Microarray of DNA probes on carboxylate functional beads surface

The microarray of DNA probes with 5′-NH₂ and 5′-Tex/3′-NH₂ modified terminus on 10 μm carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) is characterized in the present paper. It was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentration of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.     

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.     

Computer simulation study of probe-target hybridization in model DNA microarrays: effect of probe surface density and target concentration

We use lattice Monte Carlo simulations to study the thermodynamics of hybridization of single-stranded "target" genes in solution with complementary "probe" DNA molecules immobilized on a microarray surface. The target molecules in our system contain 48 segments and the probes tethered on a hard surface contain 8-24 segments. The segments on the probe and target are distinct, with each segment representing a sequence of nucleotides that interacts exclusively with its unique complementary target segment with a single hybridization energy; all other interactions are zero. We examine how surface density (number of probes per unit surface area) and concentration of target molecules affect the extent of hybridization. For short probe lengths, as the surface density increases, the probability of binding long stretches of target segments increases at low surface density, reaches a maximum at an intermediate surface density, and then decreases at high surface density. Furthermore, as the surface density increases, the target is less likely to bind completely to one probe; instead, it binds simultaneously to multiple probes. At short probe lengths, as the target concentration increases, the fraction of targets binding completely to the probes (specificity) decreases. At long probe lengths, varying the target concentration does not affect the specificity. At all target concentrations as the probe length increases, the fraction of target molecules bound to the probes by at least one segment (sensitivity) increases while the fraction of target molecules completely bound to the probes (specificity) decreases. This work provides general guidelines to maximizing microarray sensitivity and specificity. Our results suggest that the sensitivity and specificity can be maximized by using probes 130-180 nucleotides long at a surface density in the range of 7 x 10(-5)- 3 x 10(-4) probe molecules per nm(2).     

Nanoscale-controlled spacing provides DNA microarrays with the SNP discrimination efficiency in solution phase

We have prepared solid substrates modified with a cone-shaped dendron that generates mesospacing (3.2 nm on average) on the surface. This nanoscale-controlled surface provided an ideal DNA microarray in which each probe DNA strand was given ample space for the incoming target DNA, resulting in selectivity as high as that in solution (100: < 1). In addition, high hybridization yield confirms that DNA probes on the mesospaced surface are sterically unhindered for the hybridization.     

Molecular beacon-metal nanowire interface: effect of probe sequence and surface coverage on sensor performance

We report the effect of surface coverage and sequence on the performance of 5' thiolated, 3' fluorophore-labeled DNA hairpin probes bound to Au/Ag striped ("barcoded") metal nanowires. Coverage was controlled by varying probe concentration, buffer ionic strength, and by addition of short hydroxy-terminated alkanethiol diluent molecules during probe assembly onto the nanowire surface. Surface dilution of the surface-bound probes with a omega-hydroxyl alkanethiol, a commonly accepted practice in the surface-bound DNA literature, did not appreciably improve sensor performance as compared to similar probe coverages without hydroxyalkanethiol diluents; this finding underscores the differences between the molecular beacon probes used here and more traditional nonfluorescent, random coil probes. We found that intermediate probe coverage of approximately 10 (12) molecules/cm (2) gave the best discrimination between presence and absence of a target sequence. Because we are interested in multiplexed assays, we also compared several beacon probe sequences having different stabilities for secondary structure formation in solution; we found that both probe surface coverage and sensor performance varied for different probe sequences. When five different molecular beacon probes, each bound to barcoded nanowires, were used in a multiplexed, wash-free assay for target oligonucleotides corresponding to viral nucleic acid sequences, these differences in probe performance did not prevent accurate target identification. We anticipate that the findings described here will also be relevant to other applications involving molecular beacons or other structured nucleic acid probes immobilized on metal surfaces.     

Surface-modified ZnSe waveguides for label-free infrared attenuated total reflection detection of DNA hybridization

This communication presents a novel label-free biosensing method to monitor DNA hybridization via infrared attenuated total reflection (IR-ATR) spectroscopy using surface-modified ZnSe waveguides. Well-defined carboxyl-terminated monolayers were formed at H-terminated ZnSe by direct photochemical activation. Chemical activation of the acidic function was obtained by using succinimide/carbodiimide linkers. The sequential surface modification reactions were characterized by XPS and IR-ATR spectroscopy. Finally, a single stranded DNA probe with a C6-NH(2) 5' modifier was coupled to the ester-terminated surface via peptide bonding, and the hybridization of the immobilized DNA sequence with its complementary strand was directly evaluated by IR-ATR spectroscopy in the mid-infrared (MIR) spectral regime (3-20 μm) without requiring an additional label. A shift of the vibrational modes corresponding to the phosphodiester and deoxyribose structures of the DNA backbone was observed. Hence, this approach substantiates a novel strategy for label-free DNA detection utilizing mid-infrared spectroscopy as the optical sensing platform.     

A spatially resolved nucleic acid biochip based on a gradient of density of immobilized probe oligonucleotide

The potential for a new biochip design based on a continuous gradient of density of immobilized single-stranded DNA oligonucleotide probes (ssDNA) is explored. This gradient resolved information platform (GRIP) can provide sequence identification based on the spatial location and extent of hybridization by a target sequence. Surfaces based on indium-tin oxide (ITO) on glass were first functionalized by 3-aminopropyltriethoxysilane (APTES) followed by attachment of glutaraldehyde, prior to immobilization of oligonucleotide probe that was terminated with amine. The use of Cy₃ and Cy₅ dye-labelled ssDNA probes and targets allowed estimation of density and correlation of the location of binding of labelled targets. Probe molecules of 20 mer lengths were loaded to produce density gradients in the range of 1.0-200 ng/mm². The biochips could resolve a mixture of fully complementary five base-pair mismatched targets by the location of binding on the surface. Thermal control provided additional selectivity. Thermal cycling and washing provided for regeneration of the surface, and the fluorescence intensities showed no deterioration in at least five cycles of hybridization reactions.     

Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers

Microarray-based technology is in need of flexible and cost-effective chemistry for fabrication of oligonucleotide microarrays. We have developed a novel method for the fabrication of oligonucleotide microarrays with unmodified oligonucleotide probes on nanoengineered three-dimensional thin films that are deposited on glass slides by consecutive layer-to-layer adsorption of polyelectrolytes. Unmodified oligonucleotide probes were spotted and immobilized on these multilayered polyelectrolyte thin films (PET) by electrostatic adsorption and entrapment on the porous structure of the PET film. The PET provides higher probe binding capacity and thus higher hybridization signal than that of the traditional two-dimensional aminosilane and poly-L-lysine coated slides. Immobilized probe densities of 3.4 x 10(12)/cm2 were observed for microarray spots on PET with unmodified 50-mer oligonucleotide probes, which is comparable to the immobilized probe densities of alkyamine-modified 50-mer probes end-tethered on an aldehyde-functionalized slide. The study of hybridization efficiency showed that 90% of immobilized probes on PET film are accessible to target DNA to form duplex format in hybridization. The DNA microarray fabricated on PET film has wider dynamic range (about 3 orders of magnitude) and lower detection limit (0.5 nM) than the conventional amino- and aldehyde-functionalized slides. Oligonucleotide microarrays fabricated on these PET-coated slides also had consistent spot morphology. In addition, discrimination of single nucleotide polymorphism of 16S rRNA genes was achieved with the PET-based oligonucleotide microarrays. The PET microarrays constructed by our self-assembly process is cost-effective, versatile, and well suited for immobilizing many types of biological active molecules so that a wide variety of microarray formats can be developed.     

基因芯片-玻璃表面两种不同DNA探针固定化方法的比较研究

研究了基因芯片相关的DNA探针在芯片表面最佳固定化方法。用两种不同的双功能试剂1,4-苯二异硫氰酸酯和戊二醛分别把5'-端氨基衍生的21-mer寡脱氧核苷酸探针直接共价固定到玻片表面,固定化的寡脱氧核苷酸探针与5'-端FITC标记的互补靶序列进行分子杂交,杂交后用配有CCD的IX70型荧光倒置显微镜成像检测。结果表明,两种固定化方法的效果都比较好,能检测到靶序列的最低终浓度为1.5×10^-9mol/L,优化了探针固定化时间、杂交时间、杂交温度等对DNA芯片分析性能的影响,为构建高灵敏度基因芯片打下良好基础。     

Tethered thiazole orange intercalating dye for development of fibre-optic nucleic acid biosensors

Single-stranded DNA (ssDNA) oligonucleotide in solution, or that is immobilized onto a surface to create a biosensor, can be used as a selective probe to bind to a complementary single-stranded sequence. Fluorescence enhancement of thiazole orange (TO) occurs when the dye intercalates into double-stranded DNA (dsDNA). TO dye has been covalently attached to probe oligonucleotides (homopolymer and mixed base 10mer and 20mer) through the 5′ terminal phosphate group using polyethylene glycol linker. The tethered TO dye was able to intercalate when dsDNA formed in solution, and also at fused silica surfaces using immobilized ssDNA. The results indicated the potential for development of a self-contained biosensor where the fluorescent label was available as part of the immobilized oligonucleotide probe chemistry. The approach was shown to be able to operate in a reversible manner for multiple cycles of detection of targeted DNA sequences.     

An Electrochemical Study of the Surface Hybridization Process of Morpholino‐DNA: Thermodynamics and Kinetics

Morpholino (MO) is a neutral analogue of DNA, which shows promise in the development of DNA biosensors and diagnostic devices. The present study explores the hybridization process of a surface‐attached MO 22‐mer with 10‐mer and 20‐mer DNA targets on a gold electrode. The melting process of the MO‐DNA duplex at the electrode/buffer interface is recorded using cyclic voltammetry. These results show that the length of target DNA, the binding location of the target DNA on the surface‐immobilized MO chain, and electrostatic forces from neighbouring duplexes all modulate the stability and hybridization kinetics of the DNA targets with the MO probes. Melting temperatures for immobilized MO‐DNA duplexes are found to be insensitive to ionic strength, provided the duplexes do not have a linker. Although the melting temperature does not shift appreciably with ionic strength, the maximum hybridization yield does. This somewhat surprising observation is considered to originate from an electrostatic limit on the extent of attainable hybridization. It is also reported that hybridization tends to initiate at the upper half of MO probes.     

Electrochemical Detection of Avian Influenza Virus Genotype Using Amino‐ssDNA Probe Modified Gold Electrodes

A DNA biosensor for the detection of specific oligonucleotide sequences of Avian Influenza Virus type H5N1 has been proposed. The NH₂‐ssDNA probe was deposited onto a gold electrode surface to form an amide bond between the carboxyl group of thioacid and the amino group from ssDNA probe. The signals generated as a result of hybridization were registered in square wave voltammetry and electrochemical impedance spectroscopy in the presence of [Fe(CN)₆]^3?/4? as a redox marker. The genosensor is capable to determine 20‐mer and 180‐bp (PCR products) oligonucleotides complementary sequences with detection limit in the fM range. The genosensor displays good selectivity and sensitivity. The 20‐mer as well as 180‐bp oligonucleotides without a complementary sequence generate very low signal.     

Probing hydroxyl radicals and their imaging in living cells by use of FAM-DNA-Au nanoparticles

The incorporation of gold nanoparticles (Au NPs) as quencher modules in fluorescent probes for DNA damage caused by intracellular hydroxyl radicals (HO*) is reported. Au NPs of 15 nm diameter were decorated with DNA oligomers terminating in thiol functions in their 3' positions and possessing 5' fluorophore modifications. The Au NPs, which have high extinction coefficients, functioned as excellent fluorescent quenchers in the fluorophore-Au NP composites. FRET is switched off as a factor of HO*-induced strand breakage in the single-stranded DNAs, restoring the fluorescence of the quenched fluorophores, which can be followed by spectrofluorimetry. In vitro assays with HO*-generating Fenton reagent demonstrated increases in fluorescence intensity with a linear range from 8.0 nM to 1.0 microM and a detection limit as low as 2.4 nM. Confocal microscopic imaging of macrophages and HepG2 revealed that the probe is cell-permeable and intracellular HO*-responsive. The unique combination of good selectivity and high sensitivity establishes the potential value of the probe for facilitating investigations of HO*-mediated cellular homeostasis and injury.     

Bioreactive surfaces prepared via the self-assembly of dendron thiols and subsequent dendrimer bridging reactions

Here, we report a novel route to prepare bioreactive surfaces on gold by the self-assembly of generation-three hydroxyl-terminated dendron thiols (G3-OH) and subsequent bridging reactions using generation-two amine-terminated dendrimers (G2-NH(2)). It has been shown that G3-OH dendron thiols form a stable and uniform self-assembled monolayer on gold, which can be activated by the homobifunctional cross-linker N,N-disuccinimidyl carbonate (DSC). Subsequent derivatization of the activated monolayer via dendrimer bridging reactions with G2-NH(2) enhances the stability, reactivity, and versatility of the prepared surface. Each step of the surface formation reaction has been monitored, and the resulting surface has been characterized by wetting, electrochemistry, scanning tunneling microscopy (STM), and infrared (IR) spectroscopy measurements. The reactivity of this surface was demonstrated by a Schiff base coupling reaction with 4-cyanobenzaldehyde, by immobilizing biotin molecules onto the peripheral amine groups using one of the conjugation methods, and by further binding avidin onto the biotinylated surface. We believe that the prepared bioreactive surface with a high density of amine groups will be useful for the immobilization of biological macromolecules for various biosensor applications, such as the fabrication of DNA microarrays and protein chips.     

Photophysical properties of a new series of water soluble iridium bisterpyridine complexes functionalised at the 4' position

Four new hetero- and homo-leptic iridium(III) bisterpyridine complexes have been prepared which incorporate aniline (tpy-φ-NH(2)), benzoic acid (tpy-φ-COOH), and benzyl alcohol (tpy-φ-CH(2)OH) substituents at the 4' positions of the tpy ligands (tpy = 2,2':6',2'-terpyridine, φ = phenylene). The electrochemical behaviour and ground and excited state spectroscopic properties of the complexes are reported, and the X-ray crystal structures of a homoleptic benzyl alcohol [Ir(tpy-φ-CH(2)OH)(2)](PF(6))(3), homoleptic aniline [Ir(tpy-φ-NH(2))(2)](PF(6))(3), and heteroleptic benzyl alcohol/aniline substituted complex [Ir(tpy-φ-CH(2)OH)(tpy-φ-NH(2))](PF(6))(3) have been solved. Complexes with aniline substituents were found to display absorption bands at around 430 nm corresponding to intraligand charge transfer (ILCT) that are sensitive to changes in solvent and pH. Strong emission in the visible region involving the ILCT state is observed in two of the complexes (Φ(e) = 0.7% and 2.6%) in acetonitrile. In the heteroleptic aniline/benzyl alcohol complex the Stokes shift is shown to be linearly related to solvent polarisability according to the Lippert equation, but only for solvents with weak hydrogen bonding interactions. Additionally, in water, emission from the ILCT state is quenched and only weak ligand centred (LC) emission is observed. The long lifetimes and quantum yields of these complexes make them interesting candidates for probes in sensing applications, especially [Ir(tpy-φ-CH(2)OH)(tpy-φ-NH(2))(2)](PF(6))(3) due to its unusual sensitivity to the solvent environment.     

稀土上转换发光材料标记抗体的制备及在免疫组化中的应用

采用微波辐射法合成了具有上转换发光特性的六方相纳米粒子NaGdF₄: Yb³⁺,Er³⁺(UCNPs), 其晶粒大小约为65 nm, 且粒子在980 nm的激发光下显示绿光(550 nm). 进一步在NaGdF₄: Yb³⁺,Er³⁺纳米晶的表面包覆了一层二氧化硅层, 进行氨基功能化后获得了表面共价结合氨基基团的粒径为70 nm的上转换发光纳米微球NaGdF₄: Yb³⁺,Er³⁺@SiO₂-NH₂(UCNPs@SiO₂-NH₂). 通过共价键将UCNPs@SiO₂-NH₂与多克隆抗体免疫球蛋白联接, 将标记后的多克隆抗体应用于传统的免疫组化检测子宫内膜腺细胞中基质金属蛋白酶组织抑制剂-4(TIMP-4)蛋白的表达. 结果表明, 微波合成的稀土上转换发光纳米材料形貌规则且粒径均一, 包覆硅壳后材料具有良好的分散性和水溶性, 荧光强度高且稳定, 在980 nm激发光下对生物组织无背景荧光, 可以很好地检测组织中蛋白质的表达.     

Colorimetric detection of DNA by modulation of thrombin activity on gold nanoparticles

A colorimetric, non-cross-linking aggregation-based gold-nanoparticle (AuNP) probe has been developed for the detection of DNA and the analysis of single-nucleotide polymorphism (SNP). The probe acts by modulating the enzyme activity of thrombin relative to fibrinogen. A thrombin-binding aptamer with a 29-base-long oligonucleotide (TBA(29)) assembled on the nanoparticles (TBA(29)-AuNPs) through sandwich DNA hybridization was found to possess ultra-high anticoagulant potency. The enzyme inhibition of thrombin was determined by thrombin-induced aggregation of fibrinogen-functionalized 56 nm AuNPs (Fib-AuNPs). The potency of the inhibition of TBA(29)-AuNPs relative to thrombin--and thus the degree of aggregation of the Fib-AuNPs--is highly dependent on the concentration of perfectly matched DNA (DNA(pm)). Under optimal conditions [Tris-HCl (20 mM, pH 7.4), KCl (5 mM), MgCl(2) (1 mM), CaCl(2) (1 mM), NaCl (150 mM), thrombin (10 pM), and TBA(29)-AuNPs (20 pM)], the new TBA(29)-AuNP/Fib-AuNP probe shows linear sensitivity to DNA(pm) in the concentration range 20-500 pM with a correlation coefficient of 0.96. The limit of detection for DNA(pm) was experimentally determined to be 12 pM, based on a signal-to-noise ratio (S/N) of 3. The new probe was successfully applied to the analysis of an SNP that is responsible for sickle cell anemia. Relative to conventional molecular-beacon-based probes, the new probe offers the advantages of higher sensitivity and selectivity towards DNA and lower cost, showing its great potential for practical studies of SNPs.     

Kinetic discrimination of sequence-specific DNA-drug binding measured by surface plasmon resonance imaging and comparison to solution-phase measurements

We demonstrate the use of surface plasmon resonance (SPR) imaging for direct detection of small-molecule binding to surface-bound DNA probes. Using a carefully designed array surface, we quantitatively discriminate between the interactions of a model drug with different immobilized DNA binding sites. Specifically, we measure the association and dissociation intercalation rates of actinomycin-D (ACTD) to and from double-stranded 5'-TGCT-3' and 5'-GGCA-3' binding sites. The rates measured provide mechanistic information about the DNA-ACTD interaction; ACTD initially binds nonspecifically to DNA but exerts its activity by dissociating slowly from strong affinity sites. We observe a slow dissociation time of kd-1 = 3300 +/- 100 s for ACTD bound to the strong affinity site 5'-TGCT-3' and a much faster dissociation time (210 +/- 15 s) for ACTD bound weakly to the site 5'-GGCA-3'. These dissociation rates, which differ by an order of magnitude, determine the binding affinity for each site (8.8 x 10(6) and 1.0 x 10(6) M(-1), respectively). We assess the effect the surface environment has on these biosensor measurements by determining kinetic and thermodynamic constants for the same DNA-ACTD interactions in solution. The surface suppresses binding affinities approximately 4-fold for both binding sites. This suppression suggests a barrier to DNA-drug association; ACTD binding to duplex DNA is approximately 100 times slower on the surface than in solution.     

Thermodynamics of DNA hybridization on surfaces

Hybridization of single-stranded DNA (ssDNA) targets to surface-tethered ssDNA probes was simulated using an advanced coarse-grain model to identify key factors that influence the accuracy of DNA microarrays. Comparing behavior in the bulk and on the surface showed, contrary to previous assumptions, that hybridization on surfaces is more thermodynamically favorable than in the bulk. In addition, the effects of stretching or compressing the probe strand were investigated as a model system to test the hypothesis that improving surface hybridization will improve microarray performance. The results in this regard indicate that selectivity can be increased by reducing overall sensitivity by a small degree. Taken as a whole, the results suggest that current methods to enhance microarray performance by seeking to improve hybridization on the surface may not yield the desired outcomes.     

A self-assembled deoxyribonucleic acid concatemer for sensitive detection of single nucleotide polymorphism

Polymerase-free and label-free strategies for DNA detection have shown excellent sensitivity and specificity in various biological samples. Herein, we propose a method for single nucleotide polymorphism (SNP) detection by using self-assembled DNA concatemers. Capture probes, bound to magnetic beads, can joint mediator probes by T4 DNA ligase in the presence of target DNA that is complementary to the capture probe and mediator probe. The mediator probes trigger self-assembly of two auxiliary probes on magnetic beads to form DNA concatemers. Separated by a magnetic rack, the double-stranded concatemers on beads can recruit a great amount of SYBR Green I and eventually result in amplified fluorescent signals. In comparison with reported methods for SNP detection, the concatemer-based approach has significant advantages of low background, simplicity, and ultrasensitivity, making it as a convenient platform for clinical applications. As a proof of concept, BRAF^T1799A oncogene mutation, a SNP involved in diverse human cancers, was used as a model target. The developed approach using a fluorescent intercalator can detect as low as 0.1 fM target BRAF^T1799A DNA, which is better than those previously published methods for SNP detection. This method is robust and can be used directly to measure the BRAF^T1799A DNA in complex human serum with excellent recovery (94–103%). It is expected that this assay principle can be directed toward other SNP genes by simply changing the mediator probe and auxiliary probes.