Macroporous Silicon Electrical Sensor for DNA Hybridization Detection

Biosensing platforms based on silicon nanostructures: A critical review

Biosensors are revolutionizing the health-care systems worldwide, permitting to survey several diseases, even at their early stage, by using different biomolecules such as proteins, DNA, and other biomarkers. However, these sensing approaches are still scarcely diffused outside the specialized medical and research facilities. Silicon is the undiscussed leader of the whole microelectronics industry, and novel sensors based on this material may completely change the health-care scenario. In this review, we will show how novel sensing platforms based on Si nanostructures may have a disruptive impact on applications with a real commercial transfer. A critical study for the main Si-based biosensors is herein presented with a comparison of their advantages and drawbacks. The most appealing sensing devices are discussed, starting from electronic transducers, with Si nanowires field-effect transistor (FET) and porous Si, to their optical alternatives, such as effective optical thickness porous silicon, photonic crystals, luminescent Si quantum dots, and finally luminescent Si NWs. All these sensors are investigated in terms of working principle, sensitivity, and selectivity with a specific focus on the possibility of their industrial transfer, and which ones may be preferred for a medical device.

Advances in Nanoparticle-based Delivery of Next Generation Peptide Nucleic Acids

BACKGROUND

Peptide nucleic acids (PNAs) belong to the next generation of synthetic nucleic acid analogues. Their high binding affinity and specificity towards the target DNA or RNA make them the reagent of choice for gene therapy-based applications.

OBJECTIVE

To review important gene therapy based applications of regular and chemically modified peptide nucleic acids in combination with nanotechnology.

METHOD

Selective research of the literature.

RESULTS

Poor intracellular delivery of PNAs has been a significant challenge. Among several delivery strategies explored till date, nanotechnology-based strategies hold immense potential. Recent studies have shown that advances in nanotechnology can be used to broaden the range of therapeutic applications of PNAs. In this review, we discussed significant advances made in nanoparticle-based on PLGA polymer, silicon, oxidized carbon and graphene oxide for the delivery of PNAs.

CONCLUSION

Nanoparticles delivered PNAs can be implied in diverse gene therapy based applications including gene editing as well as gene targeting (antisense) based strategies.

Photoluminescent and biodegradable porous silicon nanoparticles for biomedical imaging

A set of unique properties including biodegradability, intrinsic photoluminescence, and mesoporous structure allows porous silicon nanoparticles to address current challenges of translational nanomedicine, especially in biomedical imaging.

Nanostructured Electrochemical Biosensors for Label-Free Detection of Water- and Food-Borne Pathogens

The emergence of nanostructured materials has opened new horizons in the development of next generation biosensors. Being able to control the design of the electrode interface at the nanoscale combined with the intrinsic characteristics of the nanomaterials engenders novel biosensing platforms with improved capabilities. The purpose of this review is to provide a comprehensive and critical overview of the latest trends in emerging nanostructured electrochemical biosensors. A detailed description and discussion of recent approaches to construct label-free electrochemical nanostructured electrodes is given with special focus on pathogen detection for environmental monitoring and food safety. This includes the use of nanoscale materials such as nanotubes, nanowires, nanoparticles, and nanosheets as well as porous nanostructured materials including nanoporous anodic alumina, mesoporous silica, porous silicon, and polystyrene nanochannels. These platforms may pave the way toward the development of point-of-care portable electronic devices for applications ranging from environmental analysis to biomedical diagnostics.

In situ synthesis of peptide nucleic acids in porous silicon for drug delivery and biosensing

Peptide nucleic acids (PNA) are a unique class of synthetic molecules that have a peptide backbone and can hybridize with nucleic acids. Here, a versatile method has been developed for the automated, in situ synthesis of PNA from a porous silicon (PSi) substrate for applications in gene therapy and biosensing. Nondestructive optical measurements were performed to monitor single base additions of PNA initiated from (3-aminopropyl)triethoxysilane attached to the surface of PSi films, and mass spectrometry was conducted to verify synthesis of the desired sequence. Comparison of in situ synthesis to postsynthesis surface conjugation of the full PNA molecules showed that surface mediated, in situ PNA synthesis increased loading 8-fold. For therapeutic proof-of-concept, controlled PNA release from PSi films was characterized in phosphate buffered saline, and PSi nanoparticles fabricated from PSi films containing in situ grown PNA complementary to micro-RNA (miR) 122 generated significant anti-miR activity in a Huh7 psiCHECK-miR122 cell line. The applicability of this platform for biosensing was also demonstrated using optical measurements that indicated selective hybridization of complementary DNA target molecules to PNA synthesized in situ on PSi films. These collective data confirm that we have established a novel PNA–PSi platform with broad utility in drug delivery and biosensing.

Engineering multi-stage nanovectors for controlled degradation and tunable release kinetics

Nanovectors hold substantial promise in abating the off-target effects of therapeutics by providing a means to selectively accumulate payloads at the target lesion, resulting in an increase in the therapeutic index. A sophisticated understanding of the factors that govern the degradation and release dynamics of these nanovectors is imperative to achieve these ambitious goals. In this work, we elucidate the relationship that exists between variations in pore size and the impact on the degradation, loading, and release of multistage nanovectors. Larger pored vectors displayed faster degradation and higher loading of nanoparticles, while exhibiting the slowest release rate. The degradation of these particles was characterized to occur in a multi-step progression where they initially decreased in size leaving the porous core isolated, while the pores gradually increased in size. Empirical loading and release studies of nanoparticles along with diffusion modeling revealed that this prolonged release was modulated by the penetration within the porous core of the vectors regulated by their pore size.

Porous silicon-based nanostructured microparticles as degradable supports for solid-phase synthesis and release of oligonucleotides

We describe the preparation of several types of porous silicon (pSi) microparticles as supports for the solid-phase synthesis of oligonucleotides. The first of these supports facilitates oligonucleotide release from the nanostructured support during the oligonucleotide deprotection step, while the second type of support is able to withstand the cleavage and deprotection of the oligonucleotides post synthesis and subsequently dissolve at physiological conditions (pH = 7.4, 37°C), slowly releasing the oligonucleotides. Our approach involves the fabrication of pSi microparticles and their functionalisation via hydrosilylation reactions to generate a dimethoxytrityl-protected alcohol on the pSi surface as an initiation point for the synthesis of short oligonucleotides.

Application of peptide nucleic acid towards development of nanobiosensor arrays

Peptide nucleic acid (PNA) is the modified DNA or DNA analogue with a neutral peptide backbone instead of a negatively charged sugar phosphate. PNA exhibits chemical stability, resistant to enzymatic degradation inside living cell, recognizing specific sequences of nucleic acid, formation of stable hybrid complexes like PNA/DNA/PNA triplex, strand invasion, extraordinary thermal stability and ionic strength, and unique hybridization relative to nucleic acids. These unique physicobiochemical properties of PNA enable a new mode of detection, which is a faster and more reliable analytical process and finds applications in the molecular diagnostics and pharmaceutical fields. Besides, a variety of unique characteristic features, PNAs replace DNA as a probe for biomolecular tool in the molecular genetic diagnostics, cytogenetics, and various pharmaceutical potentials as well as for the development of sensors/arrays/chips and many more investigation purposes. This review paper discusses the various current aspects related with PNAs, making a new hot device in the commercial applications like nanobiosensor arrays.

Trapping and detection of single molecules in water

An innovative nanoprobe-based device that can measure and adjust the pH, can mimic biochemistry, can create microscale vortices in water, and can be used to trap single molecules is presented. Because the analytes in question to trap and detect are small in dimensions, we start by presenting scaling issues and challenging limitations for miniaturized chemical nanosensors. Advantages of using nanoprobes e.g., isolated nanowires, as the components in chemical sensing are discussed. How the observation of the physical property can beneficially change with isomorphic scaling is highlighted. Some of the technology-related constrains are presented for specific sensors. Solutions to overcome such problems are also given. Different aspects, e.g., sample size and sensitivity, for chemical sensing at the nanoscale are highlighted.

Mesoporous silicon in drug delivery applications

During the last few years, a number of interesting drug delivery applications of mesoporous materials have been demonstrated. Mesoporous silicon has many important properties advantageous to drug delivery applications. The small size of the pores confines the space of a drug and engages the effects of surface interactions of the drug molecules and the pore wall. The size of the pores and the surface chemistry of the pore walls may be easily changed and controlled. Depending on the size and the surface chemistry of the pores, increased or sustained release of the loaded drug can be obtained. Drug loading from a solution at room temperature enables the use of porous silicon (PSi) also with sensitive therapeutic compounds susceptible to degradation, like peptides and proteins. This article reviews the fabrication and chemical modifications of PSi for biomedical applications, and also the potential advantages of PSi in drug delivery.

Computer modeling in biotechnology: a partner in development

Computational modeling can be a useful partner in biotechnology, in particular, in nanodevice engineering. Such modeling guides development through nanoscale views of biomolecules and devices not available through experimental imaging methods. We illustrate the role of computational modeling, mainly of molecular dynamics, through four case studies: development of silicon bionanodevices for single molecule electrical recording, development of carbon nano-tube-biomolecular systems as in vivo sensors, development of lipoprotein nanodiscs for assays of single membrane proteins, and engineering of oxygen tolerance into the enzyme hydrogenase for photosynthetic hydrogen gas production. The four case studies show how molecular dynamics approaches were adapted to the specific technical uses through (i) multi-scale extensions, (ii) fast quantum chemical force field evaluation, (iii) coarse graining, and (iv) novel sampling methods. The adapted molecular dynamics simulations provided key information on device behavior and revealed development opportunities, arguing that the "computational microscope" is an indispensable nanoengineering tool.

Preliminary dielectric measurement and analysis protocol for determining the melting temperature and binding energy of short sequences of DNA in solution

Measurement of the real dielectric constant of bulk buffer solutions containing short sequences of DNA as a function of temperature through the DNA melting or denaturiztion transition can be used to determine melting temperatures, T(m), and to estimate the binding energy of the complimentary strands. We describe a preliminary dielectric measurement and analysis protocol to determine these parameters and its application to two known short sequences. The relative real dielectric constant for the bulk solutions was determined over the frequency range of 50 Hz-20 kHz and temperature range of <40-65 degrees C. The measurements were performed on dilute solutions and utilized low electric field strengths. Based on fits to the data by modified sigmoid functions, the melting temperatures, width of transition, and binding energy for the two sequences in solution were estimated. It was observed that the order of the transition appeared to be second order. The results were then compared against predictions of a number of models from the literature that provide theoretical estimates for the melting temperatures of known short sequences of DNA.

Kinetics of oligonucleotide hybridization to DNA probe arrays on high-capacity porous silica substrates

We have investigated the kinetics of DNA hybridization to oligonucleotide arrays on high-capacity porous silica films that were deposited by two techniques. Films created by spin coating pure colloidal silica suspensions onto a substrate had pores of approximately 23 nm, relatively low porosity (35%), and a surface area of 17 times flat glass (for a 0.3-microm film). In the second method, latex particles were codeposited with the silica by spin coating and then pyrolyzed, which resulted in larger pores (36 nm), higher porosity (65%), and higher surface area (26 times flat glass for a 0.3-microm film). As a result of these favorable properties, the templated silica hybridized more quickly and reached a higher adsorbed target density (11 vs. 8 times flat glass at 22 degrees C) than the pure silica. Adsorption of DNA onto the high-capacity films is controlled by traditional adsorption and desorption coefficients, as well as by morphology factors and transient binding interactions between the target and the probes. To describe these effects, we have developed a model based on the analogy to diffusion of a reactant in a porous catalyst. Adsorption values (k(a), k(d), and K) measured on planar arrays for the same probe/target system provide the parameters for the model and also provide an internally consistent comparison for the stability of the transient complexes. The interpretation of the model takes into account factors not previously considered for hybridization in three-dimensional films, including the potential effects of heterogeneous probe populations, partial probe/target complexes during diffusion, and non-1:1 binding structures. The transient complexes are much less stable than full duplexes (binding constants for full duplexes higher by three orders of magnitude or more), which may be a result of the unique probe density and distribution that is characteristic of the photolithographically patterned arrays. The behavior at 22 degrees C is described well by the predictive equations for morphology, whereas the behavior at 45 degrees C deviates from expectations and suggests that more complex phenomena may be occurring in that temperature regime.

Label-free quantitative detection of protein using macroporous silicon photonic bandgap biosensors

A label-free biosensor was demonstrated using macroporous silicon (pore size >100 nm) one-dimensional photonic band gap structures that are very sensitive to refractive index changes. In this study, we employed Tir-IBD (translocated Intimin receptor-Intimin binding domain) and Intimin-ECD (extracellular domain of Intimin) as the probe and target, respectively. These two recombinant proteins comprise the extracellular domains of two key proteins responsible for the pathogenicity of enteropathogenic Escherichia coli (EPEC). The optical response of the sensor was characterized so that the capture of Intimin-ECD could be quantitatively determined. Our result shows that the concentration sensitivity limit of the sensor is currently 4 microM of Intimin-ECD. This corresponds to a detection limit of approximately 130 fmol of Intimin-ECD. We have also investigated the dependence of the sensor performance on the Tir-IBD probe molecule concentration and the effect of immobilization on the Tir-IBD/Intimin-ECD equilibrium dissociation constant. A calibration curve generated from purified Intimin-ECD solutions was used to quantify the concentration of Intimin-ECD in an E. coli BL21 bacterial cell lysate, and results were validated using gel electrophoresis. This work demonstrates for the first time that a macroporous silicon microcavity sensor can be used to selectively and quantitatively detect a specific target protein with micromolar dissociation constant (Kd) in a milieu of bacterial proteins with minimal sample preparation.

High surface area silicon materials: fundamentals and new technology

Crystalline silicon forms the basis of just about all computing technologies on the planet, in the form of microelectronics. An enormous amount of research infrastructure and knowledge has been developed over the past half-century to construct complex functional microelectronic structures in silicon. As a result, it is highly probable that silicon will remain central to computing and related technologies as a platform for integration of, for instance, molecular electronics, sensing elements and micro- and nanoelectromechanical systems. Porous nanocrystalline silicon is a fascinating variant of the same single crystal silicon wafers used to make computer chips. Its synthesis, a straightforward electrochemical, chemical or photochemical etch, is compatible with existing silicon-based fabrication techniques. Porous silicon literally adds an entirely new dimension to the realm of silicon-based technologies as it has a complex, three-dimensional architecture made up of silicon nanoparticles, nanowires, and channel structures. The intrinsic material is photoluminescent at room temperature in the visible region due to quantum confinement effects, and thus provides an optical element to electronic applications. Our group has been developing new organic surface reactions on porous and nanocrystalline silicon to tailor it for a myriad of applications, including molecular electronics and sensing. Integration of organic and biological molecules with porous silicon is critical to harness the properties of this material. The construction and use of complex, hierarchical molecular synthetic strategies on porous silicon will be described.

Assessment of porous silicon substrate for well-characterised sensitive DNA chip implement

A biochip approach based on porous silicon as substrate is presented. The goal is to enhance the sensitivity of the biochip by increasing the specific surface area on the support. The elaboration of porous silicon layers has been optimized to guarantee good accessibility for large bio-molecule targets. Oligonucleotide probes are synthesised directly on the surface using phosphoramidite chemistry. The high specific surface area of porous silicon allows the direct characterisation, by infrared spectroscopy, of the porous layer formation and the functionalisation steps. The monolayer grafting and derivatisation protocol is additionally characterized by wettability and fluorescence microscopy. The surface modification of porous layers (i.e. thermal oxidation and chemical derivatisation) ensures the stability of the structure against strong chemical reagents used during the direct oligonucleotide synthesis. Finally the protocol is successfully transferred to a flat Si/SiO(2) substrate, and validated by biological target specific recognition during hybridisation tests. In particular, radioactive measurements show a 10-fold enhancement of the oligonucleotide surface density on the porous silicon substrate compared to the flat thermal silica.