Colorimetric DNA detection of transgenic plants using gold nanoparticles functionalized with L-shaped DNA probes

In this study, a DNA colorimetric detection system based on gold nanoparticles functionalized with L-shaped DNA probes was prepared and evaluated. We investigated the hybridization efficiency of the L-shaped probes and studied the effect of nanoparticle size and the L-shaped DNA probe length on the performance of the as-prepared system. Probes were attached to the surface of gold nanoparticles using an adenine sequence. An optimal sequence of 35S rRNA gene promoter from the cauliflower mosaic virus, which is frequently used in the development of transgenic plants, and the two complementary ends of this gene were employed as model target strands and probe molecules, respectively. The spectrophotometric properties of the as-prepared systems indicated that the large NPs show better changes in the absorption spectrum and consequently present a better performance. The results of this study revealed that the probe/Au-NPs prepared using a vertical spacer containing 5 thymine oligonucleotides exhibited a stronger spectrophotometric response in comparison to that of larger probes. These results in general indicate the suitable performance of the L-shaped DNA probe-functionalized Au-NPs, and in particular emphasize the important role of the gold nanoparticle size and length of the DNA probes in enhancing the performance of such a system.     

Increasing the stability of DNA-functionalized gold nanoparticles using mercaptoalkanes

In this work, the stability of DNA functionalized gold nanoparticles was examined in relation to their size, temperature, as well as the presence of mono- and bivalent ions. Furthermore, we report on the stabilizing effect of an additional post-functionalization with mercaptoalkanes, optionally bearing triethylene glycol (TEG) units. Although such so-called backfilling molecules are commonly used for planar gold surfaces, they have rarely been reported in combination with DNA-functionalized nanoparticles. Our results show that, conform the DLVO theory, smaller citrate-capped gold nanoparticles were more stable towards higher concentrations of salt. Citrate nanoparticles of 30 nm in size were only stable in sodium chloride concentrations up to ~0.05 M and up to 45 °C. The stability of these uncoated nanoparticles was even lower when bivalent salts were used (i.e. <2 × 10⁻⁴ M). Immobilization of DNA on these nanoparticles, on the other hand, improved the stability in salt solutions with at least one order of magnitude. The additional use of backfilling molecules stabilized the gold nanoparticles even further, without negatively affecting the DNA hybridization efficiency. DNA functionalization also had a positive impact on the thermal stability of the nanoparticles. Unfortunately, this beneficial effect was not observed after a subsequent backfilling step.

     

Melting transition of directly linked gold nanoparticle DNA assembly

DNA melting and hybridization is a fundamental biological process as well as a crucial step in many modern biotechnology applications. DNA confined on surfaces exhibits a behavior different from that in free solutions. The system of DNA-capped gold nanoparticles exhibits unique phase transitions and represents a new class of complex fluids. Depending on the sequence of the DNA, particles can be linked to each other through direct complementary DNA sequences or via a ‘linker’ DNA, whose sequence is complementary to the sequence attached to the gold nanoparticles. We observed different melting transitions for these two distinct systems.     

Colorimetric Biosensors Based on DNAzyme-Assembled Gold Nanoparticles

Taking advantage of recent developments in the field of metallic nanoparticle-based colorimetric DNA detection and in the field of in vitro selection of functional DNA/RNA that can recognize a wide range of analytes, we have designed highly sensitive and selective colorimetric biosensors for many analytes of choice. As an example of the sensor design strategy, a highly sensitive and selective colorimetric lead biosensor based on DNAzyme-directed assembly of gold nanoparticles is reviewed. The DNAzyme consists of an enzyme and a substrate strand, which can be used to assemble DNA-functionalized gold nanoparticles. The aggregation brings gold nanoparticles together, resulting in a blue-colored nanoparticle assembly. In the presence of lead, the DNAzyme catalyzes specific hydrolytic cleavage of the substrate strand, which disrupts the formation of the nanoparticle assembly, resulting in red-colored individual nanoparticles. The application of the sensor in lead detection in leaded paint is also demonstrated. In perspective, the use of allosteric DNA/RNAzymes to expand the range of the nanoparticle-based sensor design method is described.     

Gold nanoparticle growth on self-assembled monolayers of ferrocenyl-substituted terpyridine on graphite

In this contribution we demonstrate that densely packed gold nanoparticles can be grown by Volmer–Weber mode on ferrocenyl functionalized terpyridine (FcTerp) on graphite. FcTerp forms highly ordered and dense self-assembled monolayers (SAMs) on graphite which significantly reduces the diffusion length of gold atoms and increases the sticking coefficient compared to bare graphite. Both effects lead to an increased nucleation and thus, to the growth of densely packed gold nanoparticles with diameters in the nanometer range. The optical properties of the nanoparticles as well as their morphology and the structure of the SAMs were characterized by optical extinction spectroscopy and scanning tunneling microscopy.     

Hydrophobically modified chitosan/gold nanoparticles for DNA delivery

Present study dealt an application of modified chitosan gold nanoparticles (Nac-6-Au) for the immobilization of necked plasmid DNA. Gold nanoparticles stabilized with N-acylated chitosan were prepared by graft-onto approach. The stabilized gold nanoparticles were characterized by different physico-chemical techniques such as UV-vis, TEM, ELS and DLS. MTT assay was used for in vitro cytotoxicity of the nanoparticles into three different cell lines (NIH 3T3, CT-26 and MCF-7). The formulation of plasmid DNA with the nanoparticles corresponds to the complex forming capacity and in-vitro/in-vivo transfection efficiency was studied via gel electrophoresis and transfection methods, respectively. Results showed the modified chitosan gold nanoparticles were well-dispersed and spherical in shape with average size around 10～12 nm in triple distilled water at pH 7.4, and showed relatively no cytotoxicity at low concentration. Addition of plasmid DNA on the aqueous solution of the nanoparticles markedly reduced surface potential (50.0～66.6%) as well as resulted in a 13.33% increase in hydrodynamic diameters of the formulated nanoparticles. Transfection efficiency of Nac-6-Au/DNA was dependent on cell type, and higher β-galactosidase activity was observed on MCF-7 breast cancer cell. Typically, this activity was 5 times higher in 4.5 mg/ml nanoparticles concentration than that achieved by the nanoparticles of other concentrations (and/or control). However, this activity was lower in in-vitro and dramatically higher in in-vivo than that of commercially available transfection kit (Lipofectin®) and DNA. From these results, it can be expected to develop alternative new vectors for gene delivery.     

磷钼酸作为光催化还原剂制备纳米金溶胶

选择二甲基甲酰(DMF)为电子牺牲剂,以磷钼杂多酸作为光催化还原剂制备了纳米金溶胶,由于DMF与磷钼杂多阴离子间的电荷转移作用,导致钼系杂多酸可成为制备纳米金溶胶的光催化还原剂.实验结果表明,紫外光照作用及光照时间、DMF用量等是影响纳米金的形成和形貌的主要因素,选择适宜的合成条件可以得到粒径均匀、分散性好的纳米金溶胶.     

Antibody and DNA dual-labeled gold nanoparticles: Stability and reactivity

Gold nanoparticles labeled by both antibody (IgG) and single stranded DNA (ss-DNA) have been synthesized and characterized. The stability and reactivity of the dual-labeled nanoparticles were compared with the conventional IgG or ss-DNA modified nanoparticles. It was found that the IgG adsorption significantly improved the stability of the nanoparticles in aqueous solution, which is beneficial for attaching ss-DNA. The presence of IgG also effectively prohibits the desorption of ss-DNA against dithiothreitol (DTT) displacement. The coverage on dual-labeled nanoparticles was found to be 50 ± 15 ss-DNA/nanoparticle and 10 ± 2 IgG/nanoparticle, respectively, compared to the value of 70 ± 15 ss-DNA/nanoparticle of only ss-DNA-labeled gold nanoparticles. Dot-immuno and cross-linking experiments confirmed that both the IgG and ss-DNA retained their bioactivity on the nanoparticle surface. The dual-labeled nanoparticles have potential to be used as novel bio-probes for ultrasensitive detection.     

Phase transfer synthesis of N,N′(1,2-phenylene)bis-hippuricamide tethered metal based functionalized nanoparticles: A study on some novel microbial targeting peptide-mimic nanoparticles

This paper presents the novel synthesis of peptide, N,N′(1,2-phenylene)bis-hippuricamide tethered metal [Cu(II), Zn(II), Ni(II) and Co(II)] based functionalized nanoparticles via modified Brust-Schiffrin methodology. The growth, organic composition and morphology of these functionalized nanoparticles have been evaluated by UV-Vis, FT-IR spectroscopy and scanning electron microscopy. They are structurally and thermally characterized by X-ray diffraction and thermogravimetric analysis. Moreover, the interfacial dealings of these functionalized nanoparticles with Calf-thymus DNA and pUC19 DNA reveal that the functionalized nanoparticles of cobalt is an effective DNA damaging agent under physiological conditions. This has been supported by its efficient antimicrobial character against few fungal and bacterial strains, thereby steering its way towards biomedical applications as a metal based nanocarrier.     

X-ray photoelectron spectroscopic investigations of modifications in plasmid DNA after interaction with Hg nanoparticles

The electronic structure of plasmid DNA both prior to and after its conjugation with Hg nanoparticles (NP) has been investigated here. The DNA molecules undergo severe perturbation on their interaction with Hg-NP. The circular plasmid DNA becomes predominantly linearised on interaction with 10 mM Hg salt solution. These perturbations are also reflected in the electronic structure of C1s and O1s suggesting severe modifications in the exocyclic groups, of the nucleic acid bases, participating in the hydrogen bondings. The results reflect the rupturing of the purine-pyrimidine bonds after interaction with the NP. The study also suggests selective and specific interactions of DNA bases with the Hg nanoparticles leading to the formation of metal-purine-pyrimidine complexes through rupturing of G-C base pairs. Hg-NP exclusively interact with the nitrogen bases of the DNA molecule and do not cause any significant modification to the phosphate backbone of DNA.     

Anisotropically DNA-functionalized nanoparticle dimers

Self-assembly of complex, non-periodic nanostructures can only be achieved by using anisotropic building-blocks. The building blocks need to have at least four bonds pointing in separate directions [J. Comput. Theor. Nanosci. 3, 391 (2006)]. We have previously presented a method for the synthesis of such building-blocks using DNA-functionalized gold nanoparticles. Here, we report on the progress in the experimental realization of this scheme. The first goal, in a process to make programmable self-assembly building-blocks using nanoparticles, is the production of dimers with different DNA-functions on the two component particles. We report on the fabrication of anisotropically functionalized dimers of nanoparticles of two different sizes. As a result of their anisotropy, these demonstrator building blocks can be made to assemble into spherical structures.     

A SPECTROSCOPIC STUDY ON THE DNA BINDING BEHAVIOR OF THE ANTICANCER DRUG DACARBAZINE

ABSTRACT

The selective binding of some drug to DNA has been explored in this study to elucidate the structure-function relationship of the anticancer agent. In the case of the binding behavior of the anticancer drug dacarbazine [5-(3,3-dimethy-1-triazenyl)imidazole-4-carboxamide; DTIC], it was found that DNA causes significant decrease of the absorption intensity of DTIC without any shift of the peak position. Besides, nuclear magnetic resonance (NMR) study shows that only slight upfield shift was observed upon addition of DNA. These results as well as our nanostructural study by atomic force microscopy (AFM) illustrate the DNA recognition specificity of DTIC though this anticancer drug interacts with DNA by using non-intercalation mode.     

Selfassembly of gold nanoparticles onto the surface of multiwall carbon nanotubes functionalized with mercaptobenzene moieties

We have developed a new and effective method to robustly self-assemble gold nanoparticles onto the surface of multiwall carbon nanotubes (MWNTs) functionalized with mercaptobenzene moieties. Fourier transform infrared and electron diffraction spectroscopy were used to verify whether or not the mercaptobenzene moieties have been attached to the π-conjugated body of MWNTs. Transmission electron microscope images give direct evidences for the success of selfassembly of gold nanoparticles onto the functionalized MWNTs.     

Direct immobilization and hybridization of DNA on group III nitride semiconductors

A key concern for group III-nitride high electron mobility transistor (HEMT) biosensors is the anchoring of specific capture molecules onto the gate surface. To this end, a direct immobilization strategy was developed to attach single-stranded DNA (ssDNA) to AlGaN surfaces using simple printing techniques without the need for cross-linking agents or complex surface pre-functionalization procedures. Immobilized DNA molecules were stably attached to the AlGaN surfaces and were able to withstand a range of pH and ionic strength conditions. The biological activity of surface-immobilized probe DNA was also retained, as demonstrated by sequence-specific hybridization experiments. Probe hybridization with target ssDNA could be detected by PicoGreen fluorescent dye labeling with a minimum detection limit of 2 nM. These experiments demonstrate a simple and effective immobilization approach for attaching nucleic acids to AlGaN surfaces which can further be used for the development of HEMT-based DNA biosensors.     

Ultrasonic, chemical stability and preparation of self-assembled fullerene[C60]-gold nanoparticle films

C(60)-functionalized gold nanoparticle films were self-assembled on the reactive surface of glass slides functionalized with 3-aminopropyltrimethoxysilane. The functionalized glass slides were alternately soaked in the solutions containing unmodified C(60) and 4-aminothiophenoxide/hexane thiolate-protected gold nanoparticles. Organic reaction (amination) facilitated the layer-by-layer multilayer film assembly. C(60)-functionalized gold nanoparticle films have grown up to several layers (upto 5 layers were examined) depending on the immersion time. The assembled nanoparticle films were characterized using UV-vis spectroscopy. The chemical stability of C(60)-gold nanoparticle films was studied by monitoring the changes in absorbance after the immersion of the films in acidic solutions. The ultrasonic stability of these nanoparticle films was studied by exposing them to ultrasonic irradiated surrounding, which results in the aggregation of nanoparticles on solid surfaces.     

Functionalization of magnetic gold/iron-oxide composite nanoparticles with oligonucleotides and magnetic separation of specific target

Magnetic composite nanoparticles of gold and iron-oxide synthesized with gamma-rays or ultrasonics were functionalized with thiol-modified oligonucleotides. The amount of oligonucleotides bound to the functionalized nanoparticle probes via hybridization was quantified with fluorescently-labeled target oligonucleotides. Our composite nanoparticles magnetically separated the specific target oligonucleotides without the non-specific adsorption.     

Lithography-free fabrication of large-area plasmonic nanostructures using colloidal gold nanoparticles

We report simple and efficient fabrication of large-area gold nanostructures using solution-processible gold nanoparticles, where lithography and vacuum evaporation techniques are not involved in the fabrication processes. These gold nanoisland structures exhibit strong particle plasmon resonance that is characterized by optical extinction spectroscopy in the visible spectral range. The tunability of the optical response is realized by controlling the annealing temperature and by changing the concentration of the colloidal solutions of gold nanoparticles. This enables a low-cost route for exploiting new photonic devices, biosensors, and optoelectronic devices with localized field-enhancement.     

Obtaining DNA aptamers to human interleukin-6 for biomagnetic immunoassay nanosensors

We used aptamers, which are functional equivalents of antibodies, in order to develop a nanosensor immunoassay system based on magnetic nanoparticles and a SQUID magnetometer. Selection was used to obtain DNA aptamers to interleukin-6; their affinity to the target protein was characterized by surface plasmon resonance. It was shown that the biotinylated aptamer binds to magnetic nanoparticles that were functionalized with streptavidin.     

Thiol-Capped Gold Nanoparticle Biosensors for Rapid and Sensitive Visual Colorimetric Detection of <Emphasis Type="Italic">Klebsiella pneumoniae</Emphasis>

In the last few years, gold nanoparticle biosensors have been developed for rapid, precise, easy and inexpensive with high specificity and sensitivity detection of human, plant and animal pathogens. Klebsiella pneumoniae serotype K2 is one of the common gram-negative pathogens with high prevalence. Therefore, it is essential to provide the effective and exclusive method to detect the bacteria. Klebsiella pneumoniae serotype K2 strain ATCC9997 genomic DNA was applied to establish the detection protocol either with thiol-capped oligonucleotide probes and gold nanoparticles or polymerase chain reaction based on K2A gene sequence. In the presence of the genomic DNA and oligonucleotide probes, a change in the color of gold nanoparticles and maximum changes in wavelength at 550-650 nm was achieved. In addition, the result showed specificity of 15?×?10⁵ CFU/mL and 9 pg/μL by gold nanoparticles probes. The lower limit of detection obtained by PCR method was 1 pg/μL. Moreover, results demonstrated a great specificity of the designed primers and probes for colorimetric detection assay and PCR. Colorimetric detection using gold nanoparticle probe with advantages such as the lower time required for detection and no need for expensive detection instrumentation compared to the biochemical and molecular methods could be introduced for rapid, accurate detection of the bacteria.     

Biophysical and electrochemical properties of Self-assembled noncovalent SWNT/DNA hybrid and electroactive nanostructure

DNA self-assembled hybrid nanostructures are widely used in recent research in nanobiotechnology. Combination of DNA with carbon based nanoparticles such as single-walled carbon nanotube (SWNT), multi-walled carbon nanotube (MWNT) and carbon quantum dot were applied in important biological applications. Many examples of biosensors, nanowires and nanoelectronic devices, nanomachine and drug delivery systems are fabricated by these hybrid nanostructures. In this study, a new hybrid nanostructure has been fabricated by noncovalent interactions between single or double stranded DNA and SWNT nanoparticles and biophysical properties of these structures were studied comparatively. Biophysical properties of hybrid nanostructures studied by circular dichroism, UV–vis and fluorescence spectroscopy techniques. Also, electrochemical properties studied by cyclic voltammetry, linear sweep voltammetry, square wave voltammetry, choronoamperometry and impedance spectroscopy (EIS). Results revealed that the biophysical and electrochemical properties of SWNT/DNA hybrid nanostructures were different compare to ss-DNA, ds-DNA and SWNT singly. Circular dichroism results showed that ss-DNA wrapped around the nanotubes through π-π stacking interactions. The results indicated that after adding SWNT to ss-DNA and ds-DNA intensity of CD and UV–vis spectrum peaks were decreased. Electrochemical experiments indicated that the modification of single-walled carbon nanotubes by ss-DNA improves the electron transfer rate of hybrid nanostructures. It was demonstrated SWNT/DNA hybrid nanostructures should be a good electroactive nanostructure that can be used for electrochemical detection or sensing.