DNA Biosensors and Microarrays

Toxicity and environmental risks of nanomaterials: challenges and future needs

Nanotechnology has gained a great deal of public interest because of the needs and applications of nanomaterials in many areas of human endeavors including industry, agriculture, business, medicine, and public health. Environmental exposure to nanomaterials is inevitable as nanomaterials become part of our daily life, and, as a result, nanotoxicity research is gaining attention. This review presents a summary of recent research efforts on fate, behavior, and toxicity of different classes of nanomaterials in the environment. A critical evaluation of challenges and future needs for the safe environmental nanotechnology are discussed.

An ionic liquid supported CeO2 nanoshuttles-carbon nanotubes composite as a platform for impedance DNA hybridization sensing

A novel nanocomposite membrane, comprising of nanosized shuttle-shaped cerium oxide (CeO(2)), single-walled carbon nanotubes (SWNTs) and hydrophobic room temperature ionic liquid (RTIL) 1-butyl-3-methylimidazolium hexafluorophosphate (BMIMPF(6)), was developed on the glassy carbon electrode (GCE) for electrochemical sensing of the immobilization and hybridization of DNA. The properties of the CeO(2)-SWNTs-BMIMPF(6)/GCE, the characteristics of the immobilization and hybridization of DNA were studied by cyclic voltammetry and electrochemical impedance spectroscopy (EIS) using [Fe(CN)(6)](3-/4-) as the redox indicator. The synergistic effect of nano-CeO(2), SWNTs and RTIL could dramatically enhance the sensitivity of DNA hybridization recognition. The electron transfer resistance (R(et)) of the electrode surface increased after the immobilization of probe ssDNA on the CeO(2)-SWNTs-BMIMPF(6) membrane and rose further after the hybridization of the probe ssDNA with its complementary sequence. The remarkable difference between the R(et) value at the probe DNA-immobilized electrode and that at the hybridized electrode could be used for label-free EIS detection of the target DNA. The sequence-specific DNA of phosphoenolpyruvate carboxylase (PEPCase) gene from transgenically modified rape was detected by this DNA electrochemical biosensor. Under optimal conditions, the dynamic range for detecting the sequence-specific DNA of the PEPCase gene was from 1.0x10(-12) mol/L to 1.0x10(-7) mol/L, and the detection limit was 2.3x10(-13) mol/L, suggesting that the CeO(2)-SWNTs-BMIMPF(6) nanocomposite hold great promises for the applications in sensitive electrochemical biosensor.

Chemical strategies for generating protein biochips

Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.

Cationic copolymer-mediated DNA immobilization: interfacial structure and composition as determined by ellipsometry, dual polarization interferometry, and neutron reflection

DNA immobilization onto support surfaces is required in biotechnological applications such as microarrays and gene delivery. This important interfacial molecular process can be mediated from a preadsobred cationic polymer. There is, however, a lack of understanding over the control of the interfacial composition and structural distribution of the DNA immobilized. We have used a combined approach of spectroscopic ellipsometry (SE), dual polarization interferometry (DPI) and neutron reflection (NR) to determine the interfacial polymer adsorption and the subsequent DNA binding. Cationic diblock copolymers incorporating 30 phosphorylcholine (PC) groups and different diethylaminoethyl groups, referred to as MPC30-DEAn, were chosen because of their well-defined molecular architecture. While our studies revealed different effects of surface charge and hydrophobicity, the amount of copolymers adsorbed on both model surfaces showed a broad trend of increase with solution pH, indicating a strong effect arising from pH-dependent charge density on the copolymers. In contrast, the copolymer structure and solution concentration showed a weak effect under the conditions studied. The subsequent DNA binding at pH 7 showed that on both surfaces the amount of DNA immobilized followed an approximate 1:1 charge interaction for all different DNA samples studied, irrespective of single or double strand, or different DNA size, indicating the dominant effect of electrostatic interaction between the two species. Both DPI and NR revealed consistent thickness increase upon DNA binding. Furthermore, with increasing DNA size, the interfacial layer became much thicker, and charge interaction drove more extensive interfacial mixing between the two species. Our results show that the amount of DNA immobilized is controlled by the amount of cationic copolymer preadsorbed that is in turn controlled by the solution pH and surface chemistry but that is barely affected by the type and concentration of DNA or cationic copolymer.

Signal enhancement for gene detection based on a redox reaction of [Fe(CN)(6)](4-) mediated by ferrocene at the terminal of a peptide nucleic acid as a probe with hybridization-amenable conformational flexibility

Electrochemically enhanced DNA detection was demonstrated by utilizing the couple of a synthesized ferrocene-terminated peptide nucleic acid (PNA) with a cysteine anchor and a sacrificial electron donor [Fe(CN)(6)](4-). DNA detection sensors were prepared by modifying a gold electrode surface with a mixed monolayer of the probe PNA and 11-hydroxy-1-undecanethiol (11-HUT), protecting [Fe(CN)(6)](4-) from any unexpected redox reaction. Before hybridization, the terminal ferrocene moiety of the probe was subject to a redox reaction due to the flexible probe structure and, in the presence of [Fe(CN)(6)](4-), the observed current was amplified based on regeneration of the ferrocene moiety. Hybridization decreased the redox current of the ferrocene. This occurred because hybridization rigidified the probe structure: the ferrocene moiety was then removed from the electrode surface, and the redox reaction of [Fe(CN)(6)](4-) was again prevented. The change in the anodic current before and after hybridization was enhanced 1.75-fold by using the electron donor [Fe(CN)(6)](4-). Sequence-specific detection of the complementary target DNA was also demonstrated.

An Electrochemical DNA Biosensor Developed on a Nanocomposite Platform of Gold and Poly(propyleneimine) Dendrimer

An electrochemical DNA nanobiosensor was prepared by immobilization of a 20mer thiolated probe DNA on electro-deposited generation 4 (G4) poly(propyleneimine) dendrimer (PPI) doped with gold nanoparticles (AuNP) as platform, on a glassy carbon electrode (GCE). Field emission scanning electron microscopy results confirmed the co-deposition of PPI (which was linked to the carbon electrode surface by C-N covalent bonds) and AuNP ca 60 nm. Voltammetric interrogations showed that the platform (GCE/PPI-AuNP) was conducting and exhibited reversible electrochemistry (E°′ = 235 mV) in pH 7.2 phosphate buffer saline solution (PBS) due to the PPI component. The redox chemistry of PPI was pH dependent and involves a two electron, one proton process, as interpreted from a 28 mV/pH value obtained from pH studies. The charge transfer resistance (R_ct) from the electrochemical impedance spectroscopy (EIS) profiles of GCE/PPI-AuNP monitored with ferro/ferricyanide (Fe(CN)₆^3-/4-) redox probe, decreased by 81% compared to bare GCE. The conductivity (in PBS) and reduced R_ct (in Fe(CN)₆^3-/4-) values confirmed PPI-AuNP as a suitable electron transfer mediator platform for voltammetric and impedimetric DNA biosensor. The DNA probe was effectively wired onto the GCE/PPI-AuNP via Au-S linkage and electrostatic interactions. The nanobiosensor responses to target DNA which gave a dynamic linear range of 0.01 - 5 nM in PBS was based on the changes in R_ct values using Fe(CN)₆^3-/4- redox probe.

Selective enzymatic labeling to detect packing-induced denaturation of double-stranded DNA at interfaces

The adsorption of DNA on surfaces is a widespread procedure and is a common way for fabrication of biosensors, DNA chips, and nanoelectronic devices. Although the biologically relevant and prevailing in vivo structure of DNA is its double-stranded (dsDNA) conformation, the characterization of DNA on surfaces has mainly focused on single-stranded DNA (ssDNA). Studying the structure of dsDNA on surfaces is of invaluable importance to microarray performance since their effectiveness relies on the ability of two DNA molecules to hybridize and remain stable. In addition, many of the enzymatic transactions performed on DNA require dsDNA, rather than ssDNA, as a substrate. However, it is not established that adsorbed dsDNA remains in its structure and does not denature. Here, two methodologies have been developed for distinguishing between surface-adsorbed single- and double-stranded DNA. We demonstrate that, upon formation of a dense monolayer, the nonthiolated strand comprising the dsDNA is released and the monolayer consists of mostly ssDNA. The fraction of dsDNA within the ssDNA monolayer depends on the length of the oligomers. A likely mechanism leading to this rearrangement is discussed.

Status of biomolecular recognition using electrochemical techniques

The use of nanoscale materials (e.g., nanoparticles, nanowires, and nanorods) for electrochemical biosensing has seen explosive growth in recent years following the discovery of carbon nanotubes by Sumio Ijima in 1991. Although the resulting label-free sensors could potentially simplify the molecular recognition process, there are several important hurdles to be overcome. These include issues of validating the biosensor on statistically large population of real samples rather than the commonly reported relatively short synthetic oligonucleotides, pristine laboratory standards or bioreagents; multiplexing the sensors to accommodate high-throughput, multianalyte detection as well as application in complex clinical and environmental samples. This article reviews the status of biomolecular recognition using electrochemical detection by analyzing the trends, limitations, challenges and commercial devices in the field of electrochemical biosensors. It provides a survey of recent advances in electrochemical biosensors including integrated microelectrode arrays with microfluidic technologies, commercial multiplex electrochemical biosensors, aptamer-based sensors, and metal-enhanced electrochemical detection (MED), with limits of detection in the attomole range. Novel applications are also reviewed for cancer monitoring, detection of food pathogens, as well as recent advances in electrochemical glucose biosensors.

Immobilization-free sequence-specific electrochemical detection of DNA using ferrocene-labeled peptide nucleic acid

An electrochemical method for sequence-specific detection of DNA without solid-phase probe immobilization is reported. This detection scheme starts with a solution-phase hybridization of ferrocene-labeled peptide nucleic acid (Fc-PNA) and its complementary DNA (cDNA) sequence, followed by the electrochemical transduction of Fc-PNA-DNA hybrid on indium tin oxide (ITO)-based substrates. On the bare ITO electrode, the negatively charged Fc-PNA-DNA hybrid exhibits a much reduced electrochemical signal than that of the neutral-charge Fc-PNA. This is attributed to the electrostatic repulsion between the negatively charged ITO surface and the negatively charged DNA, hindering the access of Fc-PNA-DNA to the electrode. On the contrary, when the transduction measurement is done on the ITO electrode coated with a positively charged poly(allylamine hydrochloride) (PAH) layer, the electrostatic attraction between the (+) PAH surface and the (-) Fc-PNA-DNA hybrid leads to a much higher electrochemical signal than that of the Fc-PNA. The measured electrochemical signal is proportional to the amount of cDNA present. In terms of detection sensitivity, the PAH-modified ITO platform was found to be more sensitive (with a detection limit of 40 fmol) than the bare ITO counterpart (with a detection limit of 500 fmol). At elevated temperatures, this method was able to distinguish fully matched target DNA from DNA with partial mismatches. Unpurified PCR amplicons were detected using a similar format with a detection limit down to 4.17 amol. This detection method holds great promise for single-base mismatch detection as well as electrochemistry-based detection of post-PCR products.

Nanotechnology, nanotoxicology, and neuroscience

Nanotechnology, which deals with features as small as a 1 billionth of a meter, began to enter into mainstream physical sciences and engineering some 20 years ago. Recent applications of nanoscience include the use of nanoscale materials in electronics, catalysis, and biomedical research. Among these applications, strong interest has been shown to biological processes such as blood coagulation control and multimodal bioimaging, which has brought about a new and exciting research field called nanobiotechnology. Biotechnology, which itself also dates back approximately 30 years, involves the manipulation of macroscopic biological systems such as cells and mice in order to understand why and how molecular level mechanisms affect specific biological functions, e.g., the role of APP (amyloid precursor protein) in Alzheimer's disease (AD). This review aims (1) to introduce key concepts and materials from nanotechnology to a non-physical sciences community; (2) to introduce several state-of-the-art examples of current nanotechnology that were either constructed for use in biological systems or that can, in time, be utilized for biomedical research; (3) to provide recent excerpts in nanotoxicology and multifunctional nanoparticle systems (MFNPSs); and (4) to propose areas in neuroscience that may benefit from research at the interface of neurobiologically important systems and nanostructured materials.

One-step photochemical attachment of NHS-terminated monolayers onto silicon surfaces and subsequent functionalization

N-Hydroxysuccinimide (NHS)-ester-terminated monolayers were covalently attached in one step onto silicon using visible light. This mild photochemical attachment, starting from omega-NHS-functionalized 1-alkenes, yields a clean and flat monolayer-modified silicon surface and allows a mild and rapid functionalization of the surface by substitution of the NHS-ester moieties with amines at room temperature. Using a combination of analytical techniques (infrared reflection absorption spectroscopy (IRRAS), extensive X-ray photoelectron spectroscopy (XPS) in combination with density functional theory calculations of the XPS chemical shifts of the carbon atoms, atomic force microscopy (AFM), and static contact angle measurements), it was shown that the NHS-ester groups were attached fully intact onto the surface. The surface reactivity of the NHS-ester moieties toward amines was qualitatively and quantitatively evaluated via the reaction with para-trifluoromethyl benzylamine and biotin hydrazide.

Multifunctional mixed SAMs that promote both cell adhesion and noncovalent DNA immobilization

The ability of DNA strands to influence cellular gene expression directly and to bind with high affinity and specificity to other biological molecules (e.g., proteins and target DNA strands) makes them a potentially attractive component of cell culture substrates. On the basis of the potential importance of immobilized DNA in cell culture and the well-defined characteristics of alkanethiol self-assembled monolayers (SAMs), the current study was designed to create multifunctional SAMs upon which cell adhesion and DNA immobilization can be independently modulated. The approach immobilizes the fibronectin-derived cell adhesion ligand Arg-Gly-Asp-Ser-Pro (RGDSP) using carbodiimide activation chemistry and immobilizes DNA strands on the same surface via cDNA-DNA interactions. The surface density of hexanethiol-terminated DNA strands on alkanethiol monolayers (30.2-69.2 pmol/cm2) was controlled using a backfill method, and specific target DNA binding on cDNA-containing SAMs was regulated by varying the soluble target DNA concentration and buffer characteristics. The fibronectin-derived cell adhesion ligand GGRGDSP was covalently linked to carboxylate groups on DNA-containing SAM substrates, and peptide density was proportional to the amount of carboxylate present during SAM preparation. C166-GFP endothelial cells attached and spread on mixed SAM substrates and cell adhesion and spreading were specifically mediated by the immobilized GGRGDSP peptide. The ability to control the characteristics of noncovalent DNA immobilization and cell adhesion on a cell culture substrate suggests that these mixed SAMs could be a useful platform for studying the interaction between cells and DNA.

An improved synthesis of arsenic-biotin conjugates

An amide linked conjugate of p-aminophenylarsine oxide and biotin is conveniently prepared in a one-pot procedure by the reaction of biotinyl chloride, formed in situ, with p-aminophenyldichloroarsine. The reaction of the arsine oxide-biotin conjugate with 1,2-ethanedithiol produces the stabilized dithiarsolane. These reagents are now readily available for a variety of applications.

Functionalized carbon nanotubes and nanofibers for biosensing applications

This review summarizes recent advances in electrochemical biosensors based on carbon nanotubes (CNTs) and carbon nanofibers (CNFs) with an emphasis on applications of CNTs. CNTs and CNFs have unique electric, electrocatalytic and mechanical properties, which make them efficient materials for developing electrochemical biosensors.We discuss functionalizing CNTs for biosensors. We review electrochemical biosensors based on CNTs and their various applications (e.g., measurement of small biological molecules and environmental pollutants, detection of DNA, and immunosensing of disease biomarkers). Moreover, we outline the development of electrochemical biosensors based on CNFs and their applications. Finally, we discuss some future applications of CNTs.