Functional Nanopores Enabled with DNA

Membrane-spanning nanopores are used in label-free single-molecule sensing and next-generation portable nucleic acid sequencing, and as powerful research tools in biology, biophysics, and synthetic biology. Naturally occurring protein and peptide pores, as well as synthetic inorganic nanopores, are used in these applications, with their limitations. The structural and functional repertoire of nanopores can be considerably expanded by functionalising existing pores with DNA strands and by creating an entirely new class of nanopores with DNA nanotechnology. This review outlines progress in this area of functional DNA nanopores and outlines developments to open up new applications.     

Improved sensitivity of headspace gas chromatography for organic aromatic compounds

Summary The effect of adding an electrolyte and increasing the temperature on the preconcentration of volatile compounds in headspace analysis has been investigated. Quantification of the interactive effects of temperature and addition of salt on the vapor concentration is of interest for the determination of trace organic impurities in pharmaceutical base materials. This study was undertaken to investigate the quantitative effects of the addition of salts alcohols, and acetone, and of increasing the temperature on the vapor concentrations and distribution coefficients of volatile aromatic compounds (benzene, toluene, ando-xylene). It was found that the concentration of aromatic compound residues in the headspace could be increased by adding an inert salt to the water, but this effect was not very significant because of the low orginal solubility of the aromatic compounds in water. The reverse effect can be achieved by use of polar organic additives; this can be explained by the high polarizability of aromatic compounds and their greater solubility in the presence of these solvents. Presented at Balaton Symposium on High-Performance Separation Methods, Siófok, Hungary, September 1–3, 1999.     

New analytical procedure based on a cellulose bag and ionic exchanger with p-aminobenzoic acid groups for differentiation of labile and inert metal species in aquatic systems

A new procedure was developed for the in situ characterization of the lability of metal species in aquatic systems by using a system equipped with a diffusion membrane and cellulose organomodified with p-aminobenzoic acid groups (DM-Cell-PAB). To this end, the DM-Cell-PAB system was prepared by adding cellulose organomodified with p-aminobenzoic acid groups (Cell-PAB) to pre-purified cellulose bags. After the DM-Cell-PAB system was sealed, it was examined in the laboratory to evaluate the influence of complexation time, mass of exchanger, pH, metal ions (Cu, Cd, Fe, Mn, and Ni), and concentration of organic matter on the relative lability of metal species. It was found that the pH and kinetics strongly influence the process of metal complexation by the DM-Cell-PAB system. At all pH levels, Cd, Mn, and Ni showed lower complexation with Cell-PAB resin than Cu and Fe metals. Note that relative lability of metals complexed to aquatic humic substances (AHS) in the presence of Cell-PAB resin showed the following order: Cu≅Fe≫Ni>Mn=Cd. The results presented here also indicate that increasing the AHS concentration decreases the lability of metal species by shifting the equilibrium to AHS–metal complexes. Our results indicate that the system under study offers an interesting alternative that can be applied to in situ experiments for differentiation of labile and inert metal species in aquatic systems.     

Cellulose functionalization via high-energy irradiation-initiated grafting of glycidyl methacrylate and cyclodextrin immobilization

Cotton-cellulose was functionalized using gamma-irradiation-induced grafting of glycidyl methacrylate (GMA) to obtain a hydrophobic cellulose derivative with epoxy groups suitable for further chemical modification. Two grafting techniques were applied. In pre-irradiation grafting (PIG) cellulose was irradiated in air and then immersed in a GMA monomer solution, whereas in simultaneous grafting (SG) cellulose was irradiated in an inert atmosphere in the presence of the monomer. PIG led to a more homogeneous fiber surface, while SG resulted in higher grafting yield but showed clear indications of some GMA-homopolymerization. Effects of the reaction parameters (grafting method, absorbed dose, monomer concentration, solvent composition) were evaluated by SEM, gravimetry (grafting yield) and FTIR spectroscopy. Water uptake of the cellulose decreased while adsorption of a pesticide molecule increased upon grafting. The adsorption was further enhanced by β-cyclodextrin immobilization during SG. This method can be applied to produce adsorbents from cellulose based agricultural wastes.     

Hydrothermally shrunk alumina nanopores and their application to DNA sensing

Hydrothermal treatment of anodized alumina membranes has been known for years and is believed to seal the pores by transforming aluminium oxide into lower density hydroxides. We demonstrate that, at least for 60 nm diameter pores grown from anodization in oxalic acid at 40 V, the hydrothermal treatment significantly shrinks but does not fully seal the nanopores. The pores shrink to a neck of less than 10 nm in diameter and 2-4 microm in length, in which the diffusion coefficient of ions is five orders of magnitude smaller than in the bulk. Because of a high electrolyte resistance through hydrothermally treated shrunken nanopores, they can be used for electrical sensing applications, as demonstrated using the example of DNA sensing. Hybridization of target DNA with a complementary ssDNA covalently immobilized inside the nanopores causes an increase in impedance by more than 50% while a noncomplementary ssDNA has no measurable effect.     

电化学间接测量法研究谷胱甘肽在多壁碳纳米管和活性炭上的吸附

选取谷胱甘肽(GSH)作为小分子代表物,利用Cr(VI)与GSH的相互作用,即K2Cr2O7/H2SO4溶液加入GSH前后Cr(VI)还原峰电流值的差异,通过差分脉冲伏安法(DPV)的测定,可以间接测出GSH的含量.尝试将这种电化学间接测量法应用于研究多壁碳纳米管(MWCNTs)与商业活性炭(AC)对GSH的吸附行为.利用该方法可以确立GSH在二者的吸附量(Q)与吸附平衡浓度(Ce)的关系,绘制吸附等温曲线.根据Langmuir方程和Freundlich方程的拟合分析,证明了与商业活性炭相比,GSH在MWCNTs上的吸附更倾向Freundlich模型,即多分子层吸附.利用扫描电子显微镜(SEM)和透射电子显微镜(TEM)进行形貌表征,发现MWCNTs具有发达的堆积孔结构,有利于GSH小分子内扩散和吸附,与实验结果一致.     

Synthesis of a Porous [14]Annulene Graphene Nanoribbon and a Porous [30]Annulene Graphene Nanosheet on Metal Surfaces

The electrical and mechanical properties of graphene-based materials can be tuned by the introduction of nanopores, which are sensitively related to the size, morphology, density, and location of nanopores. The synthesis of low-dimensional graphene nanostructures containing well-defined nonplanar nanopores has been challenging due to the intrinsic steric hindrance. Herein, we report the selective synthesis of one-dimensional (1D) graphene nanoribbons (GNRs) containing periodic nonplanar [14]annulene pores on Ag(111) and two-dimensional (2D) porous graphene nanosheet containing periodic nonplanar [30]annulene pores on Au(111), starting from a same precursor. The formation of distinct products on the two substrates originates from the different thermodynamics and kinetics of coupling reactions. The reaction mechanisms were confirmed by a series of control experiments, and the appropriate thermodynamic and kinetic parameters for optimizing the reaction pathways were proposed. In addition, the combined scanning tunneling spectroscopy (STS) and density functional theory (DFT) calculations revealed the electronic structures of porous graphene structures, demonstrating the impact of nonplanar pores on the π-conjugation of molecules.     

Coagulation kinetics of amorphous colloidal silica suspensions with and without hydroxypropyl cellulose polymer

The coagulation rate constant of submicron silica has been measured as a function of solution pH, salt concentration and hydroxypropyl cellulose (HPC) polymer concentration. Results show that the colloidal stability of silica is dominated by the cation concentration in the presence of salt in the pH range 3–9.5. The stability increases as cation concentration decreases. At low salt concentration and a minimum colloid stability was found in the intermediate pH range 4–8. These results show that differences in the literature values of the critical coagulation constant by relative light-scattering experiments can be explained by the use of the coagulation rate constant analysis. When HPC polymer was present in the solution, the colloid stability of the silica increased. The adsorption of polymer stabilizes the silica suspensions, both at low pH near the isoelectric point and at high ionic strength where it coagulates without the polymer. A monolayer coverage was necessary to provide steric stabilization. At 10^–3 M KCl a smaller equilibrium concentration of HPC in solution is needed to give monolayer coverage and steric stabilization than at 1 M KCl and pH 4.2.     

离子型芘衍生物同聚电解质键合平衡的模拟

利用平衡键合模型模拟了聚电解质同荧光探针离子键合过程的计量关系 ,以及添加盐竞争键合时的计量关系 .计算的结果能够描述荧光实验结果 .芘离子探针PyMeA·HCl的IE IM 随着探针浓度的增加 ,会出现一个极大值 ,此极大值能够定量地给出饱和键合计量关系 .当盐浓度和聚电解质荷电单元浓度相当时 ,盐离子和芘离子探针发生明显的竞争键合 ,部分离子探针被排挤入水相 ,实验的IE IM 随盐浓度增大急剧减小     

Rheological studies of the interactions in cellulose/ethylene diamine/salt systems

Degree of polymerization (DP) of cellulose was measured to confirm that aging time and salt concentration did not cause cellulose degradation. Dynamic rheological studies of cellulose solutions were carried out to probe the evolving interactions between cellulose and ethylene diamine (EDA)/salt solvent system. Potassium thiocyanate (KSCN) was used as the salt in these studies. Steady shear studies indicated that all solutions exhibited shear‐thinning behavior. The empirical Cox‐Merz rule did not hold true for the cellulose system with weak gel microstructure. The shear viscosities at the shear rates explored decreased with aging time. The zero‐shear viscosity, however, increased with increasing salt concentration. Oscillatory shear studies were investigated and the time temperature superposition (TTS) method was used to extend the experimental frequency range of the instrument. The results showed that the average relaxation time of the cellulose system decreased as the sample aged and increased with increasing salt concentration, indicative of dynamic interactions between cellulose and the solvent system in solution. The conformations of cellulose chains were constantly changing over time. The system gelled when the salt concentration was increased to a critical point. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 2326–2334, 2008     

Effects of carbonyl and aldehyde groups in the graft copolymerization of methyl methacrylate on cellulose with a ceric salt

Graft copolymerization of methyl methacrylate on cellulosic materials of various carbonyl and aldehyde contents with the use of a ceric salt as an initiator was studied. It was found that the concentration of the ceric salt which gives the maximum per cent grafting is in good agreement with the equivalent of total carbonyl content in the cellulosic material, and the number of grafted chains in copolymers is roughly proportional to it. However, the molar ratio of the number of grafted chains to total carbonyl content is quite small, being approximately 1:50, and the graft copolymerization can be explained kinetically on the assumption that the number of radicals produced on cellulose by the ceric salt leading to branching is very much smaller than the number of radicals destroyed by the ceric salt, and growing radicals can be stabilized by the termination reaction with the ceric salt or with a cellulose radical. Although both aldehyde and carbonyl groups contribute to the formation of grafted chains, the former are effective mainly at low concentrations of the ceric salt; both groups participate in the production of graft copolymers showing the maximum per cent grafting.     

Coupled transport membranes III: the rate-limiting step in uranium transport with a tertiary amine

This is the second paper describing the coupled transport of uranium ions through liquid membranes. The membranes consist of a microporous polymeric support with an organic solution of a tertiary amine complexing agent held within the pores by capillary forces. p]Both the composition of the organic solution and the structure of the microporous support have a marked effect on uranium flux. With increasing concentration of the agent in an inert diluent, both the amount of uranium that can be extracted into the membrane and the viscosity of the organic solution increase. These opposing effects result in a maximum flux at about 30 vol.% agent in the diluent. The size of the pores in the support also affects the flux; it appears that interaction with the pore walls in membranes with small pores hinders diffusion. p]Two types of interfacial effects have also been observed. The first of these is concentration polarization in the aqueous solution adjacent to the membrane surface. This effect can be reduced by increased stirring. Second, the transmembrane flux of uranium can be limited by the rate of formation (or dissociation) of the uranium complex at the membrane—solution interfaces.     

The investigation of complex formation equilibria at constant ionic strength

The inert salts used for the investigations of complex formation are briefly discussed in relation to the effects of their ions on the equilibria studied. In general, some association with the inert salt ions cannot be completely avoided. In case of very stable complexes measured at low ionic strength, their effects can be quantified even though they are not caused by the anion if NO(-)(3) or ClO(-)(4) are used. In the case of weak complexes, when ionic strengths I > or =1 are used, the concentration of the complex of interest can be 1000 times lower than that of the associates of the same cation with the anion of the inert salt causing difficulties with the investigation of the latter systems. If the experimental results for K(1) of the alkaline-earth metal ions with fluoride in sodium perchlorate and sodium nitrate are correct, as their equilibrium constants have very similar values, it follows that the behavior of two anions is very similar. However, if NO(-)(3) associates with the above cations, as found, the same behavior is expected for ClO(-)(4). A more accurate analysis can only be done if activity coefficients in these solutions are known.     

Quasi one-dimensional nanopores in single-wall carbon nanohorn colloids using grand canonical Monte Carlo simulation aided adsorption technique

The average interstitial nanopore structure of single-wall carbon nanohorn (SWNH) assemblies was determined using X-ray diffraction and grand canonical Monte Carlo (GCMC) simulation aided N(2) adsorption at 77 K. The interstitial nanopores of SWNH assemblies can be regarded as quasi one-dimensional pores due to the partial orientation of the SWNH particles; the average pore width of the interstitial pores is 0.6 nm. Good agreement between the GCMC simulation of a structural model with one-dimensional interstitial nanopores and an experimental adsorption isotherm below P/P(0) = 10(-4) is evidence of the quasi one-dimensionality of the interstitial nanopores. A snapshot from the GCMC simulation showed one-dimensional growth of adsorbed N(2) molecules.     

Electric-field-controlled water and ion permeation of a hydrophobic nanopore

The permeation of hydrophobic, cylindrical nanopores by water molecules and ions is investigated under equilibrium and out-of-equilibrium conditions by extensive molecular-dynamics simulations. Neglecting the chemical structure of the confining pore surface, we focus on the effects of pore radius and electric field on permeation. The simulations confirm the intermittent filling of the pore by water, reported earlier under equilibrium conditions for pore radii larger than a critical radius R(c). Below this radius, water can still permeate the pore under the action of a strong electric field generated by an ion concentration imbalance at both ends of the pore embedded in a structureless membrane. The water driven into the channel undergoes considerable electrostriction characterized by a mean density up to twice the bulk density and by a dramatic drop in dielectric permittivity which can be traced back to a considerable distortion of the hydrogen-bond network inside the pore. The free-energy barrier to ion permeation is estimated by a variant of umbrella sampling for Na(+), K(+), Ca(2+), and Cl(-) ions, and correlates well with known solvation free energies in bulk water. Starting from an initial imbalance in ion concentration, equilibrium is gradually restored by successive ion passages through the water-filled pore. At each passage the electric field across the pore drops, reducing the initial electrostriction, until the pore, of radius less than R(c), closes to water and hence to ion transport, thus providing a possible mechanism for voltage-dependent gating of hydrophobic pores.     

Side reaction of cellulose with common 1-alkyl-3-methylimidazolium-based ionic liquids

Ionic liquids with 1-alkyl-3-methyl-imidazolium cations react at C-2 with cellulose at its reducing end, forming a carbon-carbon bond. The reaction is strongly catalyzed by bases, such as the commonly present impurities in ILs, imidazole, and 1-methylimidazole. The direct reaction was verified by means of ¹³C-isotopical labeling and with the help of an IL that carried a fluorescence label which was transferred to cellulose upon the reaction. In solutions of cellulose in alkylmethylimidazolium ILs, both the ionic liquid and the cellulose are evidently not inert.     

Development of a new analytical approach based on cellulose membrane and chelator for differentiation of labile and inert metal species in aquatic systems

A new procedure was developed in this study, based on a system equipped with a cellulose membrane and a tetraethylenepentamine hexaacetate chelator (MD-TEPHA) for in situ characterization of the lability of metal species in aquatic systems. To this end, the DM-TEPHA system was prepared by adding TEPHA chelator to cellulose bags pre-purified with 1.0 mol L⁻¹ of HCl and NaOH solutions. After the MD-TEPHA system was sealed, it was examined in the laboratory to evaluate the influence of complexation time (0-24 h), pH (3.0, 4.0, 5.0, 6.0 and 7.0), metal ions (Cu, Cd, Fe, Mn and Ni) and concentration of organic matter (15, 30 and 60 mg L⁻¹) on the relative lability of metal species by TEPHA chelator. The results showed that Fe and Cu metals were complexed more slowly by TEPHA chelator in the MD-TEPHA system than were Cd, Ni and Mn in all pH used. It was also found that the pH strongly influences the process of metal complexation by the MD-TEPHA system. At all the pH levels, Cd, Mn and Ni showed greater complexation with TEPHA chelator (recovery of about 95-75%) than did Cu and Fe metals. Time also affects the lability of metal species complexed by aquatic humic substances (AHS); while Cd, Ni and Mn showed a faster kinetics, reaching equilibrium after about 100 min, and Cu and Fe approached equilibrium after 400 min. Increasing the AHS concentration decreases the lability of metal species by shifting the equilibrium to AHS-metal complexes. Our results indicate that the system under study offers an interesting alternative that can be applied to in situ experiments for differentiation of labile and inert metal species in aquatic systems.     

Coupling Effects of Electrostatic Interactions and Salt Concentration Gradient in Polymer Translocation through a Nanopore: A Coarse-Grained Molecular Dynamics Simulations Study

We study the influence of polymer pore interactions and focus on the role played by the concentration gradient of salt in the translocation of polyelectrolytes (PE) through nanopores explicitly using coarse-grained Langevin dynamics simulations. The mean translocation time is calculated by varying the applied voltage, the pH, and the salt concentration gradient. Changing the pH can alter the electrostatic interaction between the protein pore and the polyelectrolyte chain. The polymer pore interaction is weakened by the increase in the strength of the externally applied electric field that drives translocation. Additionally, the screening effect of the salt can reduce the strong charge-charge repulsion between the PE beads which can make translocation faster. The simulation results show there can be antagonistic or synergistic coupling between the salt concentration-induced screening effect and the drift force originating from the salt concentration gradient thereby affecting the translocation time. Our simulation results are explained qualitatively with free energy calculations.     

Biosensing with conically shaped nanopores and nanotubes

In this review we consider recent results from our group that are directed towards developing "smart" synthetic nanopores that can mimic the functions of biological nanopores (transmembrane proteins). We first discuss the preparation and characterization of conical nanopores synthesized using the track-etch process. We then consider the design and function of conical nanopores that can rectify the ionic current that flows through these pores under an applied transmembrane potential. Finally, two types of sensors that we have developed with these conical nanopores are described. The first sensor makes use of molecular recognition elements that are bound to the nanopore mouth to selectively block the nanopore tip, thus detecting the presence of the analyte. The second sensor makes use of conical nanopores in a resistive-pulse type experiment, detecting the analyte via transient blockages in ionic current.     

Hydrogen confinement in carbon nanopores: extreme densification at ambient temperature

In-situ small-angle neutron scattering studies of H(2) confined in small pores of polyfurfuryl alcohol-derived activated carbon at room temperature have provided for the first time its phase behavior in equilibrium with external H(2) at pressures up to 200 bar. The data were used to evaluate the density of the adsorbed fluid, which appears to be a function of both pore size and pressure and is comparable to the density of liquid H(2) in narrow nanopores at ～200 bar. The surface-molecule interactions responsible for densification of H(2) within the pores create internal pressures that exceed the external gas pressure by a factor of up to ～50, confirming the benefits of adsorptive storage over compressive storage. These results can be used to guide the development of new carbon adsorbents tailored for maximum H(2) storage capacities at near-ambient temperatures.