A fiber-optic evanescent wave DNA biosensor based on novel molecular beacons

We have prepared a novel optical fiber evanescent wave DNA biosensor using a newly developed molecular beacon DNA probe. The molecular beacons (MB) are oligonucleotide probes that become fluorescent upon hybridization with target DNA/RNA molecules. Biotinylated MBs have been designed and immobilized on an optical fiber core surface via biotin-avidin or biotin-streptavidin interactions. The DNA sensor based on a MB does not need labeled analyte or intercalation reagents. It can be used to directly detect, in real-time, target DNA/RNA molecules without using competitive assays. The sensor is rapid, stable, highly selective, and reproducible. We have studied the hybridization kinetics of the immobilized MB by changing the ionic strength of the hybridization solution and target DNA concentration. Our result shows divalent cations play a more important role than monovalent cations in stabilizing the MB stem hybrids and in accelerating the hybridization reaction with target DNA/RNA molecules. The concentration detection limit of the MB evanescent wave biosensor is 1.1 nM. The MB DNA biosensor has been applied to the analysis of specific gamma-actin mRNA sequences amplified by polymerase chain reaction.     

Enzyme-free and amplified fluorescence DNA detection using bimolecular beacons

In this work, we propose a simple and enzyme-free strategy for sensitive and selective DNA detection by using two different types of molecular beacons (MBs), MB1 and MB2. In this method, the target DNA binds with and restores the fluorescence of MB1 first. Then, MB2 hybridizes with MB1 and free the target, which is used to trigger another reaction cycle. The cycling use of the target and the employment of bi-MBs amplify the fluorescence intensity for sensitive DNA detection. The detection limit of this method was obtained as 10 pM, which is about 2 orders of magnitude sensitive than the conventional MB-based approaches.     

MicroRNA profiling by simultaneous selective isotachophoresis and hybridization with molecular beacons

We present and demonstrate a novel assay for the detection and quantification of microRNA (miRNA) that leverages isotachophoresis (ITP) and molecular beacon (MB) hybridization. We use ITP to selectively preconcentrate miRNA from total RNA. We simultaneously focus MBs and use the ITP zone as a 10 pL reactor with active mixing where MBs fluoresce upon hybridization to target miRNA. To increase both sensitivity and selectivity, we leverage a multistage ITP strategy composed of three discrete regions of different concentrations of denaturant, sieving matrix, and magnesium chloride. We show that ITP hybridization is specific and selective to the miRNA target. We demonstrate ITP hybridization of miRNA in a biologically relevant case by detecting and quantifying miR-122 in human kidney and liver. ITP hybridization is a cheap, simple, high-speed, and amplification-free miRNA profiling method which requires small amounts (order 100 ng) of sample. The technique therefore represents an attractive alternative to PCR or Northern blot for miRNAs.     

Noncovalent assembly of carbon nanotubes and single-stranded DNA: an effective sensing platform for probing biomolecular interactions

In this paper, we report the assembly of single-walled carbon nanotubes (SWNTs) and single-stranded DNA to develop a new class of fluorescent biosensors which are able to probe and recognize biomolecular interactions in a homogeneous format. This novel sensing platform consists of a structure formed by the interaction of SWNTs and dye-labeled DNA oligonucleotides such that the proximity of the nanotube to the dye effectively quenches the fluorescence in the absence of a target. Conversely, and very importantly, the competitive binding of a target DNA or protein with SWNTs for the oligonucleotide results in the restoration of fluorescence signal in increments relative to the fluorescence without a target. This signaling mechanism makes it possible to detect the target by fluorescence spectroscopy. In the present study, the schemes for such fluorescence changes were examined by fluorescence anisotropy and fluorescence intensity measurements for DNA hybridization and aptamer-protein interaction studies.     

Rapid detection of urinary tract infections using isotachophoresis and molecular beacons

We present a novel assay for rapid detection and identification of bacterial urinary tract infections using isotachophoresis (ITP) and molecular beacons. We applied on-chip ITP to extract and focus 16S rRNA directly from bacterial lysate and used molecular beacons to achieve detection of bacteria specific sequences. We demonstrated detection of E. coli in bacteria cultures as well as in patient urine samples in the clinically relevant range 1E6-1E8 cfu/mL. For bacterial cultures we further demonstrate quantification in this range. The assay requires minimal sample preparation (a single centrifugation and dilution), and can be completed, from beginning of lysing to detection, in under 15 min. We believe that the principles presented here can be used for design of other rapid diagnostics or detection methods for pathogenic diseases.     

Monitoring molecular beacon/DNA interactions using atomic force microscopy

The molecular beacon (MB) is a new fluorescence probe containing a single-stranded oligonucleotide with a probe sequence embedded in complementary sequences that form a hairpin stem. Due to the inherent fluorescent signal transduction mechanism, an MB functions as a sensitive probe with a high signal-to-background ratio for real-time monitoring and provides a variety of exciting opportunities in DNA, RNA, and protein studies. To better understand the properties of MBs, the specific interactions between MB and target DNA (complementary and one-base mismatch) have been directly investigated by atomic force microscopy. The interaction force between a linear DNA probe and the target DNA was also detected and compared to that between MB and target DNA. The results demonstrate the high specificity of the MB/target DNA compared to the linear DNA/target DNA interaction.     

Using biofunctionalized nanoparticles to probe pathogenic bacteria

In this paper, we report a method for fabricating biofunctionalized nanoparticles by attaching human immunoglobulin (IgG) onto their surfaces through either electrostatic interactions or covalent binding. We found that these IgG-presenting nanoparticles can bind selectively to the cell walls of pathogens that contain IgG-binding sites based on the investigation of transmission electron microscopy images. Our results demonstrate that such Au-IgG nanoparticles may serve as useful nanoscale probes for exploring the interactions between IgG and pathogens. Furthermore, the IgG-presenting magnetic nanoparticles have been employed as effective affinity probes for selectively concentrating traces of target bacteria from sample solutions. The trapped bacteria were then characterized by using matrix-assisted laser desorption/ionization mass spectrometry. The lowest cell concentration we detected for both Staphylococcus saprophyticus and Staphylococcus aureus in aqueous sample solutions (0.5 mL) was approximately 3 x 10(5) cfu/mL, while the detectable cell concentration for S. saprophyticus in a urine sample was approximately 3 x 10(7) cfu/mL.     

Efficient fluorescence turn-on probe for zirconium via a target-triggered DNA molecular beacon strategy

It is well-known that Zr(4+) could selectively bind with two phosphate-functionalized molecules through a coordinate covalent interaction to form a sandwich-structured complex (-PO(3)(2-)-Zr(4+)-PO(3)(2-)-). In this paper, we for the first time converted such interaction into fluorescence sensing systems for Zr(4+) via a target-triggered DNA molecular beacon strategy. In the new designed sensing system, two phosphorylated and pyrene-labeled oligonucleotides were chosen as both recognition and reporter units, which will be linked by target Zr(4+) to form a hairpin structure and bring the two labeled pyrene molecules into close proximity, resulting in a "turn-on" excimer fluorescence signal. Moreover, γ-cyclodextrin was introduced to afford an amplified fluorescence signal and, therefore, provided an improved sensitivity for the target Zr(4+). This allows detection of Zr(4+) with high sensitivity (limit of detection, LOD = 200 nM) and excellent selectivity. The proposed sensing system has also been used for detection of Zr(4+) in river water samples with satisfactory result.     

Using gold nanorods to probe cell-induced collagen deformation

In biological tissue, complex mechanisms of cellular response are closely linked to the mechanical environment that cells experience. The key to understanding these mechanisms may lie in measurement of local mechanical fields near living cells and between cells. We have developed a novel optical measurement technique which combines the light elastically scattered from gold nanorods with digital image analysis to track local deformations that occur in vitro between cells, in real time, under darkfield optical microscopy. We find that measurable tension and compression exist in the intercellular matrix at the length scale of micrometers, as the cells assess, adapt, and rearrange their environment.     

Study of single-stranded DNA binding protein-nucleic acids interactions using unmodified gold nanoparticles and its application for detection of single nucleotide polymorphisms

We have developed a label-free homogeneous phase bioassay to characterize the DNA binding properties of single-stranded DNA binding (SSB) protein, a key protein involved in various DNA processes such as DNA replication and repair. This assay uses gold nanoparticles (AuNPs) as sensing probe and is based on the phenomenon that preformed SSB-single-stranded DNA (ssDNA) complexes can protect AuNPs against salt-induced aggregation better than SSB or ssDNA alone. With the controlled particle aggregation/dispersion as measure, this assay can be used to detect the formation of SSB complexes with ssDNA of different length and nucleotide composition and to assess their binding properties without tedious and complicated assay procedures. On the basis of the inverse relationship between DNA hybridization efficiency and the tendency of SSB to form protection complex with unhybridized ssDNA to AuNPs, this assay is further developed to detect DNA hybridization with single nucleotide polymorphism selectivity. Owing to the high affinity between SSB and dissociated ssDNA, single-base mismatch discrimination in a long sequence of 30-mer DNA was achieved for both the end- and center-base mismatch. Unlike the conventional techniques for DNA and protein analysis, current AuNPs-based sensing strategy is simple in design, fast in detection, and economical for operation without the need of sophisticated equipment.     

Micromethod for the investigation of the interactions between DNA and redox-active molecules

A novel microscale and surface-based method for the study of the interactions of DNA with other redox-active molecules using DNA-modified electrodes is described. The method is simple, convenient, reliable, reagent-saving, and applicable for DNA studies, especially those involving microsamples. Information such as binding site size (s, in base pairs), binding constant (K), ratio (K0x/KRed) of the binding constants for the oxidized and reduced forms of a bound species, binding free energy (delta Gb), and interaction mode, including changes in the mode of interaction, and "limiting" ratio K0x0/KRed0 at zero ionic strength can be obtained using only 3-15 micrograms of DNA samples. The method was developed using [Co(Phen)3]3+/2+ (Phen = 1,10-phenanthroline)/double-stranded DNA (dsDNA)-modified gold electrodes and [Co(bpy)3]3+/2+ (2,2'-bipyridyl)/dsDNA-modified gold electrodes as model systems. For the [Co(Phen)3]3+/2+/dsDNA-modified gold electrode system, a K2+ of (2.5 +/- 0.3) x 10(5) M-1 and an s of 5 bp were obtained in 5 mM pH 7.1 Tris-HCl buffer solution containing 50 mM NaCl. For [Co(bpy)3]3+/2+/dsDNA-modified gold electrodes, K3+ and s values of (1.3 +/- 0.3) x 10(5) M-1 and 3 bp, respectively, were obtained. While the s values are consistent with those reported in the literature obtained by solution methods, the K values are almost an order of magnitude larger. A transition in the nature of the interaction between dsDNA and [Co(Phen)3]3+/2+, from electrostatic to intercalative with increasing ionic strength, was found in our studies. Negative values of delta E0' for [Co(bpy)3]3+/2+ bound to dsDNA suggest that its interaction with dsDNA is predominantly electrostatic over the ionic strength range of 5-105 mM. The "limiting" ratio K3+0/K2+0 of 22 obtained for [Co(Phen)3]3+/2+ bound to dsDNA at zero ionic strength suggests that electrostatic interactions are predominant over intercalative ones under these limiting conditions. The ratio for [Co(bpy)3]3+/2+ of 16 also indicates that the 3+ form binds to dsDNA more strongly than the 2+ form at zero ionic strength. For [Co(Phen)3]3+/2+/single-stranded DNA (ssDNA)-modified gold electrodes, the nonuniformity of the surface structure of ssDNA-modified gold electrodes greatly complicates the analysis. A system consisting of a dsDNA-modified gold electrode and [Co(tppz)2]3+/2+ (tppz = tetra-2-pyridyl-1,4-pyrazine) was studied by this method, with a K2+ value of (5 +/- 1) x 10(5) M-1 and an 8 value of 7 bp being obtained.     

Immobilization of Au nanoparticles on Au electrode for hydrazine detection: Using thiolated single-stranded DNA as a linker

In this article, we report a method for effective immobilization of Au nanoparticles (AuNPs) on thiolated single-stranded DNA (thiol-ssDNA) modified Au electrode (AuE) surface via coordination interactions between the nitrogen atoms of DNA bases and AuNPs. It suggests that the resultant AuNP-immobilized AuE exhibits notable catalytic performance for hydrazine oxidation and the loading of AuNPs on the AuE surface and hence the effective catalytic area can be tuned by the immobilization time of thiol-ssDNA and adsorption time of AuNPs. This hydrazine sensor has a fast amperometric response time of less than 4 s. The linear range and detection limit are estimated to be from 0.1 mM to 100 mM (r = 0.998) and 0.56 μM at a signal-to-noise ratio of 3, respectively.     

Using the intrinsic chirality of a molecule as a label-free probe to detect molecular adsorption to a surface by second harmonic generation

Chiral second harmonic generation (C-SHG) has been used for the label-free detection of (R)-(+)-1,1'-bi-2-naphthol (RBN) and (S)-(+)-1,1'-bi-2-naphthol (SBN) binding to planar-supported lipid bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphotidylcholine (POPC) based on the intrinsic chirality of the molecules. C-SHG adsorption isotherms of RBN and SBN reveal Langmuir adsorption behavior with binding constants of 2.7 +/- 0.2 x 10(5) M(-1) and 3.0 +/- 0.1 x 10(5) M(-1), respectively. The kinetics of RBN binding to a POPC bilayer was also measured. It was determined that the adsorption rate for RBN was 5.7 +/- 0.4 x 10(3) s(-1)M(-1) and the desorption rate was 2.1 +/- 0.8 x 10(-2) s(-1). From the kinetic data a binding constant of 2.7 +/- 1.0 x 10(5) M(-1) was calculated, which agrees well with the thermodynamic measurement. The C-SHG technique was correlated with surface tension measurements in order to determine the RBN surface excess within the POPC membrane. The maximum surface excess of RBN in a monolayer of POPC was 4.3 +/- 0.5 x 10(-11) mol cm2. Using the maximum surface excess in conjunction with the C-SHG binding data a lower limit of detection of 1.5 +/- 0.1 x 10(-13) mols cm(-2) was calculated. The results of these studies show that C-SHG is a powerful tool for the study of chiral molecular interactions at surfaces.     

Redox polymer and probe DNA tethered to gold electrodes for enzyme-amplified amperometric detection of DNA hybridization

The detection of nucleic acids based upon recognition surfaces formed by co-immobilization of a redox polymer mediator and DNA probe sequences on gold electrodes is described. The recognition surface consists of a redox polymer, [Os(2,2'-bipyridine)2(polyvinylimidazole)(10)Cl](+/2+), and a model single DNA strand cross-linked and tethered to a gold electrode via an anchoring self-assembled monolayer (SAM) of cysteamine. Hybridization between the immobilized probe DNA of the recognition surface and a biotin-conjugated target DNA sequence (designed from the ssrA gene of Listeria monocytogenes), followed by addition of an enzyme (glucose oxidase)-avidin conjugate, results in electrical contact between the enzyme and the mediating redox polymer. In the presence of glucose, the current generated due to the catalytic oxidation of glucose to gluconolactone is measured, and a response is obtained that is binding-dependent. The tethering of the probe DNA and redox polymer to the SAM improves the stability of the surface to assay conditions of rigorous washing and high salt concentration (1 M). These conditions eliminate nonspecific interaction of both the target DNA and the enzyme-avidin conjugate with the recognition surfaces. The sensor response increases linearly with increasing concentration of target DNA in the range of 1 x 10(-9) to 2 x 10(-6) M. The detection limit is approximately 1.4 fmol, (corresponding to 0.2 nM of target DNA). Regeneration of the recognition surface is possible by treatment with 0.25 M NaOH solution. After rehybridization of the regenerated surface with the target DNA sequence, >95% of the current is recovered, indicating that the redox polymer and probe DNA are strongly bound to the surface. These results demonstrate the utility of the proposed approach.     

纳米金与细胞相互作用机理的蛋白质组学研究

应用蛋白质组学结合生物信息学方法研究纳米金与人皮肤成纤维细胞(HDF-f )的作用机理.首先采用柠檬酸钠还原氛金酸法制备20nm的纳米金,然后应用MTT法和流式细胞术评价纳米金的细胞毒性及对细胞周期和细胞凋亡的影响.接着应用蛋白质组学技术和生物信息学方法筛选纳米金作用后细胞发生差异表达的蛋白质并进行基因本体论分析.MT...     

Measuring adhesion forces between model polysaccharide films and PLA bead to mimic molecular interactions in flax/PLA biocomposite

Natural fiber-reinforced polymers or biocomposites are becoming increasingly popular as an environment friendly alternative to traditional glass fiber-reinforced thermoplastics. The mechanical properties of reinforced biocomposites, such as flax/polylactic acid (PLA), are largely governed by the level of interfacial interactions between the two constituents apart from their intrinsic properties. The hierarchical organization of various polysaccharides present in natural fibers results in complex mechanisms at the interface which are still poorly understood and difficult to analyze through a traditional approach that rely on indirect assessments. The possibility of measuring direct adhesion force between individual particles using the colloidal force microscopy has been exploited here by developing an experimental set-up in which a micrometer colloidal PLA bead is brought into close contact with molecularly smooth polysaccharide surfaces that mimic the main constituents of flax fibers, cellulose, hemicellulose, and pectins. Adhesion force measurements performed under ambient and low relative humidity conditions indicate that cellulose/PLA is the weakest interface in the biocomposite. Moreover, the results emphasize the important role of water molecules for the more hydrophilic polymers in flax fibers that takes place in the fundamental forces involved in the adhesion phenomena at the biocomposite interface.     

The promotion of secondary structures in single-stranded DNA by drugs that bind to duplex DNA: an atomic force microscopy study

We study the behavior of single-stranded DNA (ssDNA) in the presence of well-known drugs with either an intercalating binding mode, such as daunorubicin, actinomycin D, and chloroquine, or a minor groove binding mode, such as netropsin and berenil, by atomic force microscopy (AFM). At very low salt conditions, ssDNA molecules adopt an unstructured conformation without secondary structures. We observe that under these conditions additions of?drugs that bind to double-stranded DNA (dsDNA) promote the formation of secondary structures in ssDNA. Furthermore, with an increase of concentration of the drugs, the extension as well as the thermal stabilization of these hairpins was observed.     

Use of potentiometric sensors to study (bio)molecular interactions

Potentiometric sensors were used to study molecular interactions in liquid environments with sensorgram methodology. This is demonstrated with a lipophilic rubber-based and a collagen-based hydrogel sensor coating. The investigated molecules were promazine and tartaric acid, respectively. The sensors were placed in a hydrodynamic wall-jet system for the recording of sensorgrams. Millivolt sensor responses were first converted to a signal, expressing the concentration of adsorbed organic ions. Using a linearization method, a pseudo-first order-kinetic model of adsorption was shown to fit the experimental results perfectly. K(assoc), k(on), and k(off) values were calculated. The technique can be used over 4 decades of concentration, and it is very sensitive to low-MW compounds as well as to multiply charged large biomolecules. This study is the first to demonstrate the application of potentiometric sensors as an alternative and complement to surface plasmon resonance methods.