Facile and Controllable Loading of Single-Stranded DNA on Gold Nanoparticles

Dynamic light scattering on bioconjugated laser generated gold nanoparticles

Gold nanoparticles (AuNPs) conjugated to DNA are widely used for biomedical targeting and sensing applications. DNA functionalization is easily reached on laser generated gold nanoparticles because of their unique surface chemistry, not reproducible by other methods. In this context, we present an extensive investigation concerning the attachment of DNA to the surface of laser generated nanoparticles using Dynamic Light Scattering and UV-Vis spectroscopy. The DNA conjugation is highlighted by the increase of the hydrodynamic radius and by the UV-Vis spectra behavior. Our investigation indicates that Dynamic Light Scattering is a suitable analytical tool to evidence, directly and qualitatively, the binding between a DNA molecule and a gold nanoparticle, therefore it is ideal to monitor changes in the conjugation process when experimental conditions are varied.

Detection of single DNA molecule hybridization on a surface by atomic force microscopy

Improving the detection of DNA hybridization is a critical issue for several challenging applications encountered in microarray and biosensor domains. Herein, it is demonstrated that hybridization between complementary single-stranded DNA (ssDNA) molecules loosely adsorbed on a mica surface can be achieved thanks to fine-tuning of the composition of the hybridization buffer. Single-molecule DNA hybridization occurs in only a few minutes upon encounters of freely diffusing complementary strands on the mica surface. Interestingly, the specific hybridization between complementary ssDNA is not altered in the presence of large amounts of nonrelated DNA. The detection of single-molecule DNA hybridization events is performed by measuring the contour length of DNA in atomic force microscopy images. Besides the advantage provided by facilitated diffusion, which promotes hybridization between probes and targets on mica, the present approach also allows the detection of single isolated DNA duplexes and thus requires a very low amount of both probe and target molecules.

Surface modification of plasmonic nanostructured materials with thiolated oligonucleotides in 10 seconds using selective microwave heating

This study demonstrates the proof-of-principle of rapid surface modification of plasmonic nanostructured materials with oligonucleotides using low power microwave heating. Due to their interesting optical and electronic properties, silver nanoparticle films (SNFs, 2 nm thick) deposited onto glass slides were used as the model plasmonic nanostructured materials. Rapid surface modification of SNFs with oligonucleotides was carried out using two strategies (1) Strategy 1: for ss-oligonucleotides, surface hybridization and (2) Strategy 2: for ds-oligonucleotides, solution hybridization), where the samples were exposed to 10, 15, 30 and 60 seconds microwave heating. To assess the efficacy of our new rapid surface modification technique, identical experiments carried out without the microwave heating (i.e., conventional method), which requires 24 hours for the completion of the identical steps. It was found that SNFs can be modified with ss- and ds-oligonucleotides in 10 seconds, which typically requires several hours of incubation time for the chemisorption of thiol groups on to the planar metal surface using conventional techniques.

One-step conjugation chemistry of DNA with highly scattered silver nanoparticles for sandwich detection of DNA

DNA-silver nanoparticle (AgNP) conjugates were facilely prepared through a one-step method, and then used for the quantitative detection of HIV DNA with a sandwich strategy based on their strong plasmon resonance scattering signals.

Instantaneous and quantitative functionalization of gold nanoparticles with thiolated DNA using a pH-assisted and surfactant-free route

The attachment of thiolated DNA to gold nanoparticles (AuNPs) has enabled many landmark works in nanobiotechnology. This conjugate chemistry is typically performed using a salt-aging protocol where, in the presence of an excess amount of DNA, NaCl is gradually added to increase DNA loading over 1-2 days. To functionalize large AuNPs, surfactants need to be used, which may generate difficulties for downstream biological applications. We report herein a novel method using a pH 3.0 citrate buffer to complete the attachment process in a few minutes. More importantly, it allows for quantitative DNA adsorption, eliminating the need to quantify the number of adsorbed DNA and allowing the adsorption of multiple DNAs with different sequences at predetermined ratios. The method has been tested for various DNAs over a wide range of AuNP sizes. Our work suggests a synergistic effect between pH and salt in DNA attachment and reveals the fundamental kinetics of AuNP aggregation versus DNA adsorption, providing a novel means to modulate the interactions between DNA and AuNPs.

Gold nanoparticle fluorescent molecular beacon for low-resolution DQ2 gene HLA typing

Coeliac disease is an inflammation of the small intestine triggered by gluten ingestion. We present a fluorescent genosensor, exploiting molecular-beacon-functionalized gold nanoparticles, for the identification of human leukocyte antigen (HLA) DQ2 gene, a key genetic factor in coeliac disease. Optimization of sensor performance was achieved by tuning the composition of the oligonucleotide monolayer immobilized on the gold nanoparticle and the molecular beacon design. Co-immobilization of the molecular beacon with a spacing oligonucleotide (thiolated ten-thymine oligonucleotide) in the presence of ten-adenine oligonucleotides resulted in a significant increase of the sensor response owing to improved spacing of the molecular beacons and extension of the distance from the nanoparticle surface, which renders them more available for recognition. Further increase in the response (approximately 40%) was shown to be achievable when the recognition sequence of the molecular beacon was incorporated in the stem. Improvement of the specificity of the molecular beacons was also achieved by the incorporation within their recognition sequence of a one-base mismatch. Finally, gold nanoparticles functionalized with two molecular beacons targeting the DQA1*05* and DQB1*02* alleles allowed the low-resolution typing of the DQ2 gene at the nanomolar level.

Quantifying the nanomachinery of the nanoparticle-biomolecule interface

A study is presented of the nanomechanical phenomena experienced by nanoparticle-conjugated biomolecules. A thermodynamic framework is developed to describe the binding of thrombin-binding aptamer (TBA) to thrombin when the TBA is conjugated to nanorods. Binding results in nanorod aggregation (viz. directed self-assembly), which is detectable by absorption spectroscopy. The analysis introduces the energy of aggregation, separating it into TBA-thrombin recognition and surface-work contributions. Consequently, it is demonstrated that self-assembly is driven by the interplay of surface work and thrombin-TBA recognition. It is shown that the work at the surface is about -10 kJ mol(-1) and results from the accumulation of in-plane molecular forces of pN magnitude and with a lifetime of <1 s, which arises from TBA nanoscale rearrangements fuelled by thrombin-directed nanorod aggregation. The obtained surface work can map aggregation regimes as a function of different nanoparticle surface conditions. Also, the thermodynamic treatment can be used to obtain quantitative information on surface effects impacting biomolecules on nanoparticle surfaces.

Stable dye-labelled oligonucleotide-nanoparticle conjugates for nucleic acid detection

Metallic nanoparticles functionalized with oligonucleotides are used for a number of nucleic acid detection strategies. However, oligonucleotide-nanoparticle conjugates suffer from a lack of stability when exposed to certain conditions associated with DNA detection assays. In this study, we report the synthesis of thiol and thioctic acid-modified oligonucleotide gold nanoparticle (OGNs) conjugates functionalized with a dye label and varying spacer groups. The thioctic acid-modified conjugates exhibit increased stability when treated with dithiothreitol (DTT) compared to the more commonly used thiol modification. When the dye labelled oligonucleotide nanoparticle conjugates are exposed to the same conditions there is a pronounced increase in the stability for both thioctic acid and thiol modified sequences. These results open up the possibility of simply using a dye label to enhance the stability of oligonucleotide-nanoparticle conjugates in DNA detection assays where the enhanced stability of the conjugate system can be advantageous in more complex biological environments.

A microfluidic-assisted microarray for ultrasensitive detection of miRNA under an optical microscope

In this article, we report on direct detection of microRNAs (miRNAs) on a microarray by differential interference contrast (DIC) imaging technique. While the best resolution achieved with a fluorescence scanner is ∼1 μm, the DIC imaging technique adopted in our study offers the possibility of imaging individual reporting gold nanoparticles, or, in other words, individual miRNA strands. Due to its unrivalled resolution, the present technique could detect as low as 300 copies of target miRNAs in a sample volume of 1.0 μl. With the greatly improved sensitivity, the amount of total RNA needed in the assay is reduced to only a few nanograms, offering an excellent opportunity for fast and direct miRNA profiling without engaging any labeling and amplification procedure. Expression patterns of hsa-let-7 family members in healthy versus cancer cells analyzed on our microarray, are found to be consistent with the patterns obtained on a commercial microarray and those reported in the literature.

Sequence-selective recognition of nucleic acids under extremely low salt conditions using nanoparticle probes

Extensive secondary structures in nucleic acid targets seriously impede the binding of complementary oligonucleotide probes. We report here a method to conduct the detection under extremely low salt conditions where the secondary structures are less stable and more accessible. A new type of nanoparticle probes prepared by functionalizing gold nanoparticles with nonionic morpholino oligos is employed. Because of the salt-independent hybridization of the probes with nucleic acid targets, nanoparticle assemblies can be formed in 2 mM Tris buffer solutions containing 0-5 mM NaCl, leading to the colorimetric target recognition. The sharp melting transitions of the target-probe hybrids allow discrimination of single-base imperfection, including substitution, deletion, and insertion. The method works effectively in detecting sequences that are likely to form secondary structure. In addition, the study provides direct evidence of the relationship between the aggregate structure and the melting behavior of the DNA-linked nanoparticles.

Hybridization efficiency of molecular beacons bound to gold nanowires: effect of surface coverage and target length

Surface-bound nucleic acid probes designed to adopt specific secondary structures are becoming increasingly important in a range of biosensing applications but remain less well characterized than traditional single-stranded probes, which are typically designed to avoid secondary structure. We report the hybridization efficiency for surface-immobilized hairpin DNA probes. Our probes are molecular beacons, carrying a 3' dye moiety and a 5' thiol for attachment to gold nanowires, which serve as both scaffolds for probe attachment and quenchers. Hybridization efficiency was dependent on probe surface coverage, reaching a maximum of ∼90% at intermediate coverages of (1-2) × 10(12) probes/cm(2) and dropping to ≤20% at higher or lower coverages. Fluorescence intensity did not track with the number of target molecules bound, and was highest for high probe coverage despite the lower bound targets per square centimeter. Backfilling with short thiolated oligoethylene glycol spacers increased hybridization efficiency at low hairpin probe coverages (∼(3-4) × 10(11) probes/cm(2)), but not at higher probe coverages (1 × 10(12)/cm(2)). We also evaluated the effect of target length by adding up to 50 nonhybridizing nucleotides to the 3' or 5' end of the complementary target sequence. Additional nucleotides on the 3' end of the complementary target sequence (i.e., the end near the nanowire surface) had a much greater impact on hybridization efficiency as compared to nucleotides added to the 5' end. This work provides guidance in designing sensors in which surface-bound probes designed to adopt secondary structures are used to detect target sequences from solution.

High-sensitivity biosensors fabricated by tailoring the localized surface plasmon resonance property of core-shell gold nanorods

An enhanced sensitive biosensor has been developed to detect biological targets by tailoring the localized surface plasmon resonance property of core-shell gold nanorods. In this new concept, a shell layer is produced on gold nanorods by generating a layer of chalcogenide on the gold nanorod surface after attachment of the recognition reagent, namely, goat IgG and antigen of schistosomiasis japonica. The bioactivity of these attached biomolecules is retained and the sensitivity of this biosensor is thus enhanced significantly. The plasmonic properties of the gold nanorods attached with the biomolecules can be adjusted and the plasmon resonance wavelength can be red-shifted up to several hundred nanometers in the visible or near infrared (NIR) region, which is extremely important to biosensing applications. This leads to a lager red-shift in the localized surface plasmon resonance absorption compared to the original gold nanorod-based sensor and hence offers greatly enhanced sensitivity in the detection of schistosomiasis japonica. The human serum infected with schistosomiasis japonica diluted to 1:50,000 (volume ratio, serum/buffer solution) can be detected readily. The technique offers enhanced sensitivity and can be easily extended to other sensing applications based on not only immuno-recognition but also other types of specific reactions.

Increased stability of mercapto alkane functionalized Au nanoparticles towards DNA sensing

The use of gold nanoparticles (GNPs) in bioassays is often hampered by their colloidal stability. In this study, gold nanoparticles coated with different mercapto alkanes were investigated towards their stability. Hereto, the effects of the alkane chain length (5-11 methylene groups), the type of functional end-group (-OH or -COOH) and the amount of incorporated poly-ethylene oxide units (none, 3 or 6) on the GNP stabilization was evaluated. Based on these results, an optimal mercapto alkane (HS(CH(2))(11)PEO(6)COOH) was selected to increase the colloidal stability up to 2 M NaCl. Furthermore, it was proved that this mercapto alkane is ideally suited to enhance the stability of DNA functionalized GNPs in high electrolytic hybridization buffers. The effectiveness of these DNA functionalized GNPs was demonstrated in a sandwich assay using a surface plasmon resonance biosensor. The superior stability of these nanoparticles during hybridization may lead to enhanced biosensor technologies.

Controlled and efficient hybridization achieved with DNA probes immobilized solely through preferential DNA-substrate interactions

Quantitative and reproducible data can be obtained from surface-based DNA sensors if variations in the conformation and surface density of immobilized single-stranded DNA capture probes are minimized. Both the conformation and surface density can be independently and deterministically controlled by taking advantage of the preferential adsorption of adenine nucleotides (dA) on gold, as previously demonstrated using a model system in Opdahl, A.; Petrovykh, D. Y.; Kimura-Suda, H.; Tarlov, M. J.; Whitman, L. J. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 9-14. Here, we describe the immobilization and subsequent hybridization properties of a 15-nucleotide DNA probe sequence that has additional m adenine nucleotides, (dA)(m), at the 5' end. Quantitative analysis of immobilization and hybridization for these probes indicates that the (dA)(m) block preferentially adsorbs on gold, forcing the probe portion of the strand to adopt an upright conformation suited for efficient hybridization. In addition, a wide range of probe-to-probe lateral spacing can be achieved by coimmobilizing the probe DNA with a lateral spacer, a strand of k adenine nucleotides, (dA)(k). Altering either the length or relative concentration of the (dA)(k) spacers added during probe immobilization controls the average surface density of probes; the density of probes, in turn, systematically modulates their hybridization with solution targets.