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

SONOCHEMICAL PREPARATION OF GOLD/IRON OXIDE COMPOSITE MAGNETIC NANOPARTICLES AND SELECTIVE MAGNETIC SEPARATION OF BIOMOLECULES

We have successfully prepared Au nanoparticles by the sonochemically reducing Au(III) ions and immobilized them on the surface of magnetic γ- Fe 2 O 3 nanoparticles. Au particles with average diameter of about 10 nm were homogeneously dispersed on the surface of γ- Fe 2 O 3 (average diameter : 26 nm) without aggregation. Au nanoparticles are known to selectively adsorb the molecules having sulfur. Aiming at the uses for magnetic carriers of specific biomolecules, we employed prepared composite nanoparticles for selective separation of biomolecules and estimated their adsorption properties. The composite nanoparticles exhibited a high affinity with glutathione, a tripeptide with mercapto group, so that separation and manipulation of glutathione in aqueous solutions could be performed by applying an external magnetic field. Magnetic separations of amino acids were also investigated. Composite nanoparticles were mixed with amino acid standard solution containing 17 kinds of amino acids and their magnetic separations were carried out by applying an external magnetic field. It was found that adsorption amounts of methionine and cystine, containing internal sulfur were larger than other amino acids. The adsorbed amounts of sulfur containing amino acids increased with relative amount of Au in the composite nanoparticles.

Homogeneous point mutation detection by quantum dot-mediated two-color fluorescence coincidence analysis

This report describes a new genotyping method capable of detecting low-abundant point mutations in a homogeneous, separation-free format. The method is based on integration of oligonucleotide ligation with a semiconductor quantum dot (QD)-mediated two-color fluorescence coincidence detection scheme. Surface-functionalized QDs are used to capture fluorophore-labeled ligation products, forming QD-oligonucleotide nanoassemblies. The presence of such nanoassemblies and thereby the genotype of the sample is determined by detecting the simultaneous emissions of QDs and fluorophores that occurs whenever a single nanoassembly flows through the femtoliter measurement volume of a confocal fluorescence detection system. The ability of this method to detect single events enables analysis of target signals with a multiple-parameter (intensities and count rates of the digitized target signals) approach to enhance assay sensitivity and specificity. We demonstrate that this new method is capable of detecting zeptomoles of targets and achieve an allele discrimination selectivity factor >10⁵.

Optical detection of DNA hybridization based on fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles

A novel system for the detection of DNA hybridization in a homogeneous format is developed. This method is based on fluorescence quenching by gold nanoparticles used as both nanoscaffolds for the immobilization of capture sequences and nanoquenchers of fluorophores attached to detection sequences. The oligonucleotide-functionalized gold nanoparticles are synthesized by derivatizing the colloidal gold solution with 5'-thiolated 12-base oligonucleotides. Introduction of sequence-specific target DNAs (24 bases) into the mixture containing dye-tagged detection sequences and oligonucleotide-functionalized gold nanoparticles results in the quenching of carboxytetramethylrhodamine-labeled DNA fluorescence because DNA hybridization occurs and brings fluorophores into close proximity with oligonucleotide-functionalized gold nanoparticles. The quenching efficiency of fluorescence increases with the target DNA concentration and provides a quantitative measurement of sequence-specific DNA in sample. A linearity is obtained within the range from 1.4 to 92 nM. The target sequence is detected down to 2 nM. This new system not only overcomes many of the drawbacks inherent in radioisotopic measurement or enzyme-linked assay but also avoids the requirement for the stem-loop structure compared with conventional molecular beacons. Furthermore, the background signal that is defined as fluorescence quenching arising from electrostatic attraction between positively charged fluorophores and negatively charged gold nanoparticles is comparatively low due to electrostatic repulsion between negatively charged oligonucleotides. In addition, this is a homogeneous assay that can offer the potential to be monitored in real time, be amenable to automation, eliminate washing steps, and reduce the risk of contamination.

Modification of gold nanorods using phosphatidylcholine to reduce cytotoxicity

Hexadecyltrimethylammonium bromide (CTAB), which is necessary for the preparation of gold nanorods (NRs), was extracted from a NR solution into a chloroform phase containing phosphatidylcholine (PC). After three extractions, the zeta potential of the NRs remained positive, but its magnitude decreased from +67 +/- 1 to +15 +/- 1 mV. Transmission electron microscopy and energy-dispersive X-ray analysis indicated that the NRs were passivated with PC. The PC layer on the NR surface contributed to the prevention of NR aggregation. The PC-passivated NRs showed low cytotoxicity in comparison with twice-centrifuged NRs. It was shown that a negligible amount of CTAB was dispersed in the NR solution after the extraction. The extraction using a chloroform phase containing PC was found to be a convenient way of replacing the CTAB with alternative capping agents such as PC. This is a key technique for preparing functional NRs that can have practical applications.

Electrochemical SNPs detection using an abasic site-containing DNA on a gold electrode

An abasic site-containing DNA combined with lumiflavin allows amperometric determination of single nucleotide polymorphism through hydrogen bond-mediated nucleobase recognition in water by using abasic sites as a molecular recognition field.

One-step preparation of positively-charged gold nanoraspberry

Self-assembling particles were prepared by a new synthetic strategy for a raspberry-like aggregate, based on three-dimensional particle-aniline oligomer-particle repeated sequences; this one-step process, without the need for extra control, organic solvents, or ligand exchange, could further help in the realization of nanoscale electronics and molecular devices.

Subfemtomolar electrochemical detection of target DNA by catalytic enlargement of the hybridized gold nanoparticle labels

After showing the failure of conventional gold-enhancement procedures to amplify the gold nanoparticle-based electrochemical transduction of DNA hybridization in polystyrene microwells, a new efficient protocol was developed and evaluated for the sensitive quantification of a 35 base-pair human cytomegalovirus nucleic acid target (tDNA). In this assay, the hybridization of the target adsorbed on the bottom of microwells with an oligonucleotide-modified Au nanoparticle detection probe (pDNA-Au) was monitored by the anodic stripping detection of the chemically oxidized gold label at a screen-printed microband electrode (SPMBE). Thanks to the combination of the sensitive Au(III) determination at a SPMBE with the large amount of Au(III) released from each pDNA-Au, picomolar detection limits of tDNA can be achieved. Further enhancement of the hybridization signal based on the autocatalytic reductive deposition of ionic gold (Au(III)) on the surface of the gold nanoparticle labels anchored on the hybrids was first envisaged by incubating the commonly used mixture of Au(III) and hydroxylamine (NH(2)OH). However, due to a considerable nonspecific current response of poor reproducibility it was not possible to significantly improve the analytical performances of the method under these conditions. Complementary transmission electronic microscopy experiments indicated the loss of most of the grown gold labels during the post-enlargement rinsing step. To circumvent this drawback, a polymeric solute containing polyethyleneglycol and sodium chloride was introduced in the growth media to act as an aggregating agent during the catalytic process and thus retain the enlarged labels on the bottom of the microwell. This strategy, which led to an efficient increase of the hybridization response, allowed detection of tDNA concentrations as low as 600 aM (i.e., 10(4) lower than without amplification), and thus offers great promise for ultrasensitive detection of other hybridization events.

A thermodynamic investigation into the binding properties of DNA functionalized gold nanoparticle probes and molecular fluorophore probes

We report the first quantitative analysis of the oligonucleotide binding thermodynamics for DNA functionalized gold nanoparticle probes and compare our findings to molecular fluorophore probes on a sequence-for-sequence basis. With proper design, nanoparticle probes show significantly increased binding over molecular fluorophore probes under identical conditions. This is significant because probe binding strength directly influences detection sensitivity limits.

Integrated nanoparticle-biomolecule hybrid systems: synthesis, properties, and applications

Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.

Stabilized and size-tunable gold nanoparticles formed in a quaternary ammonium-based room-temperature ionic liquid under gamma-irradiation

Colloidal gold nanoparticles were synthesized in a quaternary ammonium-based room-temperature ionic liquid (QAIL) by gamma-radiation for the first time. Transmission electron microscopy, x-ray diffraction and optical techniques were used to characterize the colloidal nanoparticles. By changing the experimental conditions, the size of the gold nanoparticles can be varied between 10 and 50 nm. It was found that gold nanoparticles coated by QAIL are very stable in dispersion.

Colorimetric detection of eukaryotic gene expression with DNA-derivatized gold nanoparticles

Thiol-linked DNA-gold nanoparticles were used in a novel colorimetric method to detect the presence of specific mRNA from a total RNA extract of yeast cells. The method allowed detection of expression of the FSY1 gene that encodes a specific fructose/H+ symporter in Saccharomyces bayanus PYCC 4565. FSY1 is strongly expressed when the yeast is grown in fructose as the sole carbon source, while cells cultivated in glucose as the sole carbon source repress gene expression. The presence of FSY1 mRNA is detected based on color change of a sample containing total RNA extracted from the organism and gold nanoparticles derivatized with a 15-mer of complementary single stranded DNA upon addition of NaCl. If FSY1 mRNA is present, the solution remains pink, changing to blue-purple in the absence of FSY1 mRNA. Direct detection of specific expression was possible from only 0.3 microg of unamplified total RNA without any further enhancement. This novel method is inexpensive, very easy to perform as no amplification or signal enhancement steps are necessary and takes less than 15 min to develop after total RNA extraction. No temperature control is necessary and color change can be easily detected visually.

Use of vitamin B2 for fluorescence detection of thymidine-related single-nucleotide polymorphisms

In combination with abasic site (AP site)-containing DNAs, potential use of a biotic fluorescence compound, Vitamin B2 (riboflavin), is demonstrated for the fluorescence detection of the thymine (T)-related single-nucleotide polymorphisms. Our method is based on construction of the AP site in DNA duplexes, which allows small ligands to bind to target nucleotides accompanied by fluorescence signaling: an AP site-containing probe DNA is hybridized with a target DNA so as to place the AP site toward a target nucleobase, by which hydrophobic microenvironments are provided for ligands to recognize target nucleotides through stacking and hydrogen-bonding interactions. In 10 mM sodium cacodylate buffer solutions (pH 7.0) containing 100 mM NaCl and 1.0 mM EDTA, Vitamin B2 is found to selectively bind to T (K11=1.8x10(6) M(-1) at 5 degrees C) over other nucleobases, and this is accompanied by significant quenching of its fluorescence. While the sensing functions depend on the flanking sequences to the AP site, Vitamin B2 is applicable to the detection of T/C (cytosine), T/G (guanine) and T/A (adenine) mutation sequences of the CYP2A6 gene, where the flanking nucleobases are guanines in both positions (-GXG-, X=AP site).

PDMS microfludic device for optical detection of protein immunoassay using gold nanoparticles

A simple but highly specific immunoassay system for goat anti-human IgG has been developed using gold nanoparticles and microfluidic techniques. The assay is based on the deposition of gold nanoparticles that are coated with protein antigens in the presence of their corresponding antibodies to microfluidic channel surface. The effects of time accumulation, the flow velocity, and the concentration of antibodies to the red light absorption percentage (RAP) of deposition were investigated with an ordinary optical microscope. By controlling the reaction time and flow velocity, a dynamic range of 3 orders of magnitude and a detection sensitivity of 10 ng ml(-1) of goat anti-human IgG were achieved. Because of its simplicity and flexibility, this new technique should be useful for fast, highthroughput screening of antibodies in clinical diagnostic applications.

Synthesis, characterization of dihydrolipoic acid capped gold nanoparticles, and functionalization by the electroluminescent luminol

The use of gold nanoparticles as biological probes requires the improvement of colloidal stability. Dihydrolipoic acid (DHLA), a dithiol obtained by the reduction of thioctic acid, appears therefore very attractive for the stabilization and the further functionalization of gold nanoparticles because DHLA is characterized by a carboxylic acid group and two thiol functions. The ionizable carboxylic acid groups ensure, for pH > or = 8, the water solubility of DHLA-capped gold (Au@DHLA) nanoparticles, prepared by the Brust protocol, and the stability of the resulting colloid by electrostatic repulsions. Moreover almost all DHLA, adsorbed onto gold, adopts a conformation allowing their immobilization by both sulfur ends. It is proved by sulfur K-edge X-ray absorption near edge structure spectroscopy, which appears as an appropriate tool for determining the chemical form of sulfur atoms present in the organic monolayer. Such a grafting renders the DHLA monolayers more resistant to displacement by dithiothreitol than mercaptoundecanoic acid monolayers. The presence of DHLA on gold particles allows their functionalization by the electroluminescent luminol through amine coupling reactions assisted by 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride and N-hydroxysuccinimide. As a luminol-functionalized particle is nine times as bright as a single luminol molecule, the use of the particles as a biological probe with a lower threshold of detection is envisaged.

Electrochemical detection of single a-g mismatch using biosensing surface based on gold nanoparticles

The study of small drug molecules interacting with nucleic acids is an area of intense research that has particular relevance in our understanding of relative mechanism in chemotherapeutic applications and the association between genetics (including sequence variation) and drug response. In this contribution, we demonstrate how the sequence-specific binding of an anticancer drug Dacarbazine (DTIC) to single base (A-G) mismatch could be sensitively detected by combining electrochemical detection with biosensing surface based on gold nanoparticles.

Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions

Aggregation of DNA-modified gold nanoparticles in a non-cross-linking configuration has extraordinary selectivity against terminal mismatch of the surface-bound duplex. In this paper, we demonstrate the utility of this selectivity for detection of single-base substitutions. The samples were prepared through standard protocols: DNA extraction, PCR amplification and single-base primer extension. Oligonucleotide-modified nanoparticles correctly responded to the unpurified products from the primer extension: aggregation for the full match and dispersion for all the mismatches. Applicability of this method to genomic DNA was tested with five human tumor cell lines, and verified by conventional technologies: mass spectrometry and direct sequencing. Unlike the existing methods for single-base substitution analysis, this method does not need specialized equipments, and opens up a new possibility of point-of-care diagnosis for single-nucleotide polymorphisms.

Label-free colorimetric detection of specific sequences in genomic DNA amplified by the polymerase chain reaction

We document the surprising result that single-stranded DNA adsorbs on negatively charged gold nanoparticles (Au-nps) with a rate that depends on sequence length and temperature. After ss-DNA adsorbs on Au-nps, we find that the particles are stabilized against salt-induced aggregation. These observations can be rationalized on the basis of electrostatics and form the basis for a colorimetric assay to identify specific sequences and single nucleotide polymorphisms on polymerase chain reaction (PCR)-amplified DNA. The assay is label-free, requires no covalent modification of the DNA or Au-np surfaces, and takes on the sensitivity of PCR. Most important, binding of target and probe takes place in solution where hybridization occurs in less than 1 min. As an example, we test PCR-amplified genomic DNA from clinical samples for single nucleotide polymorphisms (SNPs) associated with a fatal arrhythmia known as long QT syndrome.

Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles

We find that single- and double-stranded oligonucleotides have different propensities to adsorb on gold nanoparticles in colloidal solution. We use this observation to design a hybridization assay based on color changes associated with gold aggregation. Because the underlying adsorption mechanism is electrostatic, no covalent functionalization of the gold, the probe, or the target DNA is required. Hybridization conditions can be optimized because it is completely separated from the detection step. The assay is complete within 5 min, and <100 femtomoles of target produces color changes observable without instrumentation. Single-base-pair mismatches are easily detected.

Fluorescence detection of guanine-adenine transition by a hydrogen bond forming small compound

In combination with abasic site-containing oligodeoxynucleotides, 2-amino-4-oxopteridine (pterin) can selectively recognize guanine base over other nucleobases accompanied by fluorescence quenching, which allows clear detection of a guanine-adenine transition with the naked eye.

Single-base Mutation Detection Using Neutravidin-modified Polystyrene Nanoparticle Aggregation

A single-base mutation assay using the non-crosslinking aggregation of neutravidin-modified polystyrene nanoparticles is described. This method requires only two steps: hybridization of biotinylated probe and sample DNAs, and then mixing with neutravidin-modified nanoparticles. The aggregation was detected within 20 min in total. A combination of the DNA non-crosslinking aggregation and biotin-avidin technology has allowed sufficient performance for the detection of single nucleotide polymorphisms.