DNA Biosensors and Microarrays

A simple label-free electrochemical DNA biosensor based on carbon nanotube–DNA interaction

A DNA biosensor based on π–π interactions between DNA and MWCNTs was developed in which the MWCNTs play the role of a conductive indicator.

Multiple detection of single nucleotide polymorphism by microarray-based resonance light scattering assay with enlarged gold nanoparticle probes

A gold nanoparticle enlargement assisted DNA microarray-based RLS assay has been developed for multiplexed detection of single nucleotide polymorphism with high sensitivity.

DNA Microarray-Based Diagnostics

The DNA microarray technology is currently a useful biomedical tool which has been developed for a variety of diagnostic applications. However, the development pathway has not been smooth and the technology has faced some challenges. The reliability of the microarray data and also the clinical utility of the results in the early days were criticized. These criticisms added to the severe competition from other techniques, such as next-generation sequencing (NGS), impacting the growth of microarray-based tests in the molecular diagnostic market.Thanks to the advances in the underlying technologies as well as the tremendous effort offered by the research community and commercial vendors, these challenges have mostly been addressed. Nowadays, the microarray platform has achieved sufficient standardization and method validation as well as efficient probe printing, liquid handling and signal visualization. Integration of various steps of the microarray assay into a harmonized and miniaturized handheld lab-on-a-chip (LOC) device has been a goal for the microarray community. In this respect, notable progress has been achieved in coupling the DNA microarray with the liquid manipulation microsystem as well as the supporting subsystem that will generate the stand-alone LOC device.In this chapter, we discuss the major challenges that microarray technology has faced in its almost two decades of development and also describe the solutions to overcome the challenges. In addition, we review the advancements of the technology, especially the progress toward developing the LOC devices for DNA diagnostic applications.

Solid phase synthesis of a thrombin binding aptamer on macroporous silica for label free optical quantification of thrombin

Human α-thrombin (TB) is a serine protease with a crucial role in coagulation and hemostasis.

Sequence selective naked-eye detection of DNA harnessing extension of oligonucleotide-modified nucleotides

DNA polymerases can efficiently and sequence selectively incorporate oligonucleotide (ODN)-modified nucleotides and the incorporated oligonucleotide strand can be employed as primer in rolling circle amplification (RCA). The effective amplification of the DNA primer by Φ29 DNA polymerase allows the sequence-selective hybridisation of the amplified strand with a G-quadruplex DNA sequence that has horse radish peroxidase-like activity. Based on these findings we develop a system that allows DNA detection with single-base resolution by naked eye.

Molecularly imprinted polymers for separating and sensing of macromolecular compounds and microorganisms

The present review article focuses on gathering, summarizing, and critically evaluating the results of the last decade on separating and sensing macromolecular compounds and microorganisms with the use of molecularly imprinted polymer (MIP) synthetic receptors. Macromolecules play an important role in biology and are termed that way to contrast them from micromolecules. The former are large and complex molecules with relatively high molecular weights. The article mainly considers chemical sensing of deoxyribonucleic acids (DNAs), proteins and protein fragments as well as sugars and oligosaccharides. Moreover, it briefly discusses fabrication of chemosensors for determination of bacteria and viruses that can ultimately be considered as extremely large macromolecules.

Controlled DNA Patterning by Chemical Lift-Off Lithography: Matrix Matters

Nucleotide arrays require controlled surface densities and minimal nucleotide-substrate interactions to enable highly specific and efficient recognition by corresponding targets. We investigated chemical lift-off lithography with hydroxyl- and oligo(ethylene glycol)-terminated alkanethiol self-assembled monolayers as a means to produce substrates optimized for tethered DNA insertion into post-lift-off regions. Residual alkanethiols in the patterned regions after lift-off lithography enabled the formation of patterned DNA monolayers that favored hybridization with target DNA. Nucleotide densities were tunable by altering surface chemistries and alkanethiol ratios prior to lift-off. Lithography-induced conformational changes in oligo(ethylene glycol)-terminated monolayers hindered nucleotide insertion but could be used to advantage via mixed monolayers or double-lift-off lithography. Compared to thiolated DNA self-assembly alone or with alkanethiol backfilling, preparation of functional nucleotide arrays by chemical lift-off lithography enables superior hybridization efficiency and tunability.

Sequence specific recognition of ssDNA by fluorophore 3-hydroxyflavone

A fully water soluble 3-hydroxyflavone (3HF) derivative, N-(3-hydroxy-4'-flavonyl)-N,N,N-trimethylammonium sulfate (3HFNMe3) was synthesized. Investigation of its emissions at varying wavelengths revealed that it had three emission bands of normal (N(⁎)), anionic (A(⁎)) and tautomeric (T(⁎)), in ultrapure water. Recognition of single-stranded ten ssDNA chains, having different nucleotide sequences was studied, using the ratiometric change of the intensities of the two bands (A(⁎)/T(⁎)), depending upon the varying environment of the 3HFNMe3 with different ssDNA chains. Addition of the ssDNA chains to the 3HFNMe3 solution caused gradual quenching of the A(⁎) band and had almost no effect on the T(⁎) band. As the ratios of the two bands (A(⁎)/T(⁎)) vs increasing amount of the ssDNAs generated characteristic curves for each ssDNA chain, it became possible to identify the chains with their characteristic curves.

Light-Directed Synthesis of High-Density Peptide Nucleic Acid Microarrays

Peptide nucleic acids (PNAs) are a class of nucleic acid mimics that can bind to the complementary DNA or RNA with high specificity and sensitivity. PNA-based microarrays have distinct characteristics and have improved performance in many aspects compared to DNA microarrays. A new set of PNA monomers has been synthesized and used as the building blocks for the preparation of high density PNA microarrays. These monomers have their backbones protected by the photolabile group 2-(2-nitrophenyl)propyloxy carbonyl (NPPOC), and their exocyclic amino groups protected by amide carbonyl groups. A light-directed synthesis system was designed and applied to the in situ synthesis of a PNA microarray with a density of over 10,000 probes per square centimeter. This PNA microarray was able to detect single and multiple base-mismatches correctly with a high discrimination ratio.

Label-free, zeptomole cancer biomarker detection by surface-enhanced fluorescence on nanoporous gold disk plasmonic nanoparticles

We experimentally demonstrate a label-free biosensor for the ERBB2 cancer gene DNA target based on the distance-dependent detection of surface-enhanced fluorescence (SEF) on nanoporous gold disk (NPGD) plasmonic nanoparticles. We achieve detection of 2.4 zeptomole of DNA target on the NPGD substrate with an upper concentration detection limit of 1 nM. Without the use of molecular spacers, the NPGD substrate as an SEF platform was shown to provide higher net fluorescence for visible and NIR fluorophores compared to glass and non-porous gold substrates. The enhanced fluorescence signals in patterned nanoporous gold nanoparticles make NPGD a viable material for further reducing detection limits for biomolecular targets used in clinical assays. With patterned nanoporous gold disk (NPGD) plasmonic nanoparticles, a label-free biosensor that makes use of distance-dependent detection of surface-enhanced fluorescence (SEF) is constructed and tested for zeptomole detection of ERBB2 cancer gene DNA targets.

Preparation and Characterization of Biofunctionalized Inorganic Substrates

Integrating the function of biological molecules into traditional inorganic materials and substrates couples biologically relevant function to synthetic devices and generates new materials and capabilities by combining biological and inorganic functions. At this so-called "bio/abio interface," basic biological functions such as ligand binding and catalysis can be co-opted to detect analytes with exceptional sensitivity or to generate useful molecules with chiral specificity under entirely benign reaction conditions. Proteins function in dynamic, complex, and crowded environments (the living cell) and are therefore appropriate for integrating into multistep, multiscale, multimaterial devices such as integrated circuits and heterogeneous catalysts. However, the goal of reproducing the highly specific activities of biomolecules in the perturbed chemical and electrostatic environment at an inorganic interface while maintaining their native conformations is challenging to achieve. Moreover, characterizing protein structure and function at a surface is often difficult, particularly if one wishes to compare the activity of the protein to that of the dilute, aqueous solution phase. Our laboratory has developed a general strategy to address this challenge by taking advantage of the structural and chemical properties of alkanethiol self-assembled monolayers (SAMs) on gold surfaces that are functionalized with covalently tethered peptides. These surface-bound peptides then act as the chemical recognition element for a target protein, generating a biomimetic surface in which protein orientation, structure, density, and function are controlled and variable. Herein we discuss current research and future directions related to generating a chemically tunable biofunctionalization strategy that has potential to successfully incorporate the highly specialized functions of proteins onto inorganic substrates.

A nanostructured genosensor for the early diagnosis of systemic arterial hypertension

The rapid progress of nanomedicine, especially in areas related to medical imaging and diagnostics, has motivated the development of new nanomaterials that can be combined with biological materials for specific medical applications. One such area of research involves the detection of specific DNA sequences for the early diagnosis of genetic diseases, using nanoparticles-containing genosensors. Typical genosensors devices are based on the use of sensing electrodes - biorecognition platforms - containing immobilized capture DNA probes capable of hybridizing with specific target DNA sequences. In this paper we show that upon an appropriate design of the biorecognition platform, efficient sandwich-type genosensors based upon DNA-AuNPs nanocomplexes can be efficiently applied to the detection of a Systemic Arterial Hypertension (SAH) polymorphism located in intron 16 of the Angiotensin-converter enzyme (ACE) gene. Since SAH is intimately related to heart diseases, especially blood hypertension, its early detection is of great biomedical interest. The biorecognition platforms were assembled using mixed self-assembled monolayers (SAMmix), which provided the immobilization of organized architectures with molecular control. Detection of the DNA target sequence at concentrations down to 1 nM was carried out using electrochemical impedance spectroscopy (EIS). We show that the use of EIS combined with specific nanobiocomplexes represents an efficient method for the unambiguous detection of complementary DNA hybridization for preventative nanomedicine applications.

DNA Immobilization and Hybridization Detection by the Intrinsic Molecular Charge Using Capacitive Field-Effect Sensors Modified with a Charged Weak Polyelectrolyte Layer

Miniaturized setup, compatibility with advanced micro- and nanotechnologies, and ability to detect biomolecules by their intrinsic molecular charge favor the semiconductor field-effect platform as one of the most attractive approaches for the development of label-free DNA chips. In this work, a capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensor covered with a layer-by-layer prepared, positively charged weak polyelectrolyte layer of PAH (poly(allylamine hydrochloride)) was used for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization. The negatively charged probe single-stranded DNA (ssDNA) molecules were electrostatically adsorbed onto the positively charged PAH layer, resulting in a preferentially flat orientation of the ssDNA molecules within the Debye length, thus yielding a reduced charge-screening effect and a higher sensor signal. Each sensor-surface modification step (PAH adsorption, probe ssDNA immobilization, hybridization with complementary target DNA (cDNA), reducing an unspecific adsorption by a blocking agent, incubation with noncomplementary DNA (ncDNA) solution) was monitored by means of capacitance-voltage and constant-capacitance measurements. In addition, the surface morphology of the PAH layer was studied by atomic force microscopy and contact-angle measurements. High hybridization signals of 34 and 43 mV were recorded in low-ionic strength solutions of 10 and 1 mM, respectively. In contrast, a small signal of 4 mV was recorded in the case of unspecific adsorption of fully mismatched ncDNA. The density of probe ssDNA and dsDNA molecules as well as the hybridization efficiency was estimated using the experimentally measured DNA immobilization and hybridization signals and a simplified double-layer capacitor model. The results of field-effect experiments were supported by fluorescence measurements, verifying the DNA-immobilization and hybridization event.

Mechanisms, Capabilities, and Applications of High-Resolution Electrohydrodynamic Jet Printing

This review gives an overview of techniques used for high-resolution jet printing that rely on electrohydrodynamically induced flows. Such methods enable the direct, additive patterning of materials with a resolution that can extend below 100 nm to provide unique opportunities not only in scientific studies but also in a range of applications that includes printed electronics, tissue engineering, and photonic and plasmonic devices. Following a brief historical perspective, this review presents descriptions of the underlying processes involved in the formation of liquid cones and jets to establish critical factors in the printing process. Different printing systems that share similar principles are then described, along with key advances that have been made in the last decade. Capabilities in terms of printable materials and levels of resolution are reviewed, with a strong emphasis on areas of potential application.

Electrochemical Label-Free Nucleotide Sensors

Numerous researchers have devoted a great deal of effort over the last few decades to the development of electrochemical oligonucleotide detection techniques, owing to their advantages of simple design, inherently small dimensions, and low power requirements. Their simplicity and rapidity of detection makes label-free oligonucleotide sensors of great potential use as first-aid screening tools in the analytical field of environmental measurements and healthcare management. This review article covers label-free oligonucleotide sensors, focusing specifically on topical electrochemical techniques, including intrinsic redox reaction of bases, conductive polymers, the use of electrochemical indicators, and highly ordered probe structures.

Site-directed, on-surface assembly of DNA nanostructures

Two-dimensional DNA lattices have been assembled from DNA double-crossover (DX) motifs on DNA-encoded surfaces in a site-specific manner. The lattices contained two types of single-stranded protruding arms pointing into opposite directions of the plane. One type of these protruding arms served to anchor the DNA lattice on the solid support through specific hybridization with surface-bound, complementary capture oligomers. The other type of arms allowed for further attachment of DNA-tethered probe molecules on the opposite side of the lattices exposed to the solution. Site-specific lattice assembly and attachment of fluorophore-labeled oligonucleotides and DNA-protein conjugates was demonstrated using DNA microarrays on flat, transparent mica substrates. Owing to their programmable orientation and addressability over a broad dynamic range from the nanometer to the millimeter length scale, such supramolecular architecture might be used for presenting biomolecules on surfaces, for instance, in biosensor applications.

Focused upon hybridization: rapid and high sensitivity detection of DNA using isotachophoresis and peptide nucleic acid probes

We present a novel assay for rapid and high sensitivity detection of nucleic acids without amplification. Utilizing the neutral backbone of peptide nucleic acids (PNA), our method is based on the design of low electrophoretic mobility PNA probes, which do not focus under isotachophoresis (ITP) unless bound to their target sequence. Thus, background noise associated with free probes is entirely eliminated, significantly improving the signal-to-noise ratio while maintaining a simple single-step assay requiring no amplification steps. We provide a detailed analytical model and experimentally demonstrate the ability to detect targets as short as 17 nucleotides (nt) and a limit of detection of 100 fM with a dynamic range of 5 decades. We also demonstrate that the assay can be successfully implemented for detection of DNA in human serum without loss of signal. The assay requires 15 min to complete, and it could potentially be used in applications where rapid and highly sensitive amplification-free detection of nucleic acids is desired.

Affinity biosensors for tumor-marker analysis

The use of cancer biomarkers is emerging as one of the most promising strategies for early detection and management of cancer. Biosensors can provide advanced platforms for biomarker analysis with the advantages of being easy to use, inexpensive, rapid and offering multi-analyte testing capability. The intention of this article is to discuss recent advances and trends in affinity biosensors for cancer diagnosis, prognosis and even theragnosis. The different types of affinity biosensors will be reviewed in terms of molecular recognition element. Current challenges and trends for this technology will be also discussed, with a particular emphasis on recent developments in miRNA detection.

Microelectrode miRNA sensors enabled by enzymeless electrochemical signal amplification

Better detections of circulating microRNAs (miRNAs) as disease biomarkers could advance diseases diagnosis and treatment. Current analysis methods or sensors for research and applications are challenged by the low concentrations and wide dynamic range (from aM to nM) of miRNAs in a physiological sample. Here, we report a one-step label-free electrochemical sensor comprising a triple-stem DNA-redox probe structure on a gold microelectrode. A new signal amplification mechanism without the need of a redox enzyme is introduced. The novel strategy overcomes the fundamental limitations of microelectrode DNA sensors that fail to generate detectable current, which is primarily due to the limited amount of redox probes in response to the target analyte binding. By employing a reductant, tris(2-carboxyethyl) phosphine hydrochloride (TCEP) in the detection buffer solution, each redox molecule on the detection probe is cyclically oxidized at the electrode and reduced by the reductant; thus, the signal is amplified in situ during the detection period. The combined merits in the diagnosis power of cyclic voltammetry and the high sensitivity of pulse voltammetry enable parallel analysis for method validation and optimization previously inaccessible. As such, the detection limit of miRNA-122 was 0.1 fM via direct readout, with a wide detection range from sub fM to nM. The detection time is within minutes, which is a significant improvement over other macroscopic sensors and other relevant techniques such as quantitative reverse transcription polymerase chain reaction (qRT-PCR). The high selectivity of the developed sensors is demonstrated by the discrimination against two most similar family sequences: miR-122-3p present in serum and 2-mismatch synthetic RNA sequence. Interference such as nonspecific adsorption, a common concern in sensor development, is reduced to a negligible amount by adopting a multistep surface modification strategy. Importantly, unlike qRT-PCR, the microelectrochemical sensor offers direct absolute quantitative readout that is amenable to clinical and in-home point-of-care (POC) applications. The sensor design is flexible, capable of being tailored for detection of different miRNAs of interest. Combined with the fact that the sensor was constructed at microscale, the method can be generalized for high throughput detection of miRNA signatures as disease biomarkers.

Chemical and Physical Characteristics of Doxorubicin Hydrochloride Drug-Doped Salmon DNA Thin Films

Double-stranded salmon DNA (SDNA) was doped with doxorubicin hydrochloride drug molecules (DOX) to determine the binding between DOX and SDNA, and DOX optimum doping concentration in SDNA. SDNA thin films were prepared with various concentrations of DOX by drop-casting on oxygen plasma treated glass and quartz substrates. Fourier transform infrared (FTIR) spectroscopy was employed to investigate the binding sites for DOX in SDNA, and electrical and photoluminescence (PL) analyses were used to determine the optimum doping concentration of DOX. The FTIR spectra showed that up to a concentration of 30 μM of DOX, there was a tendency for binding with a periodic orientation via intercalation between nucleosides. The current and PL intensity increased as the DOX concentration increased up to 30 μM, and then as the concentration of DOX further increased, we observed a decrease in current as well as PL quenching. Finally, the optical band gap and second band onset of the transmittance spectra were analyzed to further verify the DOX binding and optimum doping concentration into SDNA thin films as a function of the DOX concentration.

Bridging Adhesion of a Protein onto an Inorganic Surface Using Self-Assembled Dual-Functionalized Spheres

For the bridging adhesion of different classes of materials in their intact functional states, the adhesion of biomolecules onto inorganic surfaces is a necessity. A new molecular design strategy for bridging adhesion was demonstrated by the introduction of two independent recognition groups on the periphery of spherical complexes self-assembled from metal ions (M) and bidentate ligands (L). These dual-functionalized M12L24 spheres were quantitatively synthesized in one step from two ligands, bearing either a biotin for streptavidin recognition or a titania-binding aptamer, and Pd(II) ions. The selective recognition of titania surfaces was achieved by ligands with hexapeptide aptamers (Arg-Lys-Leu-Pro-Asp-Ala: minTBP-1), whose fixation ability was enhanced by the accumulation effect on the surface of the M12L24 spheres. These well-defined spherical structures can be specifically tailored to promote interactions with both titania and streptavidin simultaneously without detrimentally affecting either recognition motif. The irreversible immobilization of the spheres onto titania was revealed quantitatively by quartz crystal microbalance measurements, and the adhesion of streptavidin to the titania surface mediated by the biotin surrounding the spheres was visually demonstrated by lithographic patterning experiments.

Iridium(III) Luminescent Probe for Detection of the Malarial Protein Biomarker Histidine Rich Protein-II

This work outlines the synthesis of a non-emissive, cyclometalated Ir(III) complex, Ir(ppy)2(H2O)2(+) (Ir1), which elicits a rapid, long-lived phosphorescent signal when coordinated to a histidine-containing protein immobilized on the surface of a magnetic particle. Synthesis of Ir1, in high yields,is complete O/N and involves splitting of the parent cyclometalated Ir(III) chloro-bridged dimer into two equivalents of the solvated complex. To confirm specificity, several amino acids were probed for coordination activity when added to the synthesized probe, and only histidine elicited a signal response. Using BNT-II, a branched peptide mimic of the malarial biomarker Histidine Rich Protein II (pfHRP-II), the iridium probe was validated as a tool for HRP-II detection. Quenching effects were noted in the BNT-II/Ir1 titration when compared to L-Histidine/Ir1, but these were attributed to steric hindrance and triplet state quenching. Biolayer interferometry was used to determine real-time kinetics of interaction of Ir1 with BNT-II. Once the system was optimized, the limit of detection of rcHRP-II using the probe was found to be 12.8 nM in solution. When this protein was immobilized on the surface of a 50 µm magnetic agarose particle, the limit of detection was 14.5 nM. The robust signal response of this inorganic probe, as well as its flexibility of use in solution or immobilized on a surface, can lend itself toward a variety of applications, from diagnostic use to imaging.

Nucleic Acid Aptamers: An Emerging Tool for Biotechnology and Biomedical Sensing

Detection of small molecules or proteins of living cells provides an exceptional opportunity to study genetic variations and functions, cellular behaviors, and various diseases including cancer and microbial infections. Our aim in this review is to give an overview of selected research activities related to nucleic acid-based aptamer techniques that have been reported in the past two decades. Limitations of aptamers and possible approaches to overcome these limitations are also discussed.

Biomolecular Crowding Arising from Small Molecules, Molecular Constraints, Surface Packing, and Nano-Confinement

The effect of macromolecular crowding on the structure, dynamics, and reactivity of biomolecules is well established and the relevant research has been extensively reviewed. Herein, we focus our discussion on crowding effects arising from small cosolvent molecules and densely packed surface conditions. In addition, we highlight recent efforts that capitalize on the excluded volume effect for various tailored biochemical and biophysical applications. Specifically, we discuss how a targeted increase in local mass density can be exploited to gain insight into the folding dynamics of the protein of interest and how confinement via reverse micelles can be used to study a range of biophysical questions, from protein hydration dynamics to amyloid formation.

DNA-Based Nanobiosensors as an Emerging Platform for Detection of Disease

Detection of disease at an early stage is one of the biggest challenges in medicine. Different disciplines of science are working together in this regard. The goal of nanodiagnostics is to provide more accurate tools for earlier diagnosis, to reduce cost and to simplify healthcare delivery of effective and personalized medicine, especially with regard to chronic diseases (e.g., diabetes and cardiovascular diseases) that have high healthcare costs. Up-to-date results suggest that DNA-based nanobiosensors could be used effectively to provide simple, fast, cost-effective, sensitive and specific detection of some genetic, cancer, and infectious diseases. In addition, they could potentially be used as a platform to detect immunodeficiency, and neurological and other diseases. This review examines different types of DNA-based nanobiosensors, the basic principles upon which they are based and their advantages and potential in diagnosis of acute and chronic diseases. We discuss recent trends and applications of new strategies for DNA-based nanobiosensors, and emphasize the challenges in translating basic research to the clinical laboratory.

Quaternized chitosan particles as ion exchange supports for label-free DNA detection using PNA probe and MALDI-TOF mass spectrometry

Quaternized chitosan particles are introduced as anion-exchanged captures to be used with a conformationally constrained pyrrolidinyl peptide nucleic acid (acpcPNA) and MALDI-TOF mass spectrometry for DNA sequence analysis. Methylated chitosan (MC) and methylated N-benzyl chitosan (MBzC) particles were obtained by heterogeneous chemical modification of ionically cross-linked chitosan particles via direct methylation and reductive benzylation/methylation, respectively. N,N,N-trimethylchitosan (TMC) and N-[(2-hydroxyl-3-trimethylammonium)propyl]chitosan chloride (HTACC) particles were prepared by ionic cross-linking of quaternized chitosan derivatives, homogeneously modified from chitosan, namely TMC and HTACC, respectively. The particles formed had a size in a sub-micrometer range and possessed positive charge. Investigation by MALDI-TOF mass spectrometry suggested that some quaternized particles in combination with acpcPNA were capable of detecting a single mismatched base out of 9-14 base DNA sequences. Potential application of this technique for the detection of wild-type and mutant K-ras DNA, a gene that mutation is associated with certain cancers, has also been demonstrated.

Electrochemistry, biosensors and microfluidics: a convergence of fields

Electrochemistry, biosensors and microfluidics are popular research topics that have attracted widespread attention from chemists, biologists, physicists, and engineers. Here, we introduce the basic concepts and recent histories of electrochemistry, biosensors, and microfluidics, and describe how they are combining to form new application-areas, including so-called "point-of-care" systems in which measurements traditionally performed in a laboratory are moved into the field. We propose that this review can serve both as a useful starting-point for researchers who are new to these topics, as well as being a compendium of the current state-of-the art for experts in these evolving areas.