Carbon nanotubes selective destabilization of duplex and triplex DNA and inducing B-A transition in solution

Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nanodevice applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mechanism. We report here, for the first time, that DNA destabilization and conformational transition induced by SWNTs are sequence-dependent. Contrasting changes for SWNTs binding to poly[dGdC]:poly[dGdC] and poly[dAdT]:poly[dAdT] were observed. For GC homopolymer, DNA melting temperature was decreased 40°C by SWNTs but no change for AT-DNA. SWNTs can induce B–A transition for GC-DNA but AT-DNA resisted the transition. Our circular dichroism, competitive binding assay and triplex destabilization studies provide direct evidence that SWNTs induce DNA B–A transition in solution and they bind to the DNA major groove with GC preference.     

DNA electrochemical sensor based on an adduct of single-walled carbon nanotubes and ferrocene

A novel electrochemical sandwich-type gene sensing system was designed by using a DNA probe (DNA-probe1) immobilized on a gold electrode, the target DNA, and another DNA probe (DNA-probe2) conjugated on a single-walled carbon nanotubes/ferrocene (Fc–SWNT) adduct. In this sandwich-type gene-sensing electrode, the Fc–SWNT adduct could significantly amplify the electrochemical response of the reduction of H₂O₂. The target DNA could be detected selectively and sensitively based on the much enhanced electrochemical catalytic property of the Fc–SWNT adduct toward H₂O₂ reduction.     

Overoxidized polypyrrole film directed single-walled carbon nanotubes immobilization on glassy carbon electrode and its sensing applications

In this paper, the films of overoxidized polypyrrole (PPyox) directed single-walled carbon nanotubes (SWNTs) have been electrochemically coated onto glassy carbon electrode (GCE). Electroactive monomer pyrrole was added into the solution containing sodium dodecyl sulfate (SDS) and SWNTs. Then, electropolymerization was proceeded at the surface of GCE, and a novel kind of conducting polymer/carbon nanotubes (CNTs) composite film with the orientation of CNTs were obtained correspondingly. Finally, this obtained polypyrrole (PPy)/SWNTs film modified GCE was oxidized at a potential of +1.8 V. It can be found that this proposed PPyox/SWNTs composite film modified GCE exhibited excellent electrocatalytic properties for some species such as nitrite, ascorbic acid (AA), dopamine (DA) and uric acid (UA), and could be used as a new sensor for practical applications. Compared with previous CNTs modified electrodes, SWNTs were oriented towards the outside of modified layer by PPyox and SDS, which made the film easily conductive. Moreover, this proposed film modified electrode was more stable, selective and applicable.     

Structural characterization of a carbon monoxide adduct of a heme–DNA complex

Abstract  

The structure of a carbon monoxide (CO) adduct of a complex between heme and a parallel G-quadruplex DNA formed from a single repeat sequence of the human telomere, d(TTAGGG), has been characterized using ¹H and ¹³C NMR spectroscopy and density function theory calculations. The study revealed that the heme binds to the 3′-terminal G-quartet of the DNA though a π–π stacking interaction between the porphyrin moiety of the heme and the G-quartet. The π–π stacking interaction between the pseudo-C ₂-symmetric heme and the C ₄-symmetric G-quartet in the complex resulted in the formation of two isomers possessing heme orientations differing by 180° rotation about the pseudo-C ₂ axis with respect to the DNA. These two slowly interconverting heme orientational isomers were formed in a ratio of approximately 1:1, reflecting that their thermodynamic stabilities are identical. Exogenous CO is coordinated to heme Fe on the side of the heme opposite the G-quartet in the complex, and the nature of the Fe–CO bond in the complex is similar to that of the Fe–CO bonds in hemoproteins. These findings provide novel insights for the design of novel DNA enzymes possessing metalloporphyrins as prosthetic groups.     

Enhancing dopamine detection using a glassy carbon electrode modified with MWCNTs, quercetin, and Nafion

Glassy carbon (GC) electrode was modified using multi-wall carbon nanotubes (MWCNTs), quercetin (Q) and Nafion^® in this sequence. The thus modified electrode was used for the detection of dopamine (DA) in the presence of equimolar ascorbic acid (AA). It is demonstrated in this study that MWCNTs can increase the current response of DA by five-fold and Q can reduce the oxidation overpotential of DA by about 60 mV, compared to these parameters obtained with a bare GC electrode. It is also shown that a layer of Nafion^® can virtually eliminate the interference of AA for the detection of DA. The GC/MWCNTs/Q/Nafion^® electrode (hereafter also called composite electrode) shows a current density of about 900 μA cm⁻² for DA, compared to the value of 80 μA cm⁻² of the GC electrode and to the value of 390 μA cm⁻² of the GC/MWCNTs electrode. The 11-fold enhancement in the sensitivity of the GC electrode for DA determination is attributed to the composite modification of the electrode, and is substantiated through various cyclic voltammetric experiments. Cyclic voltammetry (CV) and linear sweep voltammetry were used to characterize the electrodes. Calibration curves of batch and flow systems were obtained by amperometry for the detection of DA. Additionally, the composite modified electrode was tested with a human serum sample for the determination of DA and was found to be promising at our preliminary experiments.     

A sensitive voltammetric sensor for determination of synthetic corticosteroid triamcinolone, abused for doping

Edge plane pyrolytic graphite electrode (EPPGE) modified with single-wall carbon nanotubes (SWNTs) has been used as a sensor to determine triamcinolone, abused by athletes for doping. A comparison of the voltammetric behavior between SWNTs modified EPPGE and fullerene – C₆₀-modified EPPGE indicated that SWNTs modified EPPGE is more sensitive. The electrode exhibited an effective catalytic response with good reproducibility and stability. The effect of several parameters such as pH, square wave frequency and steroid concentration were studied. The square wave voltammetric response of the electrode to triamcinolone is linear in the range 0.1–25 nM with a detection limit and sensitivity of 8.9 × 10⁻¹⁰ M and 2.06 μA nM⁻¹, respectively. The method was applied for the determination of triamcinolone in several commercially available pharmaceuticals and real urine samples obtained from patients undergoing pharmacological treatment with triamcinolone. A comparison of the observed results with HPLC analysis indicated a good agreement. The product obtained after reduction of triamcinolone was also characterized using ¹H NMR and GC–MS and the site of reduction is found to be carbonyl group at position 20. The method described is rapid, simple and accurate and can be easily applied for detecting cases of doping.     

pH-dependent conformational changes of ferricytochrome c induced by electrode surface microstructure

pH-dependent processes of bovine heart ferricytochrome c have been investigated by electronic absorption and circular dichroism (CD) spectra at functionalized single-wall carbon nanotubes (SWNTs) modified glass carbon electrode (SWNTs/GCE) using a long optical path thin layer cell. These methods enabled the pH-dependent conformational changes arising from the heme structure change to be monitored. The spectra obtained at functionalized SWNTs/GCE reflect electrode surface microstructure-dependent changes for pH-induced protein conformation, pK_a of alkaline transition and structural microenvironment of the ferricytochrome c heme. pH-dependent conformational distribution curves of ferricytochrome c obtained by analysis of in situ CD spectra using singular value decomposition least square (SVDLS) method show that the functionalized SWNTs can retain native conformational stability of ferricytochrome c during alkaline transition.     

The effect of anchoring group number on molecular structures and absorption spectra of triphenylamine sensitizers: a computational study

The molecular structures and absorption spectra of triphenylamine dyes containing different numbers of anchoring groups (S1-S3) were investigated by density functional theory (DFT) and time-dependent DFT. The calculated geometries indicate that strong conjugation is formed in the dyes. The interfacial charge transfer between the TiO₂ electrode and S1-S3 are electron injection processes from the excited dyes to the semiconductor conduction band. The simulated absorption bands are assigned to π → π* transitions according to the qualitative agreement between the experimental and calculated results. The effect of anchoring group number on the molecular structures, absorption spectra and photovoltaic performance were comparatively discussed.     

Adsorption mechanism of single guanine and thymine on single-walled carbon nanotubes

Bio-nano hybrids introduce magnificent applications of nanomaterials to various fields. The choice of carbon nanotube as well as sequence selection of the nucleic acid bases play a crucial role in shaping DNA–carbon nanotube hybrids. To come up with a clear vision for the choice of carbon nanotube and nucleic acid bases to create bio-nano hybrids, we studied the adsorption mechanism of the nucleic acid bases guanine and thymine on four different types of nanotubes based on density functional theory. Nucleic acid bases exhibit differential binding strengths according to their structural geometry, inter-molecular distances, the carbon nanotube diameter, and charge transfer. The π–π interaction mechanism between the adsorbent and adsorbate is discussed in terms of charge density profile and electronic band structure analysis.     

Probing the nature of hydrogen bonds in DNA base pairs

Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler–London, polarization, electron-transfer and dispersion-energy terms, where the Heitler–London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson–Crick adenine–thymine (AT), guanine–cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (−25.4 kcal mol⁻¹ at the MP2/6-31G** level) twice that of the AT (−12.4 kcal mol⁻¹) and H-AT (−12.8 kcal mol⁻¹) pairs, compared with three conventional N-H···O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the π-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that π-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology “resonance-assisted hydrogen bonding (RHAB)” may be replaced with “resonance-assisted binding” which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds. Figure Electron density difference (EDD) maps for the GC pair: a shows the polarization effect (isodensity 1.2×10⁻³ a.u.); b shows the charge transfer effect (isodensity 2×10⁻⁴ a.u.) Dedicated to Professor Paul von Ragué Schleyer on the occasion of his 75th birthday     

Design and characterization of electrochemical dopamine–aptamer as convenient and integrated sensing platform

Here, an ultrasensitive label-free electrochemical aptasensor was developed for dopamine (DA) detection. Construction of the aptasensor was carried out by electrodeposition of gold–platinum nanoparticles (Au–PtNPs) on glassy carbon (GC) electrode modified with acid-oxidized carbon nanotubes (CNTs–COOH). A designed complementary amine-capped capture probe (ssDNA1) was immobilized at the surface of PtNPs/CNTs–COOH/GC electrode through the covalent amide bonds formed by the carboxyl groups on the nanotubes and the amino groups on the oligonucleotides. DA-specific aptamer was attached onto the electrode surface through hybridization with the ssDNA1. Methylene blue (MB) was used as an electrochemical indicator that was intercalated into the aptamer through the specific interaction with its guanine bases. In the presence of DA, the interaction between aptamer and DA displaced the MB from the electrode surface, rendering a lowered electrochemical signal attributed to a decreased amount of adsorbed MB. This phenomenon can be applied for DA detection. The peak current of probe (MB) linearly decreased over a DA concentration range of 1–30 nM with a detection limit of 0.22 nM.     

The use of single walled carbon nanotubes dispersed in a chitosan matrix for preparation of a galactose biosensor

Chitosan was chosen as a natural polymer for dispersion of single walled carbon nanotubes (SWNT) based on its ability to efficiently solubilize SWNTs to form a stable dispersion. Moreover, chitosan films deposited on a surface of a glassy carbon (GC) electrode are mechanically stable. Further stabilisation of the chitosan film containing SWNT (CHIT-SWNT) was done by chemical crosslinking with glutaraldehyde and free aldehyde groups produced a substrate used for covalent immobilisation of galactose oxidase (GalOD). Different galactose biosensor configurations were tested with optimisation of composition of inner and outer membrane; and enzyme immobilisation procedure, as well. Detection of oxygen uptake by GalOD on CHIT-SWNT layer at -400 mV is robust and, when flow injection analysis (FIA) was applied for assays, a low detection limit (25 microM) and very high assay throughput rate (150 h-1) was achieved. This new galactose biosensor offers highly reliable detection of galactose with R.S.D. well below 2% and it has been successfully applied to assaying galactose in a blood sample with recovery index between 101.2 and 102.7%.     

Creation and investigation of powerful EUV sources (λ ≈ 13.5 nm)

Results are presented from experimental studies of repetitively pulsed EUV (λ = 13.5 ± 0.135 nm) sources based on a laser-initiated discharge in tin vapor between rotating disk electrodes. Radiative characteristics of two sources with different systems of tin supply onto the electrode surface and different types of power supply have been compared. A number of new effects have been revealed at pulse repetition rates as high as ∼4000 Hz. A mean radiation power of 520 W into the 2π solid angle has been achieved in the spectral band 13.5 ± 0.135 nm at a deposited electrical power of 24 kW.     

Effect of different carbon sources on the enhanced biological phosphorus removal in a sequencing batch reactor

The effect of the different carbon sources acetate, acetate/glucose or glucose on the enhanced biological phosphorus removal (EBPR) process was studied by experiments under alternating anaerobic–aerobic conditions in one sequencing batch reactor for each carbon source. The glucose was consumed completely within the first 30 min of the anaerobic phase whereas acetate degradation was slow and incomplete. Phosphate was released independently of the carbon source during the whole anaerobic phase. The highest phosphate release (27 mg P l⁻¹) and polyhydroxyalkanoate (PHA) storage (20 mg C g⁻¹ dry matter (DM)) during the anaerobic phase as well as the highest polyphosphate (poly-P) (8 mg P g⁻¹ DM) and glycogen storage (17 mg C g⁻¹ DM) during the aerobic phase were observed with acetate. In contrast to other investigations, glycogen storage did not increase with glucose as substrate but was significantly smaller than with acetate. The PHA composition was also influenced strongly by the carbon source. The polyhydroxyvalerate (PHV) portion of the PHA was maximal 17% for acetate and 82% for glucose. Due to the strong influence of the carbon source on the PHA concentration and composition, PHA storage seems to regulate mainly the phosphate release and uptake. This revised version was published online in July 2006 with corrections to the Cover Date.     

Hollow nitrogen-doped carbon microspheres pyrolyzed from self-polymerized dopamine and its application in simultaneous electrochemical determination of uric acid, ascorbic acid and dopamine

Hollow nitrogen-doped carbon microspheres (HNCMS) as a novel carbon material have been prepared and the catalytic activities of HNCMS-modified glassy carbon (GC) electrode towards the electro-oxidation of uric acid (UA), ascorbic acid (AA) and dopamine (DA) have also been investigated. Comparing with the bare GC and carbon nanotubes (CNTs) modified GC (CNTs/GC) electrodes, the HNCMS modified GC (HNCMS/GC) electrode has higher catalytic activities towards the oxidation of UA, AA and DA. Moreover, the peak separations between AA and DA, and DA and UA at the HNCMS/GC electrode are up to 212 and 136 mV, respectively, which are superior to those at the CNTs/GC electrode (168 and 114 mV). Thus the simultaneous determination of UA, AA and DA was carried out successfully. In the co-existence system of UA, AA and DA, the linear response range for UA, AA and DA are 5-30 μM, 100-1000 μM and 3-75 μM, respectively and the detection limits (S/N = 3) are 0.04 μM, 0.91 μM and 0.02 μM, respectively. Meanwhile, the HNCMS/GC electrode can be applied to measure uric acid in human urine, and may be useful for measuring abnormally high concentration of AA or DA. The attractive features of HNCMS provide potential applications in the simultaneous determination of UA, AA and DA.     

Molecular modeling of 4-methylphthalonitrile for dye sensitized solar cells using quantum chemical calculations

The geometries, electronic structures, polarizabilities, and hyperpolarizabilities of organic dye sensitizer 4-Methylphthalonitrile was studied based on Hartree-Fock (HF) and density functional theory (DFT) using the hybrid functional B3LYP. Ultraviolet-visible (UV-Vis) spectrum was investigated by time dependent-density functional theory (TD-DFT). Features of the electronic absorption spectrum in the visible and near-UV regions were assigned based on TD-DFT calculations. The absorption bands are assigned to π → π* transitions. Calculated results suggest that three lowest energy excited states of 4-Methylphthalonitrile are due to photo induced electron transfer processes. The interfacial electron transfer between semiconductor TiO₂ electrode and dye sensitizer 4-Methylphthalonitrile is due to an electron injection process from excited dye to the semiconductor’s conduction band. The role of cyanine and methyl group in 4-Methylphthalonitrile in geometries, electronic structures, and spectral properties were analyzed.     

Intraspecific sequence variation of chloroplast DNA among the component species of deciduous broad-leaved forests in Japan

To select appropriate plant materials for a phylogeography of deciduous broad-leaved forests in Japan, we surveyed intraspecific chloroplast DNA variation in 34 species found in these forests. A relatively large number of intraspecific cpDNA variations were detected in ten species: Carpinus japonica (nucleotide diversity π=0.00083), C. laxiflora (π=0.00221), Magnolia obovata (π=0.00134), Lindera triloba (π=0.00255), L. obtusiloba (π=0.00289), Pourthiaea villosa var. leavis (π=0.00263), Acer japonicum (π=0.00170), A. micranthum (π=0.00237), Euonymus oxyphyllus (π=0.00322) and Styrax obassia (π=0.00100).     

Colonization of biofilms by bacteria capable of biodegrading sodium dodecyl sulphate (SDS) at clean and polluted riverine sites

Fifty cyanobacterial strains (10 genera) were tested in batch culture for their ability to use organic phosphorus compounds (1 mg liter⁻¹ P) as their sole P source. Two monoesters, Na₂-β-glycerophosphate and π-nitrophenyl phosphate (πNPP), supported growth of all strains, and the diester bis-π-nitrophenyl phosphate (bis-π-NPP) and herring sperm DNA supported almost all strains. ATP was either a very favorable or poor P source and failed to support growth of nine strains, seven of which were Rivulariaceae with trichomes ending in a hair or long tapered region. Phytic acid was in general the least favorable P source. P-limited cultures grown initially with inorganic phosphate to conditions of P limitation were also tested for cell-bound and extracellular phosphomonoesterase (PMEase) and phosphodiesterase (PDEase) activities at two pH values (7.6, 10.3) using πNPP and bis-πNPP as substrates. Cell-bound PMEase was inducible in all strains and cell-bound PDEase in most strains. Most showed extracellular PMEase, but not extracellular PDEase. The highest values (μM πNPP or bis-πNPP hydrolyzed mg dry weight⁻¹ hour⁻¹) all occurred in strains ofGloeotrichia as follows: cell-bound PMEase at pH 7.6, 2.7 μM in strain D602; cell-bound PMEase at pH 10.3, 5.2 μM in D602; extracellular PMEase at pH 7.6, 0.73 μM in D281; extracellular PMEase at pH 10.3, 6.6 μM in D281; cell-bound PDEase at 7.6, 0.40 μM in D613; cell-bound PDEase at pH 10.3, 1.0 μM in D613. The results were compared to see if they indicated possible relationships between phosphatase activity and taxonomic or ecological grouping. The following differences were significant (P<0.05). Rivulariaceae produced higher yields than filamentous non-Rivulariaceae with β-glycerophosphate, πNPP, and DNA. Rivulariaceae with the ability to form hairs in culture showed poorer growth in ATP than non-hair-forming Rivulariaceae, but were more effective at utilizing phytic acid. Strains from calcareous environments had higher PMEase activity at pH 10.3 than strains from noncalcareous environments (P<0.01).     

Simple detection of nucleic acids with a single-walled carbon-nanotube-based electrochemical biosensor

We report for the first time a simple approach to fabricate an electrochemical DNA (E-DNA) biosensor by introducing the single-walled carbon nanotubes (SWNTs). The SWNTs combine with the electrochemical label (methyl blue, MB)-modified single-stranded DNA (ssDNA) probes to generate a nanomaterial-biomolecule composite, which functions as a signal amplification platform to facilitate the electron-transfer between the electrochemical label and the electrode. This SWNT-based E-DNA biosensor produces a high square wave voltammetry (SWV) signal in the absence of target DNA. In the presence of target DNA, the MB-labeled ssDNA probes are removed from the SWNT-modified electrode due to the formation of a double-stranded DNA (dsDNA), generating a relatively low SWV signal. This signal-off SWNT-based E-DNA biosensor exhibits improved sensitivity and large linear dynamic range with low detection limit; it can even distinguish 1-base mismatched target DNA. Further experiments demonstrate that the SWNT-based E-DNA biosensor is superior to the multi-walled carbon nanotube (MWNT)-based one for DNA detection. Moreover, the introduction of aptamer into the SWNT-based biosensor might be further extended to detect small biomolecules such as adenosine.     

Electrochemical nitrite biosensor based on the immobilization of hemoglobin on an electrode modified by multiwall carbon nanotubes and positively charged gold nanoparticle

The report is on an electrochemical biosensor with remarkably improved sensitivity toward nitrite. In this strategy, positively charged gold nanoparticle (PCNA) is used in combination with multiwall carbon nanotubes (MWCNT) by electrostatic adsorption for fabricating PCNA/MWCNT films. Then hemoglobin (Hb) biocatalyst will easily be attached to the surface of the combination films aforementioned. After that, the Hb/PCNA films are immobilized onto the Hb/PCNA/MWCNT films through layer-by-layer assembly technique. The (Hb/PCNA)₂/MWNT/GC electrode thus prepared exhibits enhanced electrocatalytic behavior to the reduction of nitrite at −0.10 V versus SCE in 0.05 M H₂SO₄ solution_. On condition of the low detecting potential and low pH, interference caused by direct electrochemical oxidation or oxidizable substances can be prevented. Therefore, the modified electrode shows fast response time, very high sensitivity, good selectivity and stability. The current response of the sensor increases linearly with nitrite concentration from a range of 3.6 × 10⁻⁶ to 3.0 × 10⁻³ M with a detection limit(S /N = 3) of 9.6 × 10⁻⁷ M.