Adsorption of peptide nucleic acid and DNA decamers at electrically charged surfaces

Adsorption/desorption of biomacromolecules involved in catalytic hydrogen evolution

Previously, it has been shown that proteins and some polysaccharides (PSs) catalyse hydrogen evolution, producing electrochemical signals on mercury electrodes. The catalytic hydrogen evolution reaction (CHER) of the above-mentioned biomacromolecules was studied by voltammetric and chronopotentiometric stripping (CPS) methods. To obtain more information about electrode processes involving CHER, here we used protein such as BSA, and chitosan as a PS; in addition, we investigated dextran as a control PS not involved in CHER. We studied biomacromolecules by phase-sensitive alternating current (AC) voltammetry. Using phase-in AC voltammetry, for CHER-involved biomacromolecules we observed a CHER peak at highly negative potentials, similar to that observed with other voltammetric and CPS methods. On the other hand, by means of the adsorption/desorption processes studied in phase-out AC voltammetry, we uncovered a sharp and narrow decrease of capacitive current in the potential range of the CHER peak, denominated as the tensammetric minimum. This minimum was closely related to the CHER peak, as demonstrated by similar dependences on specific conditions affecting the CHER peak such as buffer capacity and pH. A tensammetric minimum was not observed for dextran. Our results suggest specific organization of biopolymer layers at negative potentials observed only in biomacromolecules involved in CHER.

A WS2 nanosheet-based platform for fluorescent DNA detection via PNA-DNA hybridization

The WS2 nanosheet, a two-dimensional layered nanomaterial, shows high fluorescence quenching ability for the dye-labeled ssDNA. Currently, most of the fluorescent DNA detection methods employ DNA as a probe for recognition of target DNA. Peptide nucleic acid (PNA) is a DNA mimic but a neutral molecule, showing superior hybridization properties to target DNA. Based on the unique properties of WS2 nanosheet and PNA-DNA hybridization, we have developed a rapid, simple, stable and sensitive approach for DNA detection based on good fluorescence quenching ability of the WS2 nanosheet as well as high binding affinity and specificity of PNA to DNA. This novel assay is capable of exhibiting high sensitivity and specificity with a detection limit of 500 pM, and discriminating between single bases.

A study of double stranded DNA adsorption on aluminum surface by means of electrochemical impedance spectroscopy

Immobilization of DNA on the solid surfaces is one of the goals in bio- and nano-technologies. Adsorption of double stranded DNA on the surface of aluminum was electrochemically studied by means of impedance spectroscopy. Nyquist diagram of aluminum in a tris (hydroxymethyl) ammoniummethane-HCl (Tris-HCl) buffer solution, pH 7.4 consisted of two overlapped capacitive semicircles. The high-frequency semicircle was related to the passivity of Cl(-)-containing aluminum species in the oxide layer, and low-frequency semicircle was attributed to metal dissolution. When DNA was added to the Tris-HCl buffer solution, Nyquist diagrams represented an inductive loop at low frequencies due to the adsorption of DNA on the pre-covered aluminum surface by hydroxy-contained species. The DNA adsorption on the aluminum surface was also confirmed by X-ray photoelectron spectroscopy. Open circuit potential variation with time also indicated the chemical adsorption of DNA on the aluminum surface.

Biorecognition on graphene: physical, covalent, and affinity immobilization methods exhibiting dramatic differences

The preparation of biorecognition layers on the surface of a sensing platform is a very crucial step for the development of sensitive and selective biosensors. Different protocols have been used thus far for the immobilization of biomolecules onto various electrode surfaces. In this work, we investigate how the protocol followed for the immobilization of a DNA aptamer affects the performance of the fabricated thrombin aptasensor. Specifically, the differences in selectivity and optimum amount of immobilized aptamer of the fabricated aptasensors adopting either physical, covalent, or affinity immobilization were compared. It was discovered that while all three methods of immobilization uniformly show a similar optimum amount of immobilized aptamer, physical, and covalent immobilization methods exhibit higher selectivity than affinity immobilization. Hence, it is believed that our findings are very important in order to optimize and improve the performance of graphene-based aptasensors.

Sequence-specific recognition of DNA oligomer using peptide nucleic acid (PNA)-modified synthetic ion channels: PNA/DNA hybridization in nanoconfined environment

Here we demonstrate the design and construction of a simple, highly sensitive and selective nanofluidic sensing device, based on a single synthetic conical nanochannel for the sequence specific detection of single-stranded DNA oligonucleotides. The biosensing performance of the device depends sensitively on the surface charge and chemical groups incorporated on the inner channel wall that act as binding sites for different analytes. Uncharged peptide nucleic acid (PNA) probes are covalently immobilized on the channel surface through carbodiimide coupling chemistry. This diminishes the channel surface charge, leading to a significant decrease in the rectified ion current flowing through the channel. The PNA-modified channel acts as a highly specific and selective device for the detection of a complementary single-stranded DNA sequence. Upon PNA/DNA hybridization, the channel surface charge density increased due to the presence of the negatively charged DNA strand. The changes in the surface charge-dependent current-voltage (I-V) curves and rectification ratio of the channel confirm the success of immobilization and PNA/DNA hybridization within a confined space at the nanoscale. In addition, a control experiment indicated that the biosensor exhibits remarkable specificity toward a cDNA strand and also has the ability to discriminate single-base mismatch DNA sequences on the basis of rectified ion flux through the nanochannel. In this context, we envision that the single conical nanochannels functionalized with a PNA probe will provide a biosensing platform for the detection and discrimination of short single-stranded DNA oligomer of unknown sequence.

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.

Alkyl-thiol Langmuir films on the surface of liquid mercury

The coverage dependent phase behavior of monolayers of alkyl thiols (CH3(CH2)(n-1)SH, denoted as CnSH) on mercury was studied for chain lengths 9 <or= n <or= 22, using surface tensiometry and surface-specific X-ray scattering methods. At low coverage, a disordered single layer of surface-parallel molecules is found for all n. At high coverage, a monolayer of standing-up molecules is formed, exhibiting well-ordered phases, the structure of which is n- and coverage-dependent. The molecular chains pack in a centered rectangular unit cell, with an approximately 27 degrees tilt from the surface normal toward nearest neighbors. The strong sulfur-mercury bond induces a noncentered unit cell for the headgroups, incorporating one mercury atom per two thiol molecules. The small but significant differences in structure of these films on gold and on mercury are discussed and assigned to the different structure of the subphase: long-range-ordered crystal for gold and short-range-ordered liquid for mercury.

Electric field isolator (EFI) for isolated and electrophoretic manipulation of charged biomolecules

This paper describes a novel technology-an electric field isolator (EFI)-that can be used for achieving isolated and electrophoretic manipulation of charged biomolecules inside a selected microscopic location. The EFI is a ground ring-shaped electrode (RE) surrounding a centre electrode (CE), which is comprised of a functional unit. When the CE is powered, the ground RE can inhibit the electric field from spreading to the neighbouring functional units. Therefore, the electrophoretic movement of the charged molecules in an electric field, which is based on the principle similar to that of electrophoresis, can be isolated inside a selected location. The ground RE causing this phenomenon is referred to as the EFI. In this paper, we clearly show the functionality of the EFI with mathematical and experimental studies.

Mercury Electrodes in Nucleic Acid Electrochemistry: Sensitive Analytical Tools and Probes of DNA Structure. A Review

This review is devoted to applications of mercury electrodes in the electrochemical analysis of nucleic acids and in studies of DNA structure and interactions. At the mercury electrodes, nucleic acids yield faradaic signals due to redox processes involving adenine, cytosine and guanine residues, and tensammetric signals due to adsorption/desorption of polynucleotide chains at the electrode surface. Some of these signals are highly sensitive to DNA structure, providing information about conformation changes of the DNA double helix, formation of DNA strand breaks as well as covalent or non-covalent DNA interactions with small molecules (including genotoxic agents, drugs, etc.). Measurements at mercury electrodes allow for determination of small quantities of unmodified or electrochemically labeled nucleic acids. DNA-modified mercury electrodes have been used as biodetectors for DNA damaging agents or as detection electrodes in DNA hybridization assays. Mercury film and solid amalgam electrodes possess similar features in the nucleic acid analysis to mercury drop electrodes. On the contrary, intrinsic (label-free) DNA electrochemical responses at other (non-mercury) solid electrodes cannot provide information about small changes of the DNA structure. A review with 188 references.

DNA and PNA sensing on mercury and carbon electrodes by using methylene blue as an electrochemical label

Described here are the electrochemical parameters for MB on binding to DNA at hanging mercury drop electrode (HMDE), glassy carbon electrode (GCE), and carbon paste electrode (CPE) in the solution and at the electrode surface. MB, which interacts with the immobilized calf thymus DNA, was detected by using single-stranded DNA-modified HMDE or CPE (ssDNA-modified HMDE or CPE), bare HMDE or CPE, and double-stranded DNA-modified HMDE or CPE (dsDNA-modified HMDE or CPE) in combination with adsorptive transfer stripping voltammetry (AdTSV), differential pulse voltammetry (DPV), and alternating current voltammetry (ACV) techniques. The structural conformation of DNA and hybridization between synthetic peptide nucleic acid (PNA) and DNA oligonucleotides were determined by the changes in the voltammetric peak of MB. The PNA and DNA probes were also challenged with excessive and equal amount of noncomplementary DNA and a mixture that contained one-base mismatched and target DNA. The partition coefficient was also obtained from the signal of MB with probe, hybrid, and ssDNA-modified GCEs. The effect of probe, target, and ssDNA concentration upon the MB signal was investigated. These results demonstrated that MB could be used as an effective electroactive hybridization indicator for DNA biosensors. Performance characteristics of the sensor are described, along with future prospects.

Condensation of nucleobases at mercury/aqueous solution interface--a structural perspective using hydrogen bonding considerations

The two-dimensional condensation behavior exhibited by nucleobases at a mercury/aqueous solution interface is analyzed on the basis of their hydrogen-bonded quadruplex structures, and the experimentally observed critical temperatures are rationalized incorporating different types of hydrogen bonding, surface coordination effects, and stacking considerations. The proposed methodology provides a structural basis for the interpretation of critical temperatures and enables the calculation of the same pertaining to different modified nucleobases. The applicability of the procedure to order-disorder transitions of water dipoles at Hg electrodes is also indicated.

An impedance study of the adsorption of nucleic acid bases at glassy carbon electrodes

Electrochemical impedance has been used to study the adsorption at glassy carbon electrodes of guanine, its corresponding nucleoside, guanosine, and adenine. Impedance studies at different concentrations and applied potentials show clearly that all three bases are adsorbed on the electrode, blocking the surface. Irradiating the electrode with low-frequency (20 kHz) ultrasound whilst recording the impedance spectra increased transport of molecules to the electrode surface with cavitation cleaning the surface and removing strongly adsorbed molecules of bases. In this way, sonoelectrochemical experiments enabled the electrode processes to be studied in the absence of adsorption.

Development of a molecular diagnosis assay based on electrohybridization at plastic electrodes and subsequent PCR

Technologies enabling specific recognition of medically relevant nucleic acid sequences will play a pivotal role in future medical diagnosis. Whereas many approaches to molecular diagnosis systems include DNA microarrays on chips and fluorometric detection, the basis of our approach is the use of inexpensive components like plastic or metal thin film electrodes with low multiplexing and an electrochemical detection unit. To increase the sensitivity, PCR can be used as an intermediate step. For selective enrichment, specific nucleic acid probes were covalently attached at their 5'-ends to conducting polycarbonate/carbon fiber electrodes. Complementary oligonucleotides were enriched at the electrodes by cyclic inversion of an electrochemical potential, transferred into a PCR vial and thermally or electrochemically desorbed. The analysis of the PCR product shows the efficiency and selectivity of the electrochemical enrichment. Hybridization of DNA was shown by electrochemical methods, in this work especially by differential pulse voltammetry (DPV) using the single strand specific hybridization redox indicator osmium(VIII)-tetroxide, and potentiometric stripping analysis (PSA). This combination of experimental methods is the basis for a molecular diagnosis system including a disposable nucleic acid modified working electrode for specific enrichment, detection and quantification, and an optional capillary PCR module for fast amplification.

DNA biosensors based on peptide nucleic acid (PNA) recognition layers. A review

Peptide nucleic acid (PNA), originally developed as a gene-targeting drug, has demonstrated remarkable hybridization properties towards complementary oligonucleotides. Biosensors based on replacement of the DNA recognition layer with a PNA one, offer greatly improved distinction between closely related sequences, as well as several other attractive advantages. The present review discusses the unique structural, hybridization, and recognition features of PNA probes, along with the opportunities accrued from the use of PNA recognition layers in DNA diagnostics.

Electrochemical biosensors for DNA hybridization and DNA damage

Recent trends in the development of DNA biosensors for nucleotide sequence-specific DNA hybridization and for the detection of the DNA damage are briefly reviewed. Changes in the redox signals of base residues in DNA immobilized at the surface of carbon or mercury electrodes can be used as a sign of the damage of DNA bases. Some compounds interacting with DNA can produce their own redox signals on binding to DNA. Covalently closed circular (usually supercoiled) DNA attached to the electrode surface can be used for a sensitive detection of a single break of the DNA sugar-phosphate backbone and for detection of agents cleaving the DNA backbone such as hydroxyl radicals, ionizing radiation, nucleases, etc. Using the peptide nucleic acid in the biosensor recognition layer greatly increased the specificity of the DNA hybridization biosensor making it possible to detect point mutations (single-base mismatches) in DNA.

Two superhelix density-dependent DNA transitions detected by changes in DNA adsorption/desorption behavior

The adsorption behavior of covalently closed circular plasmid DNA at the mercury/water interface was studied by means of AC impedance measurements. The dependence of the differential capacitance (C) of the electrode double layer on the potential (E) was measured in the presence of adsorbed DNA. It was found that the C-E curves of supercoiled DNA at native and highly negative superhelix densities (sigma), relaxed covalently closed circular DNA, and nicked DNA differed from each other. A detailed study of topoisomer distributions ranging from -sigma of 0 to 0.11 revealed two supercoiling-dependent transitions, at about -sigma = 0.04 (transition TI) and 0.07 (transition TII). Transition TI was detected by measuring the height of the adsorption/desorption peak 1 (at about -1.2 V against the saturated calomel electrode) and the decrease of capacitance (DeltaC) at -0.35 V. This transition may be due to a sudden change in the ability of the DNA to respond to the alternating voltage, probably caused by changes in the DNA tertiary and/or secondary structure. Transition TII was detected by measuring peak 3* (at about -1.3 V), which was absent in topoisomers with -sigma less than 0.05. This transition is due to changes in the DNA adsorption/desorption behavior related to increased accessibility of bases at elevated negative superhelix density. Opening of the duplex at highly negative superhelix density was also detected by the single-strand selective probe of DNA structure, osmium tetroxide, 2, 2'-bipyridine. Our results suggest that electrochemical techniques provide sensitive experimental analysis of changes in DNA structure.