Deoxyribonucleic Acid Hybridization Research Articles

DNA hybridization detection in a miniaturized electromagnetic band gap resonator

The hybridization of the deoxyribonucleic acid (DNA) is sensed in a miniaturized electromagnetic band gap resonator, which has a resonance frequency f0=17.3 GHz when unloaded. The resonance frequency f0 is shifted to the left when a single-stranded DNA is immobilized on the resonator and to the right for an immobilized double-stranded DNA. The shifted frequencies of the two states of the DNA are separated by a span of 1 GHz in the band 16-20 GHz and are explained by different effective electrical permittivity values of single- and double-stranded DNA molecules.

Effect of Surface Binding on Heterogeneous DNA Melting Equilibria: A Monte Carlo Simulation Study

Deoxyribonucleic acid (DNA) microarrays are constructed with a surface-immobilized single-stranded probe sequence that hydrogen bonds with its complementary target strand from solution and is subsequently detected, making their hybridization equilibrium of central importance. Unexpectedly, the effect of surface immobilization is that if the sequences of probe and target are exchanged, the hybridization equilibrium shifts. Here, configurational-bias Monte Carlo simulations using a coarse-grained model for DNA were carried out for an undecamer double helix both in solution and bound to a surface to determine dissociation equilibria. Four possible surface binding orientations were independently investigated. Analysis shows that the effect of surface binding is to destabilize hydrogen-bonding interactions of bases proximal to the binding site and enhance those of distal bases due to the double helix lying flat on the surface. Results have implications for predicting surface-bound DNA hybridization equilibria.

Tongue Piercing: The Effect of Material on Microbiological Findings

Biofilms on oral piercings may serve as a bacterial reservoir and lead to systemic bacteremia or local transmission of pathogenic microbiota. The use of piercing materials which are less susceptible to biofilm accumulation could contribute to prevention of problems. The present study investigated whether there are microbiological differences in bacterial samples collected from tongue piercings made of different materials. A total of 85 subjects with tongue piercings participated in this study. After a baseline dental examination, sterile piercings of four different materials were randomly allocated to the study subjects. After 2 weeks, microbiologic samples were collected and processed by checkerboard deoxyribonucleic acid- deoxyribonucleic acid hybridization methods. About 28.8% of subjects reported 61 lingual recessions (1.91 ± .96 mm), whereas 5% reported tooth chipping on one tooth each. With the exception of Aggregatibacter actinomycetemcomitans (Y4), Fusobacterium nucleatum species, and Parvimonas micra, bacteria associated with periodontitis were not commonly found in the samples from studs or piercing channels. Of the 80 bacterial species, 67 were found at significantly higher levels (p < .001) in samples from stainless steel than from polytetrafluoroethylene or polypropylene piercings. The low bacterial counts from piercing channels suggest that having a tongue pierced would not contribute to an increased risk for oral infection. The present study demonstrated that studs made of steel might promote the development of a biofilm, whereas those made of polytetrafluoroethylene or polypropylene may be rather inert to bacterial colonization. The finding of Staphylococci on steel and titanium studs may suggest an elevated risk for complication if the piercing channel is infected.

An array of field-effect nanoplate SOI capacitors for (bio-)chemical sensing

An array of individually addressable nanoplate field-effect capacitive (bio-)chemical sensors based on an SOI (silicon-on-insulator) structure has been developed. The isolation of the individual capacitors was achieved by forming a trench in the top Si layer with a thickness of 350nm. The realized sensor array allows addressable biasing and electrical readout of multiple nanoplate EISOI (electrolyte–insulator–silicon-on-insulator) capacitive biosensors on the same SOI chip as well as differential-mode measurements. The feasibility of the proposed approach has been demonstrated by realizing sensors for the pH and penicillin concentration detection as well as for the label-free electrical monitoring of polyelectrolyte multilayers formation and DNA (deoxyribonucleic acid)-hybridization event. A potential change of ∼120mV has been registered after the DNA hybridization for the sensor immobilized with perfectly matched single-strand DNA, while practically no signal changes have been observed for a sensor with fully mismatched DNA. The realized examples demonstrate the potential of the nanoplate SOI capacitors as a new basic structural element for the development of different types of field-effect biosensors.

Characterization of poly(vinylferrocenium) coated surfaces and their applications in DNA sensor technology

Poly(vinylferrocenium) (PVF+) modified gold (Au) electrode was developed in this study for the electrochemical sensing of deoxyribonucleic acid (DNA) hybridization based on the oxidation signals of polymer and guanine, and also for the electrochemical investigation of interaction of anticancer drug, mitomycin C (MC) and DNA immobilized onto PVF+ modified Au electrode. PVF+ modified Au electrode was prepared by electrooxidation of poly(vinylferrocene) PVF at +0.7 V versus Ag/AgCl reference electrode. The polymer modified electrode and DNA immobilized polymer modified electrode were characterized by X-ray photoelectron (XPS), Fourier transform infrared-attenuated total reflentance (FTIR-ATR) and alternating current (AC) impedance spectroscopy. For application studies, differential pulse voltammetry (DPV) technique was used.

Kinetics of DNA and RNA Hybridization in Serum and Serum-SDS

Cancer is recognized as a serious health challenge both in the United States and throughout the world. While early detection and diagnosis of cancer leads to decreased mortality rates, current screening methods require significant time and costly equipment. Recently, increased levels of certain micro-ribonucleic acids (miRNAs) in the blood have been linked to the presence of cancer. While blood-based biomarkers have been used for years in cancer detection, studies analyzing trace amounts of miRNAs in blood and serum samples are just beginning. Recent developments in deoxyribonucleic acid (DNA) nanotechnology and DNA computing have shown that it is possible to construct nucleic-acid-based chemical networks that accept miRNAs as inputs, perform Boolean logic functions on those inputs, and generate as an output a large number of DNA strands that can readily be detected. Since miRNAs occur in blood in low abundance, these networks would allow for amplification without using polymerase chain reaction. In this study, we report initial progress in the development of a DNA-based cross-catalytic network engineered to amplify specific cancer-related miRNAs. Subcomponents of the DNA network were tested individually, and their operation in serum, as well as a mixture of serum with sodium dodecyl sulfate, is demonstrated. Preliminary simulations of the full cross-catalytic network indicate successful operation.

DNA hybridization on silicon nanowires

Nanowire-based detection strategies provide promising new routes to bioanalysis and indeed are attractive to conventional systems because of their small size, high surface-to-volume ratios, electronic, and optical properties. A sequence-specific detection of single-stranded oligonucleotides using silicon nanowires (SiNWs) is demonstrated. The surface of the SiNWs is functionalized with densely packed organic monolayer via hydrosilylation for covalent attachment. Subsequently, deoxyribonucleic acid (DNA) is immobilized to recognize the complementary target DNA. The biomolecular recognition properties of the nanowires are tested via hybridization with γP 32 tagged complementary and non-complementary DNA oligonucleotides, showing good selectivity and reversibility. No significant non-specific binding to the incorrect sequences is observed. X-ray photoelectron spectroscopy, fluorescence imaging, and nanodrop techniques are used to characterize the modified SiNWs and covalent attachment with DNA. The results show that SiNWs are excellent substrates for the absorption, stabilization and detection of DNA sequences and could be used for DNA microarrays and micro fabricated SiNWs DNA sensors.

Electrochemical Deoxyribonucleic Acid Biosensor Based on Multiwalled Carbon Nanotubes/Ag-TiO2 Composite Film for Label-Free Phosphinothricin Acetyltransferase Gene Detection by Electrochemical Impedance Spectroscopy

Abstract A highly sensitive electrochemical deoxyribonucleic acid (DNA) biosensor based on multiwalled carbon nanotubes (MWNT)/Ag-TiO2 composite film was developed. The solution containing Ag-TiO2-MWNT composite was cast on the carbon paste electrode surface to form a robust film, which combined the advantages of the good biocompatibility of Ag-TiO2 composite and the fine conductivity, as well as the large active surface area of carbon nanotubes. The composite could greatly improve the immobilization capacity of the probe DNA. The morphologies and electrochemistry of the nanocomposite film were investigated by scanning electron microscopy and electrochemical techniques including electrochemical impedance spectroscopy and cyclic voltammetry, respectively. DNA hybridization events were monitored by a label-free method of electrochemical impedance spectroscopy. This label-free electrochemical impedance DNA biosensor showed high sensitivity and selectivity for phosphinothricin acetyltransferase gene sequence assay. The multicomponents films also displayed a high stability during repeated regeneration and hybridization process.

On the Modeling of New Tunnel Junction Magnetoresistive Biosensors

A fully integrated biochip based on a 16 × 16 scalable matrix structure of aluminum oxide magnetic tunnel junctions (MTJs) and thin-film diodes (TFDs of hydrogenated amorphous silicon) was fabricated and included as the biosensor of a portable handheld microsystem developed for biomolecular recognition detection using magnetic labels [deoxyribonucleic acid (DNA) hybridization, antibody antigen interaction, etc.]. The system uses magnetic field arraying of magnetically tagged biomolecules and can potentially be used to detect single or few biomolecules. Each biosensor matrix node is the series between a TFD (p-i-n or Schottky-barrier type) and an MTJ. In this paper, this matrix basic cell biosensor element is completely characterized and modeled. Experimental measured data are provided and compared with the proposed theoretical models results. It is shown that the diode may be used both as the matrix switching device and as an in-site temperature sensor and that the MTJ may act as the magnetoresistive sensor for detecting the fringe field of immobilized magnetic markers. Therefore, the fabricated fully integrated biochip included in the developed handheld microsystem may be used for biomolecular recognition.

Optically Characterized DNA Multilayered Assemblies and Phenomenological Modeling of Layer-by-Layer Hybridization

Layer-by-layer assemblies based on deoxyribonucleic acid (DNA) hybridization have potential for various bio- and nanotechnology applications because of their programmability, biodegradability, and ability to control the structure of the assemblies on the nanometer scale. Herein, we investigate the growth and salt stability of DNA films by the optical technique dual polarization interferometry and numerically model the film buildup. The DNA films were assembled by sequentially depositing pairs of oligonucleotides comprised of two different block sequences onto the surface. The oligonucleotides used in the assembly of the different films were as follows: a homopolymeric diblock pair of AxGx/TxCx (x = 15, 20, or 30), a homopolymeric diblock pair of A15G15/C15T15 in which the orientation of the T15C15 diblock was reversed (C15T15), and a random diblock pair of X15Y15/X′15Y′15. The characteristics of the layer growth were highly dependent on the type of the oligonucleotide pair used: the mass of DNA deposited followed a linear, stepwise, or saturated growth with increasing layer deposition. The layer growth of each film was numerically modeled by taking into account the effective hybridization rate and the effective dissociation rate of the oligonucleotides. The proposed modeling offers a framework for molecularly designing oligonucleotide pairs to obtain DNA multilayer films with desired physicochemical properties (thickness, density, stability).

Bioelectrochemical Sensing Based on Single Stranded Deoxyribonucleic Acid-Carbon Nanotubes Covalently Attached on Gold Electrodes

A biosensor based on single-stranded deoxyribonucleic acid-functionalized carbon nanotubes covalently attached to a self-assembled monolayer of 11-amino-1-undecanethiol on gold has been prepared. The preparation of the deoxyribonucleic acid sensor was followed using cyclic voltammetry. Single-walled carbon nanotubes, covalently attached to the gold surface present a nanoelectrode array behavior. To confirm the hybridization step between the probe and the target deoxyribonucleic acid, we used methylene blue, which is an indicator capable of distinguishing between single-stranded deoxyribonucleic acid and double-stranded deoxyribonucleic acid. Our results demonstrate that the modification of gold with single-walled carbon nanotubes and single-stranded deoxyribonucleic acid can be used for deoxyribonucleic acid hybridization detection.

Detection of DNA Hybridization using Functionalized InN ISFETs

AbstractUltrathin (∼10 nm) InN ion sensitive field effect transistors (ISFETs) are functionalized by immobilized label-free oligonucleotide probes with 3-mercaptopropyltrimethoxysilane (MPTMS) through molecular vapor deposition (MVD) technique. This layer on the InN surface serves the function of selectively detecting the hybridization of complementary deoxyribonucleic acid (DNA). Using MVD technique to perform the gas-phase silanization of MPTMS provided a time-saving and simple method to reach 68° water contact angle after 1.5 h treatment. High resolution X-ray photoelectron spectroscopy (HRXPS) was employed to analyze the surface characteristics after functionalization. Modified probes DNA were covalently bonded to MPTMS-covered gate surface of InN ISFETs. And further hybridized with complementary DNA For a 12-mer oligonucleotide probe, a significant drain-source current decrease (∼ 6 μA) was observed for the hybridization with complementary DNA solution of 100 nM. In contrast, the noncomplementary DNA with single-base mismatch did not show obvious current changes. Functionalized ultrathin InN ISFETs for DNA sequence detection demonstrate the promise of biological sensing and genetic diagnosis applications.

Arabidopsis cyclin D2 expressed in rice forms a functional cyclin-dependent kinase complex that enhances seedling growth

D-class cyclins play important roles in controlling the cell cycle in development and in response to external signals by forming the regulatory subunit of cyclin-dependent kinase (CDK) complexes. To evaluate the effects of D-class cyclins in transgenic rice plants, Arabidopsis cyclin D2 gene (CycD2) was linked to the maize ubiquitin1 promoter (Ubi1) and introduced into rice by the Agrobacterium-mediated transformation method. Genomic deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and Western blot hybridizations of the Ubi1:CycD2 plants revealed copy number of transgene and its increased expression in leaf and callus cells at messenger RNA (mRNA) and/or protein levels. The H1 kinase assay using the immunoprecipitates of protein extracts from the Ubi1:CycD2 plants and nontransgenic controls demonstrated that the introduced Arabidopsis CycD2 forms a functional CycD2/CDK complex with an unidentified CDK of rice. Shoot and root growth was enhanced in the Ubi1:CycD2 seedlings compared with nontransgenic controls, together, suggesting that Arabidopsis cyclin D2 interacts with a rice cyclin-dependent kinase, consequently enhancing seedling growth.

Optical detection of deoxyribonucleic acid hybridization with InGaN∕GaN multiple quantum wells

Based on the high surface sensitivity of piezoelectric polarization of strained nitride semiconductors, surface functionalized nitride light emitting devices (LEDs) provide an excellent opportunity for the development of biological sensors. To demonstrate our working principle, a probe chip based on In0.22Ga0.78N∕GaN multiple quantum wells has been constructed and exposed to target DNA solutions, matched and/or mismatched, with different concentrations. The pronounced changes of photoluminescence spectra as well as Raman scattering A1(LO) spectra in matched target DNA clearly illustrate the feasibility of our proposed mechanism. The results shown here open up a new possibility for the application of nitride LEDs in biosensor engineering.

Electrostatic repulsion and steric hindrance effects of surface probe density on deoxyribonucleic acid (DNA)/peptide nucleic acid (PNA) hybridization

In this paper, we study how probe density influences the kinetics of target capture by surface-immobilized probe strands in oligonucleotide hybridization. Surface plasmon field-enhanced fluorescence spectroscopy was employed to investigate the hybridization behaviors of natural DNA or synthetic peptide nucleic acid (PNA) double strands and quantitatively characterize surface probe density effects. Two kinds of interfacial architectures are used for the study: a self-assembled thiol/streptavidin layer (planar matrix) and a colloidal streptavidin–gold conjugate particles layer (particle matrix) coupled to a flat Au surface. For both matrices, the hybridization reactions were investigated as a function of probe density. Surface effects, including electrostatic repulsion between double stranded DNA hybrids, repulsion of negatively charged free DNA molecules in the bulk by the DNA immobilized at the surface, and steric hindrance effects, were studied. The study reveals that a monotonic decrease of the affinity constant for DNA hybridization was observed for both matrices with increasing probe density, which was attributed to steric hindrance and electrostatic repulsion. Owing to the neutral backbone of PNA, the hybridization reaction was only influenced by the variation of steric hindrance effects. The dilution of the PNA probe surface layer significantly reduced this steric hindrance and enhanced the hybridization affinity.

A Versatile Biomolecular Charge-Based Sensor Using Oxide-Gated Carbon Nanotube Transistor Arrays

Label-free deoxyribonucleic acid (DNA) hybridization detection using carbon nanotube transistor (CNT) arrays is demonstrated. The present scheme is distinguished from other CNT sensing methods as it uses a gate oxide overlayer on top of the carbon nanotubes, which function solely as charge sensors but are not participants in the chemical binding process. Because it involves DNA probe attachment on the gate oxide rather than on the CNT, this approach allows the use of conventional DNA functionalization and bioassay protocols, and is less prone to false positives. The signal sought is a few tens of millivolts in threshold voltage shift due to the increase of surface charges after target hybridization. The hybridization detection is shown to be highly specific and sensitive to a minimum concentration of about 30 nM of 61-mer DNA. Despite differences in the transistor properties due to the spread in the CNT parameters during fabrication, the yields are very high and the sensing characteristics are uniformly consistent in nearly all transistors.

Time-constant-based CMOS readout circuit for DNA detection

An RC-to-time constant interface circuit was implemented in 0.18 µm CMOS to characterise the conductive polymer labelled deoxyribonucleic acid (DNA) hybridisation activity on nano-sensor micro-arrays. Measured results show that sub-picomolar DNA (0.1–10 pM) are able to be differentiated with respect to their electrical parameters of 1–23 GΩ resistances parallel with 2.8 down to 0.1 nF capacitances.

Electrical signal amplification of DNA hybridization by nanoparticles in a nanoscale gap

We report two different methods to electrically sense deoxyribonucleic acid (DNA) hybridization and suggest that nanoparticles can act as hopping sites that amplify the conductance of the hybridized DNA strand. Single-stranded DNA has no amplification effect on conductance, but hybridized double-stranded DNA tethered to 10nm gold nanoparticles exhibits a 30-fold amplification of conductance. As to the aldehyde-derived target DNA method, silver nanoparticles from silver ion reduction in the 70nm nanogap enhance the conductance signal by 106.

DNA Sensing by Field-Effect Transistors Based on Networks of Carbon Nanotubes

We report on the sensing mechanism of electrical detection of deoxyribonucleic acid (DNA) hybridization for Au- and Cr-contacted field effect transistors based on single-walled carbon nanotube (SWCNT) networks. Barrier height extraction via low-temperature electrical measurement provides direct evidence for the notion that the energy level alignment between electrode and SWCNTs can be affected by DNA immobilization and hybridization. The study of location-selective capping using photoresist provides comprehensive evidence that the sensing of DNA is dominated by the change in metal-SWCNT junctions rather than the channel conductance.

Fluorescence amplification using colloidal photonic crystal platform in sensing dye-labeled deoxyribonucleic acids

We applied self-assembled silica colloidal photonic crystals (CPCs) for a biosensing platform. Thin-film CPCs were tested for detecting dye-labeled deoxyribonucleic acid hybridization reactions. Due to the high porosity and large internal surface area, we observed a fluorescence signal enhanced by two orders of magnitude from CPC films composed of tens of silica sphere layers in the [1 1 1]-direction. This observation agrees with the theoretical enhancement factor of 2 π / 3 per silica sphere layer. The proof-of-the-concept experiment on fluorescence amplification was then followed by other complementary experiments that clarified the concerns regarding the practicality of the CPC sensor platform, such as film thickness dependence, and the effect of non-hybridized DNAs. We also learned that the silica sphere size should be chosen carefully, since the L-point photonic bandgap of the CPC may suppress the dye fluorescence.