between Au NPs in the aggregate act as a stable "hot spot", and a SERS signal from the Raman-active molecules (sodium cacodylate) present in the hot spot is easily and sensitively detected. In contrast, a SERS signal is not detected if the hybridization is unsuccessful, because the stable hot spot does not form. This DNA sensor does not require an enzymatic reaction, fluorescent dye, precise temperature control, or complicated operating procedures.

Synthesis of circular double-stranded DNA having single-stranded recognition sequence as molecular-physical probe for nucleic acid hybridization detection based on atomic force microscopy imaging

A new class of DNA probes having a mechanically detectable tag is reported. The DNA probe, which consists of a single-stranded recognition sequence and a double-stranded circular DNA entity, was prepared by polymerase reaction. M13mp18 single strand and a 32mer oligodeoxynucleotide whose 5'-end is decorated with the recognition sequence were used in combination as template and primer, respectively. We have successfully demonstrated that the DNA probe is useful for bioanalytical purposes: by deliberately attaching target DNA molecules onto Au(111) substrates and by mechanically reading out the tag-entity using a high-resolution microscopy including atomic force microscopy, visualization/detection of the individual target/probe DNA conjugate was possible simply yet straightforwardly. The present DNA probe can be characterized as a 100%-nucleic acid product material. It is simply available by one-pod synthesis. A surface topology parameter, image roughness, has witnessed its importance as a quantitative analysis index with particular usability in the present visualization/detection method.

DNA functionalized gold nanoparticles for bioanalysis

Gold nanoparticles (Au NPs) have become one of the most interesting sensing materials because of their unique size- and shape-dependent optical properties, high extinction coefficients, and super-quenching capability. Au NPs that are bioconjugated with DNA (DNA-Au NPs) have been demonstrated for selective and sensitive detection of analytes such as mercury(ii) ions, platelet-derived growth factor (PDGF), and adenosine triphosphate (ATP). This review focuses on approaches using DNA-Au NPs for colorimetric, fluorescent, and scattering detection of biopolymers and small solutes. We highlight the important roles that the size and concentration of Au NPs, the length and sequence of DNA, the nature of the capping agents, and the ionic strength and pH of solution play in determining the specificity and sensitivity of the nanosensors for the analytes. The advantages and disadvantages of different detection methods for sensing of interesting analytes using DNA-Au NPs will be discussed.

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.

Label-free detection of specific DNA sequence-telomere using unmodified gold nanoparticles as colorimetric probes

A simple and sensitive label-free colorimetric detection of telomere DNA has been developed. It was based on the color change of gold nanoparticles (AuNPs) due to DNA hybridization. UV-vis spectra and transmission electron microscopy (TEM) were used to investigate the change of AuNPs. Under the optimized conditions, the linear range for determination of telomere DNA was 5.7 x 10(-13) to 4.5 x 10(-6)mol/L. The detection limit (3 sigma) of this method has decreased to pico-molar level.

Direct visual detection of DNA based on the light scattering of silica nanoparticles on a human papillomavirus DNA chip

A detection system for a human papillomavirus (HPV) DNA chip based on the light scattering of aggregated silica nanoparticle probes is presented. In the assay, a target HPV DNA is sandwiched between the capture DNA immobilized on the chip and the probe DNA immobilized on the plain silica nanoparticle. The spot where the sandwich reaction occurs appears bright white and is readily distinguishable to the naked eye. Scanning electron microscopy images clearly show the aggregation of the silica nanoparticle probes. When three different sized (55 nm, 137 nm, 286 nm) plain silica nanoparticles were compared, probes of the larger silica nanoparticles showed a higher scattering intensity. Using 286-nm silica nanoparticles, the spots obtained with 200 pM of target DNA were visually detectable. The demonstrated capability to detect a disease related target DNA with direct visualization without using a complex detection instrument provides the prerequisite for the development of portable testing kits for genotyping.

Sensitivity enhancement in DNA hybridization assay using gold nanoparticle-labeled two reporting probes

A simple and sensitive method for DNA detection using gold nanoparticle (AuNP) two-probe detection system (AuNP-TP) was developed. Preliminary experiment was carried out by optimizing slide types, blocking agents and hybridization times. Fluorescent-labeled probes were used along with AuNP-labeled probes to confirm specific binding event between target DNA and probes. The sensitivities between AuNP single-probe (AuNP-SP) and AuNP-TP systems using sandwich-typed assay were compared. The AuNP-TP on epoxide-coated (EP) slides increased sensitivity 1000-fold at the detection limit of 100fM when compared to the AuNP-SP. This result indicates that the assay sensitivity was simply enhanced by simultaneous adding two AuNP labeled probes which selectively recognize different regions of the target DNA. The concept of AuNP-TP could potentially be applied to a macroarray format to detect multiple DNA targets simultaneously; thereby making the assay becomes more affordable and more sensitive.

Easy design of logic gates based on aptazymes and noncrosslinking gold nanoparticle aggregation

We have developed an easy method for constructing aptazyme-based logic gates using noncrosslinking gold nanoparticle aggregation.

Single chain fragment variable recombinant antibody functionalized gold nanoparticles for a highly sensitive colorimetric immunoassay

In this report, the peptide linker connecting scFv V(H) and V(L) domains were genetically modified to contain different amino acids (i.e. cysteine (scFv-cys) or histidines (scFv-his)) to enable the scFv to adsorb or self-assemble onto the gold nanoparticles (NPs). The scFv-cys stabilized gold NPs were used to develop a highly sensitive colorimetric immunosensor. The scFv-cys stabilized gold NPs were characterized by UV-vis spectra, transmission electron microscope (TEM) and FTIR. After adding the antigen rabbit IgG, the solution of scFv-cys stabilized gold NPs shows obvious visible color change from deep red to light purple due to the aggregation of the gold nanoparticles. Based on the colorimetric aggregation of scFv-cys stabilized gold NPs, the immunosensor exhibits high sensitivity with a detection limit of 1.7 nM and good specificity. The good properties of the colorimetric aggregation immunosensor can be attributed to the small size of scFv and the covalent link between the scFv and gold NPs that improve the better orientation and enhance the probe density. With the advantages of speed, simplicity and specificity, the colorimetric immunoassay based on the functionalized scFv stabilized gold NPs represents a promising approach for protein analysis and clinical diagnostics.

Enhanced detection of early-stage oral cancer in vivo by optical coherence tomography using multimodal delivery of gold nanoparticles

Contrast in optical coherence tomography (OCT) images can be enhanced by utilizing surface plasmon resonant gold nanoparticles. To improve the poor in vivo transport of gold nanoparticles through biological barriers, an efficient delivery strategy is needed. In this study, the improved penetration and distribution of gold nanoparticles were achieved by microneedle and ultrasound, respectively, and it was demonstrated that this multimodal delivery of antibody-conjugated PEGylated gold nanoparticles enhanced the contrast in in vivo OCT images of oral dysplasia in a hamster model.

Ultrasensitive electrochemical detection of DNA based on PbS nanoparticle tags and nanoporous gold electrode

An electrochemical stripping assay for ultrasensitive detection of target DNA was reported in this work. The protocol involved nanoporous gold (NPG) electrode modified with single-stranded DNA (ssDNA) and Au nanoparticles (Au-NPs) co-loaded with two kinds of ssDNA, one was reporter DNA which was complementary to the target DNA, the other modified with PbS nanoparticles (PbS-NPs) was signal DNA which was non-complemented, reducing the cross-reaction between the targets and reporter DNA on the same Au-NP. The amount of target DNA was determined by indirect determination of the amount of lead ions through differential pulse anodic stripping voltammetry (DPASV). This protocol could detect target DNA of as low as femtomolar and exhibited excellent selectivity against one-base mismatched DNA and non-complementary DNA. Under the optimum conditions, the anodic stripping peak current of lead demonstrated a good linear relationship with the target DNA concentration in the range of 9.0x10(-16) to 7.0x10(-14) M. A detection limit of 2.6x10(-16) M of target DNA was achieved.

Individual nanoparticle detection in liquids by thermal lens microscopy and improvement of detection efficiency using a 1-microm microfluidic channel

Nanoparticles are a key material in nanoscience and nanotechnology due to their unique physicochemical properties, so an analytical method is increasingly required. In the present research, we developed a method for individual nanoparticle detection by thermal lens microscopy and microfluidic chips. Pulsed signals were clearly observed, as nanoparticles were passing through the detection volume. The scale of the microfluidic channel was reduced from 100 to 1 microm to improve the detection efficiency. As a result, a detection efficiency of 100% was demonstrated.

Colorimetric detection of mercury ion (Hg2+) based on DNA oligonucleotides and unmodified gold nanoparticles sensing system with a tunable detection range

Here, we report a simple and sensitive colorimetric detection method for Hg(2+) ions with a tunable detection range based on DNA oligonucleotides and unmodified gold nanoparticles (DNA/AuNPs) sensing system. Complementary DNA strands with T-T mismatches could effectively protect AuNPs from salt-induced aggregation. While in the presence of Hg(2+) ions T-Hg(2+)-T coordination chemistry leads to the formation of DNA duplexes, and AuNPs are less well protected thus aggregate at the same salt concentration, accompanying by color change from red to blue. By rationally varying the number of T-T mismatches in DNA oligonucleotides, the detection range could be tuned. Employing duplex oligonucleotides with 4 T-T mismatches in the sensing system, a sensitive linear range for Hg(2+) ions from 0 to 5 microM and a detection limit of 0.5 microM are obtained. Adding the number of T-T mismatches to 6 and 8, the assay region is enlarged and linear range is tuned. A low proportion of T-T mismatches makes the detection range narrow but the sensitivity high while a high proportion influences the detection limit but enlarges assay region. Besides, the sensor also shows a good selectivity for Hg(2+).

Curvature-directed assembly of gold nanocubes, nanobranches, and nanospheres

Gold nanocubes, nanobranches, and nanospheres were prepared in high yields using a seeded growth method in the presence of cationic surfactants. The resultant Au nanostructures are encapsulated with a surfactant bilayer and positively charged. The nanocubes are single-crystalline and enclosed with low-index facets. The nanobranches and nanospheres are multiply twinned. Each nanobranch possesses a varying number of sharp tips, which expose high-index facets. Glutathione was used to induce the assembly of the Au nanostructures, including both monocomponent (nanocubes and nanobranches) and bicomponent (nanocube-nanosphere and nanobranch-nanosphere) systems. The assembly was observed to occur predominantly at the vertices of the nanocubes and the sharp tips of the nanobranches. This curvature-directed assembly can be attributed to the preferential bonding of glutathione to the highly curved sites of the Au nanostructures. The fact that the curvature-directed assembly occurs for both the single-crystalline nanocubes and the multiply twinned nanobranches strongly suggests that the preferential bonding of glutathione to the curved sites is due to the less ordered surfactant bilayer at the curved sites than on the flat surfaces.

Gold nanoparticles: From nanomedicine to nanosensing

Because of their photo-optical distinctiveness and biocompatibility, gold nanoparticles (AuNPs) have proven to be powerful tools in various nanomedicinal and nanomedical applications. In this review article, we discuss recent advances in the application of AuNPs in diagnostic imaging, biosensing and binary cancer therapeutic techniques. We also provide an eclectic collection of AuNPs delivery strategies, including assorted classes of delivery vehicles, which are showing great promise in specific targeting of AuNPs to diseased tissues. However, successful clinical implementations of the promised applications of AuNPs are still hampered by many barriers. In particular, more still needs to be done regarding our understanding of the pharmacokinetics and toxicological profiles of AuNPs and AuNPs-conjugates.

Highly sensitive and selective colorimetric sensors for uranyl (UO2(2+)): development and comparison of labeled and label-free DNAzyme-gold nanoparticle systems

Colorimetric uranium sensors based on uranyl (UO2(2+)) specific DNAzyme and gold nanoparticles (AuNP) have been developed and demonstrated using both labeled and label-free methods. In the labeled method, a uranyl-specific DNAzyme was attached to AuNP, forming purple aggregates. The presence of uranyl induced disassembly of the DNAzyme functionalized AuNP aggregates, resulting in red individual AuNPs. Once assembled, such a "turn-on" sensor is highly stable, works in a single step at room temperature, and has a detection limit of 50 nM after 30 min of reaction time. The label-free method, on the other hand, utilizes the different adsorption properties of single-stranded and double-stranded DNA on AuNPs, which affects the stability of AuNPs in the presence of NaCl. The presence of uranyl resulted in cleavage of substrate by DNAzyme, releasing a single stranded DNA that can be adsorbed on AuNPs and protect them from aggregation. Taking advantage of this phenomenon, a "turn-off" sensor was developed, which is easy to control through reaction quenching and has 1 nM detection limit after 6 min of reaction at room temperature. Both sensors have excellent selectivity over other metal ions and have detection limits below the maximum contamination level of 130 nM for UO2(2+) in drinking water defined by the U.S. Environmental Protection Agency (EPA). This study represents the first direct systematic comparison of these two types of sensor methods using the same DNAzyme and AuNPs, making it possible to reveal advantages, disadvantages, versatility, limitations, and potential applications of each method. The results obtained not only allow practical sensing application for uranyl but also serve as a guide for choosing different methods for designing colorimetric sensors for other targets.

Nanofiber formation from sequence-selective DNA-templated self-assembly of a thymidylic acid-appended bolaamphiphile

Quaternary self-assembly of a thymidylic acid-appended bolaamphiphile, with heteropolymeric DNA as a template, produced supramolecular helical nanofibers in the presence of specific target DNA.