dsDNA Base Pairs Research Articles

Detection of short oligonucleotide sequences using an electrochemical DNA hybridization biosensor

Abstract An electrochemical DNA hybridization biosensor was developed for the detection of DNA hybridization using MDB and proflavine as electrochemical labels. The biosensor was based on the interaction of 7-dimethyl-amino-1,2-benzophenoxazi-nium Meldola’s Blue (MDB) and proflavine with double stranded DNA (dsDNA) The electrochemical behaviour of MDB and proflavine as well as its interaction with double stranded (dsDNA) were investigated by cyclic (CV) and square wave voltammetry (SWV) and screen printed electrodes (ScPE). Furthermore, DNA-hybridization biosensors were developed for the detection of hybridization between oligonucleotides, which was detected by studying changes in the voltammetric peaks of MDB (reduction peak at −0.251 V) and proflavine (reduction peak at 0.075 V). MDB and proflavine were found to intercalate between the base pairs of dsDNA and oligonucleotides. Several factors affecting the dsDNA or oligonucleotides immobilization, hybridization and indicator preconcentration and interaction time, were investigated. As a result of the interaction of MDB with dsDNA and hybridized oligonucleotides, the voltammetric signals of MDB increased. Furthermore, guanine’s oxidation peak (at 0.901 V) was decreased as MDB’s concentration was increased. As a result of the interaction of proflavine with dsDNA and hybridized oligonucleotides, the voltammetric signals of proflavine decreased. These results were similar for carbon paste and screen printed electrodes. A comparison of the performance between CPE and ScPE was done. Our results showed that lower concentrations of MDB and proflavine were detected using screen printed electrodes. Moreover, reproducibility was better using screen printed electrodes and the detection was faster (regarding the experimental steps), but they are more cost effective.

Carbon nanotubes/(pLys/dsDNA) n layer-by-layer multilayer films for electrochemical studies of DNA damage

Carboxylic group-functionalized carbon nanotubes (c-CNT) were modified on the surface of carbon paste electrode to obtain a conducting precursor film. Positively charged poly-l-lysine (pLys) and negatively charged double-stranded DNA (dsDNA) were alternately adsorbed on the c-CNT-modified electrode, forming (pLys/dsDNA)n layer-by-layer (LBL) films. Cyclic voltammetry and electrochemical impedance spectroscopy of the electroactive probe [Fe(CN)6]3−/4− could give the valuable dynamic information of multilayer films growth. The oxidative DNA damage induced by cadmium ion (Cd2+) in the LBL multilayer films was studied by differential pulse voltammetry (DPV) with methylene violet (MV) as the intercalation redox probe. The electrochemical signals of MV on the multilayer films were effectively amplified via LBL technology. The specific intercalation of MV into dsDNA base pairs and the amplified electrochemical response of MV, combined with the unique feature of loading reversibility of MV in the DNA layer-by-layer films, made the difference in DPV response between the intact, and damaged dsDNA films become pronounced. This biosensor exhibited that the (pLys/dsDNA)n films could be utilized for investigations of DNA damage.

The Mechanism of Benzothiazole Styrylcyanine Dyes Binding with dsDNA: Studies by Spectral-Luminescent Methods

In the presented work studies of the interaction mode of monomer and two homodimer benzothiazole styryl dyes containing spermine-like linkage/tail group with the double stranded (ds) DNA are reported. For these dyes, equilibrium constant of dye binding to DNA (K(b)), as well as the number of dsDNA base pairs occupied by one bound dye molecule (n) were determined. The data obtained show that the presence of spermine-like group containing quaternary nitrogen (Bos-5) results in increase of K(b) value as compared to this of unsubstituted analogue (Sbt). Besides, for the dimer dyes containing benzothiazole styryl chromophores, the K(b) value is either five times higher (DBos-13) or almost the same (DBsu-10) as compared to this of corresponding monomer Sbt, depending on the position in the benzothiazole ring where the linker is attached. Moreover, the n values for both dimers are significantly different as well, pointing to the bis-intercalative binding mechanism for DBos-13 and for the groove-binding one for DBsu-10. The conclusion about the dimer dyes-dsDNA binding mechanisms is also supported by the study of the fluorescent response of these dyes on the presence of AT- and GC-containing polynucleotides.

Indirect Electrochemical Sensing of DNA Hybridization Based on the Catalytic Oxidation of Cobalt (II)

A new electrochemical approach for detecting target DNA is described. The scheme involves the catalytic oxidation of a cobalt bipyridine “reporter molecule” in solution. Probe/target DNA duplexes (ds-DNA), bound on an ITO electrode, selectively recruit redox catalyst molecules from solution. This surface-bound catalyst “turns on” the redox chemistry of the reporter molecule which is otherwise kinetically inert to oxidation on ITO. The mode of selective catalyst binding is intercalation between base pairs of ds-DNA. With this approach, we demonstrate detection of a 20-mer DNA target oligonucleotide at picomolar concentrations with outstanding signal-to-noise.

Cyclic voltammetric detection of chemical DNA damage induced by styrene oxide in natural dsDNA layer-by-layer films using methylene blue as electroactive probe

In this work, an electrochemical sensor for detecting damage of natural double-stranded DNA (dsDNA) was constructed based on PSS/{PDDA/dsDNA} 3 layer-by-layer films, where PSS was poly(styrene sulfonate) and PDDA was poly(diallyldimethyl ammonium). When the PSS/{PDDA/dsDNA} 3 films assembled on pyrolytic graphite (PG) electrodes were immersed into methylene blue (MB) solution and loaded MB into the films, the formed PSS/{PDDA/dsDNA} 3-MB films in blank buffers at pH 7.0 showed a reversible cyclic voltammetric (CV) peak pair at −0.23 V vs. SCE for MB redox couple. In blank solutions, the MB loaded into the films was released gradually from the films, but the complete reloading of MB into the films could be realized by immersing the films into MB solution again, indicating the good reversibility of MB incorporation. However, after incubation in the solution of known genotoxic agent styrene oxide (SO), the damaged PSS/{PDDA/dsDNA} 3-MB films could not return to their original and fully-loaded state with reloading of MB, and showed smaller CV peak currents than those of intact PSS/{PDDA/dsDNA} 3-MB films. The relative peak current ratio, I p,I/ I p,III, where I p,I was the anodic peak current of intact DNA films in blank buffers after fully loading with MB and I p,III was that of SO-damaged DNA films after reloading with MB, increased linearly with the incubation time with SO in the range of 5–40 min with a damage rate of 0.0099 min −1. While the formation of SO adducts with dsDNA had no substantial effect on the dsDNA conformation, the steric hindrance of SO adducts with guanine or adenine blocked the intercalation of MB into the base pairs of dsDNA, resulting in the decrease of CV peak currents of loaded MB. The specific intercalation of MB into dsDNA base pairs and the sensitive electrochemical response of MB, combined with the unique feature of loading reversibility of MB in the DNA layer-by-layer films, make the difference in CV response between the intact and damaged dsDNA films become pronounced in the “loading/release/reloading” procedure. This may provide a new and general approach for constructing a biosensor for screening genetoxic chemicals in vitro.

Spectral properties and G-quadruplex DNA binding selectivities of a series of unsymmetrical perylene diimides

A series of new unsymmetrical perylene diimides have been synthesized to investigate their binding selectivities to G-quadruplex DNA structure, a unique four-stranded DNA motif, which is significant to the regulation of telomerase activity. The structures of the perylene diimides have been characterized by IR spectrophotometer, 1H NMR, 13C NMR, MS, TGA and time-resolved instruments. Spectrochemical behaviors have been investigated by visible absorption and fluorescence emission spectra. The spectral characterization of the compounds has been investigated in five common organic solvents of different polarity and in water (in 170 mM phosphate buffer at pH 6). Marked red shifts of absorbance and fluorescence emission bands of the compounds in aqueous solution are compared with the other organic solutions. The fluorescence quantum yields are determined low in more polar solvents and also calculated to be about less than about 0.05 in aqueous solution because of the aggregation effects. Photodegradation rate constants ( k p) of the synthesized compounds have been compared under xenon lamp irradiation in acetonitrile solution. Binding abilities of the synthesized perylene diimides to different form of DNA strands have been investigated by visible absorption and fluorescence spectroscopy in the phosphate buffer solutions. Also, pH-dependent aggregation and G-quadruplex DNA binding selectivity of these ligands have been compared. Among these ligands, N-(2,6-diisopropylphenyl)- N′-(4-pyridyl)-perylene-3,4,9,10-tetracarboxylic diimide (PYPER) has been found to be the most selective interactive ligand for G-quadruplex formed in the G4′-DNA structure. PYPER has shown a significant selectivity to G4′-DNA which is comprised of d(TTAGGG) repeats, known as human telomeres, in the phosphate buffer at pH 6. The absorption maximum of the PYPER/G4′-DNA complex has given bathochromic shift of 7 nm with respect to the absorption maximum of DNA-free solution of PYPER in phosphate buffer at pH 6. Fluorescence quenching experiments between PYPER and G4′-DNA show that PYPER demonstrates about a 9.3-fold selectivity for binding to G4′-DNA versus ds-DNA base pairs with the bimolecular rate constant of 0.95 × 10 12 M −1 s −1.

Imprinted polymer layer for recognizing double-stranded DNA

A method of preparing a thin polymer layer able to recognize double-stranded DNA (dsDNA) was developed by using 2-vinyl-4,6-diamino-1,3,5-triazine (VDAT) as a functional monomer for creating a DNA-imprinted polymer. The formation of hydrogen bonds between VDAT and A–T base pairs in dsDNA was confirmed by measuring the effects of VDAT on the melting point and the NMR and CD spectra of dsDNA. An imprinted polymer that can recognize dsDNA of the verotoxin gene was prepared by polymerizing VDAT, acrylamide, a crosslinking agent, and the template verotoxin dsDNA on a silanized glass surface. The specificity of this polymer layer for binding verotoxin dsDNA was investigated by using fluorescent-labelled dsDNAs. The fluorescence intensity of the polymer layer after binding verotoxin dsDNA was twice as high as after binding oligo(dG)–oligo(dC), indicating that verotoxin dsDNA was preferentially bound to the polymer imprinted with verotoxin dsDNA. The kinetics of verotoxin dsDNA binding to the imprinted polymer were analyzed by surface plasmon resonance measurements. The dissociation constant ( K D) was low, of the order of 10 −9 M.

Electrochemical Scanning Tunneling Microscope Imaging of Self-Assembled Monolayer of Double-Stranded DNA on Au(111)

Self-assembled monolayer of a double-stranded DNA, which was formed by a 20-nt 5'-thiol-modified oligonucleotide at the interface of Au(111)/solution, has been imaged and studied with electrochemical scanning tunneling microscopy (ECSTM). The results showed that the preferred directions of the adsorbed DNA were <110> and <112>. The measured width of the DNA stripes was 0.95 +/- 0.02 nm, which was consistent with the width of dsDNA base pairs. The contour of DNA in the STM image consisted of a series of blobs, which were due to the anchoring of the bases to the substrate along the dsDNA chain. The imaging of a large-scale array of DNA lying flat on the substrate offers a convenient method for the further application of high-resolution STM to the study of the interaction between DNA and a variety of molecules.

Recognition and detection of dsDNA at a thionalid self-assembled monolayer modified gold electrode

A novel method for the recognition and detection of dsDNA has been developed at a thionalid self-assembled monolayer modified gold electrode (TNL/Au SAMs). This method is based on thionalid at a gold electrode intercalating dsDNA. Attenuated total reflection-Fourier transform infrared (ATR-FTIR), cyclic voltammetry (CV) and ac impedance method are used to characterize the thionalid self-assembled monolayer modified gold electrode. Electrochemical method is adopted to investigate the interaction of thionalid and dsDNA, and fluorimetry proves further the interaction. Only dsDNA can interact with thionalid, we deduce that plane thionalid molecule insert base pairs of dsDNA forming a channel of electron transfer (ET), which is benefit to the ET of redox of gold. There are definite relations between the reductive peak value of Au and the concentration of dsDNA. A linear dependence of the reductive peak currents on the concentration of dsDNA is observed in the range 2.5×10 −5 to 2.0×10 −4 g L −1, with a detection upper limit of 2×10 −4 g L −1. Another linear dependence of the peak currents on the logarithm value of the concentration is in the range 1.0×10 −8 to 1.0×10 −5 g L −1, with a detection limit of 1.0×10 −9 g L −1. Their correlation coefficients are 0.9990 and 0.9962, respectively. For this reason, this modified electrode can be applied to quantitative analysis of dsDNA, recognize dsDNA, label degree of dsDNA hybridization and instruct design of new anticancer drug molecules.

Interaction of the mutagen ethidium bromide with DNA, using a carbon paste electrode and a hanging mercury drop electrode

The interaction of ethidium bromide (2,7-diamino-10-ethyl-9-phenylphenanthridinium bromide; EB) with double stranded (ds) calf thymus DNA and thermally denatured single stranded (ss) DNA was studied in solution and at the electrode surface by means of transfer voltammetry using a carbon paste electrode (CPE) as working electrode in 0.2M acetate buffer, pH 5.0. As a result of intercalation of this dye between the base pairs of dsDNA, the characteristic peak of dsDNA, due to the oxidation of guanine residues, decreased and after a particular concentration of EB a new peak at +0.81V appeared, probably due to the formation of a complex between dsDNA and EB. The non-intercalated EB gives another peak, but at an increased concentration of the dye. A similar behaviour was observed during the interaction of the dye with ssDNA.Furthermore, the interaction of EB with ds, ss and supercoiled (sc) DNA was studied at the hanging mercury drop electrode (HMDE) surface by means of alternating current voltammetry in 0.3M NaCl and 50mM sodium phosphate buffer (pH 8.5) as supporting electrolyte. dsDNA yields a smaller peak at −1.42V (peak III) compared to the one yielded by ssDNA, since the latter is a relaxed and more accessible form. By addition of EB into the buffer solution an increase of peak III was observed in the dsDNA form as well as in ssDNA resulting from their interaction with EB. Furthermore, the appearance of peak III in covalently closed circular scDNA after exposure to increasing concentrations of EB is a result of the introduction of ‘free ends’ in DNA affecting its structural integrity.

Electrochemical biosensor for the interaction of DNA with the alkylating agent 4,4′-dihydroxy chalcone based on guanine and adenine signals

The interaction of an alkylating agent, 4,4′-dihydroxy chalcone (DHC) with calf thymus double stranded DNA (dsDNA) and calf thymus single stranded DNA (ssDNA) was studied electrochemically based on the oxidation signals of guanine and adenine by using differential pulse voltammetry (DPV) at carbon paste electrode (CPE). As a result of the alkylation of DHC between the base pairs in dsDNA, the voltammetric signal of guanine and adenine greatly decreased. After the interaction of DHC with ssDNA, a higher decrease in the oxidation signals of guanine and adenine was observed under the same conditions. The partition coefficients of DHC at dsDNA and ssDNA modified CPEs were calculated. The interactions of DHC with synthetic polynucleotides, such as polyguanylic acid and polyadenylic acid were also observed. In addition, the detection limit and the reproducibility were determined by using DPV. The interaction of DHC with dsDNA in solution-phase was also investigated and the results were compared with the ones obtained by surface immobilized dsDNA. The application of electrochemical DNA biosensor for monitoring the DNA–alkylating agent interactions was explored.

DNA sensing on glassy carbon electrodes by using hemin as the electrochemical hybridization label.

The electrochemical behavior of hemin, an iron complex of porphyrin, on binding to DNA at a glassy carbon electrode (GCE) and in solution, is described. Hemin, which interacts with covalently immobilized calf thymus DNA, was detected by use of a bare GCE, a double-stranded DNA-modified GCE (dsDNA-modified GCE), and a single-stranded DNA-modified GCE (ssDNA-modified GCE), in combination with differential pulse voltammetry (DPV). The structural conformation of DNA was determined from changes in the voltammetric signals acquired on reduction of hemin. As a result of its large steric structure and anionic substitution on its porphyrin plane, hemin intercalates between the base pairs of dsDNA. A scan-rate study for hemin and the dsDNA-hemin complex were also performed to determine the electrochemical behavior of the complex. The partition coefficient was obtained from the peak currents measured when different concentrations of hemin were in the presence of dsDNA. By observing the oxidation signals of guanine, damage to DNA after reaction with hemin at the GCE surface was also detected. The electrochemical detection of hybridization between the covalently immobilized probe and its target sequence was detected by use of hemin. These results demonstrate the use of DNA biosensors in conjunction with hemin for electrochemical detection of hybridization and damage to DNA.

Integrity and redox properties of homogeneous and heterogeneous DNA films on gold surface probed by cyclic voltammetry

5′-thiol-labeled single-stranded DNA (22 mer ssDNA) adsorbed onto the gold surface by both non-specific binding and Au–S linkage, whereas 5′-thiol-labeled double-stranded DNA (22-bp dsDNA) formed a packed layer mainly through the Au–S linkage. The coating of homogeneous ssDNA or dsDNA films or heterogeneous DNA films mixed with n-hexadecyl mercaptan (HDM) on gold surface facilitated the redox reaction of methylene blue (MB). MB binds with ssDNA through electrostatic interaction with the charged backbone and adsorbed through the ssDNA film. MB binds with dsDNA through both electrostatic interaction and intercalation into the dsDNA base pairs and undergoes redox reaction by diffusing through the dsDNA film to the gold surface and/or electron transfer through the DNA helix. The addition of HDM enhanced the integrity and stability upon NaOH treatment for both ssDNA and dsDNA films.

Processive translocation and DNA unwinding by individual RecBCD enzyme molecules.

RecBCD enzyme is a processive DNA helicase and nuclease that participates in the repair of chromosomal DNA through homologous recombination. We have visualized directly the movement of individual RecBCD enzymes on single molecules of double-stranded DNA (dsDNA). Detection involves the optical trapping of solitary, fluorescently tagged dsDNA molecules that are attached to polystyrene beads, and their visualization by fluorescence microscopy. Both helicase translocation and DNA unwinding are monitored by the displacement of fluorescent dye from the DNA by the enzyme. Here we show that unwinding is both continuous and processive, occurring at a maximum rate of 972 +/- 172 base pairs per second (0.30 microm s(-1)), with as many as 42,300 base pairs of dsDNA unwound by a single RecBCD enzyme molecule. The mean behaviour of the individual RecBCD enzyme molecules corresponds to that observed in bulk solution.

Interactions of antitumor drug daunomycin with DNA in solution and at the surface

The interaction of the antitumor drug daunomycin with double-stranded (ds) calf thymus DNA was studied in solution and at the electrode surface by means of cyclic voltammetry and particularly by constant-current chronopotentiometric stripping analysis (CPSA) with the carbon paste electrodes (CPE). As a result of intercalation of this drug between the base pairs in dsDNA, the CPSA daunomycin peak δ decreased and a new more positive shoulder δ b appeared. This shoulder was attributed to the oxidation of the drug intercalated in DNA. Under the same conditions almost no changes in the DNA peak G ox (due to oxidation of guanine residues) were observed. It was shown that daunomycin adheres strongly to the bare CPE (resisting washing) so that a daunomycin-modified electrode can be easily prepared. Daunomycin immobilized at CPE interacted with DNA on immersion of the modified electrode into the dsDNA solution, showing a decrease of peak δ and a well-separated peak δ b instead of the shoulder (which resulted from the interaction of DNA with daunomycin in solution). When the DNA-modified CPE was immersed into a daunomycin solution the peak G ox increased in dependence on daunomycin concentration or on the time of interaction of daunomycin with dsDNA at the electrode surface. Such changes in peak G ox were observed only at submicromolar concentrations of daunomycin. At higher daunomycin concentrations or at longer interaction time intervals a daunomycin peak appeared, which was substantially smaller and more positive than the peak of free daunomycin. The increase of the DNA peak G ox was attributed to interaction of daunomycin from the side of the DNA double helix not contacting the electrode surface. Such binding may induce changes in the DNA structure including bending of the DNA molecule which may result in the increase of peak G ox. Our results thus suggest that the interaction of daunomycin with DNA anchored at the surface may significantly differ from that with DNA in solution. The prospects of using of electroanalytical methods in studies of DNA–drug interactions are discussed.

Binding of Rad51p to DNA: INTERACTION OF Rad51p WITH SINGLE- AND DOUBLE-STRANDED DNA

Like RecA, Saccharomyces cerevisiae Rad51p promotes strand exchange between circular single-stranded DNA (ssDNA) and linear double-stranded DNA (dsDNA). We have investigated several parameters characteristic of the interaction of Rad51p with ssDNA and dsDNA, particularly the effects of the nucleotide cofactors ATP and ADP and the analogs adenosine 5'-O-(thiotriphosphate) (ATPgammaS) and adenylyl-imidodiphosphate (AMP-PNP). Rad51p binding to both 1-N6-ethenoadenosine and 3-N4-ethenocytidine ssDNA (epsilonDNA) and dsDNA requires the presence of Mg2+ and ATP; no binding occurs in the presence of ADP, AMP-PNP, or ATPgammaS. Binding of Rad51p to dsDNA also requires ATP; ADP is ineffective, whereas ATPgammaS and AMP-PNP are considerably less able to promote binding and only at elevated concentrations of Rad51p. ATP binding, not ATP hydrolysis, is required for Rad51p binding to DNA. The Kd values for ATP for promoting binding of Rad51p to ssDNA and dsDNA are 1 and 3 microM, respectively. Rad51p binding occurs with a stoichiometry of one monomer of Rad51p per approximately 6.3 nucleotides of epsilonDNA and approximately 3.3 base pairs of dsDNA. Once formed, Rad51p. ssDNA complexes are stable so long as sufficient ATP levels are maintained. ATP hydrolysis causes dissociation of Rad51p from DNA. Moreover, the preformed complex is stable in the presence of a 10-fold excess of ADP or AMP-PNP over ATP. ATPgammaS, however, in the same -fold excess over ATP causes dissociation of the Rad51p. ssDNA complex.