Molecular Recognition Capabilities Research Articles

A novel method for dengue virus detection and antibody screening using a graphene-polymer based electrochemical biosensor

Dengue fever is a major disease that kills many people in the developing world every year. During early infection, a patient displays a high temperature without other signs. After this stage, and without proper treatment, serious damage to internal organs can happen, which occasionally leads to death. A rapid technique for the early detection of dengue virus (DENV) could reduce the number of fatalities. This study presents a new technique for the detection, classification and antibody screening of DENV based on electrochemical impedance spectroscopy (EIS). We found that the charge transfer resistance (Rct) of a gold electrode coated with graphene oxide reinforced polymer was influenced by virus type and quantity exposed on the surface. Molecular recognition capability established during the GO-polymer composite preparation was used to explain this observation. The linear dependence of Rct versus virus concentrations ranged from 1 to 2×103pfu/mL DENV with a 0.12 pfu/mL detection limit.

A Modular Bioplatform Based on a Versatile Supramolecular Multienzyme Complex Directly Attached to Graphene.

Developing generic strategies for building adaptable or multifunctional bioplatforms is challenging, in particular because protein immobilization onto surfaces often causes loss of protein function and because multifunctionality usually necessitates specific combinations of heterogeneous elements. Here, we introduce a generic, modular bioplatform construction strategy that uses cage-like supramolecular multienzyme complexes as highly adaptable building blocks immobilized directly and noncovalently on graphene. Thermoplasma acidophilum dihydrolipoyl acyltransferase (E2) supramolecular complexes organize as a monolayer or can be controllably transferred onto graphene, preserving their supramolecular form with specific molecular recognition capability and capacity for engineering multifunctionality. This E2-graphene platform can bind enzymes (here, E1, E2's physiological partner) without loss of enzyme function; in this test case, E1 catalytic activity was detected on E2-graphene over 6 orders of magnitude in substrate concentration. The E2-graphene platform can be multiplexed via patterned cotransfer of differently modified E2 complexes. As the E2 complexes are robust and highly customizable, E2-graphene is a platform onto which multiple functionalities can be built.

Fabrication of β-Cyclodextrin-Functionalized Reduced Graphene Oxide and Its Application for Electrocatalytic Detection of Carbendazim

We reported a graphene-based electrochemical sensor for sensitively measuring carbendazim, which is one of the effective benzimidazole fungicides popularly used in agriculture. The β-cyclodextrin-functionalized reduced graphene oxide (β-CD–RGO) nanocomposites were synthesized using hydrazine as the reducing agent at room temperature. The as-synthesized nanocomposites were characterized using different analytical methods including UV–visible spectroscopy and Fourier transform infrared spectroscopy. The nanocomposites with a combination of physicochemical properties of RGO and high molecular recognition capability of β-CD were used to modify the surface of a glassy carbon electrode for the electrochemical determination of the drug carbendazim using cyclic voltammetry and differential pulse voltammetry. The current responses of carbendazim on the β-CD–RGO-modified electrode were greatly enhanced compared to that on the bare electrode due to the electrocatalytic effect of β-CD–RGO. It was found that the peak currents increased linearly with the carbendazim concentration in the range between 0.1 and 40 μM. The obtained results suggest that β-CD–RGO composite could be a potential candidate for the preparation of effective electrochemical sensors for carbendazim or similar drugs in the future.

Protein Calligraphy: A New Concept Begins To Take Shape.

The ability to assemble molecules into supramolecular architectures of controllable size and symmetry is a long sought after goal of nanotechnology and material engineering. Proteins are particularly attractive for molecular assembly due to their inherent molecular recognition and self-assembly capabilities. Advances in the computational prediction of protein folding and quaternary assembly have enabled the design of proteins that self-assemble into complex yet predictable shapes. These protein nanostructures are opening new possibilities in biomaterials, metabolic engineering, molecular delivery, tissue engineering, and a plethora of nanomaterials. Images of protein constructs assembled from simpler structures draw comparison to characters of calligraphy. In both cases, elaborate designs emerge from basic subunits, resulting in the translation of form into function with a high degree of artistry.

Geometrical assembly of ultrastable protein templates for nanomaterials.

The fabrication of nanoscale devices requires architectural templates on which to position functional molecules in complex arrangements. Protein scaffolds are particularly promising templates for nanomaterials due to inherent molecular recognition and self-assembly capabilities combined with genetically encoded functionalities. However, difficulties in engineering protein quaternary structure into stable and well-ordered shapes have hampered progress. Here we report the development of an ultrastable biomolecular construction kit for the assembly of filamentous proteins into geometrically defined templates of controllable size and symmetry. The strategy combines redesign of protein–protein interaction specificity with the creation of tunable connector proteins that govern the assembly and projection angles of the filaments. The functionality of these nanoarchitectures is illustrated by incorporation of nanoparticles at specific locations and orientations to create hybrid materials such as conductive nanowires. These new structural components facilitate the manufacturing of nanomaterials with diverse shapes and functional properties over a wide range of processing conditions.

Preparation of per-hydroxylated pillar[5]arene decorated graphene and its electrochemical behavior

In the present work, per-hydroxylated pillar[5]arene decorated graphene was prepared and characterized with Fourier transform infrared spectroscopy, UV–vis spectroscopy, thermogravimetric analysis and transmission electron microscopy. Meanwhile, the electrochemical behavior of the electrodes coated with the as-prepared graphene derivative was explored in the presence of dopamine, ascorbic acid, uric acid and their mixture. The results indicate that the per-hydroxylated pillar[5]arene molecules are successfully linked onto the surface of graphene. The electrodes coated with the as-prepared graphene derivative possess high sensitivity to dopamine with a detectable concentration of 2.0×10−7 molL−1. More interested, the per-hydroxylated pillar[5]arene decorated graphene exhibits satisfactory capability of molecular recognition for dopamine, ascorbic acid and uric acid. When uric acid and ascorbic acid are present, the redox peaks of dopamine can be conveniently recognized on the electrodes coated with the as-prepared graphene derivative. Finally, the sensitivity and selectivity of the per-hydroxylated pillar[5]arene decorated graphene to dopamine are discussed from the viewpoints of the size/shape-fit concept and hydrogen bond catalysis mechanism.

Engineering Smart Wrappings for Next Generation Single-Walled Carbon Nanotube (SWCNT) Sensors

Semiconducting Single-Walled Carbon Nanotubes (SWCNTs) have a unique combination of optical, chemical, and physical properties that render them suitable for a broad range of applications1–3. Since SWCNTs are composed exclusively of surface atoms, the fluorescence emission of the nanotubes is very sensitive to the surrounding environment, enabling single-molecule detection limits that are especially desirable for biosensing applications. The selectivity of SWCNT-based fluorescence sensors can be tuned by engineering a polymer wrapping that covers the nanotube surface, imparting the nanotube with molecular recognition capabilities. The challenge in creating these near-infrared (NIR) fluorescence sensors lies with tuning the specificity of the sensor by altering the wrapping properties. Though the exact mechanism by which polymers render surface selectivity is an area of active area of research4, researchers have been nonetheless able to engineer wrappings by screening an assortment of SWCNTs wrapped in various polymers and monitoring fluorescence changes in response to different analytes. In contrast to this empirical approach, we have developed ”smart” wrappings capable of pre-defined molecular recognition towards a specific analyte of interest. By applying established synthetic and biological techniques for engineering specificity, our platform provides an interdisciplinary approach towards exploring the underlying molecular mechanism and versatility in tuning optical SWCNT-based sensors. The results of this work provide a seminal proof-of-concept approach in developing smart sensing technologies. References (1) Han, C.; Doepke, A.; Cho, W.; Likodimos, V.; De La Cruz, A. a.; Back, T.; Heineman, W. R.; Halsall, H. B.; Shanov, V. N.; Schulz, M. J.; Falaras, P.; Dionysiou, D. D. Adv. Funct. Mater. 2013, 23(14), 1807–1816. (2) Choi, Y.-E.; Kwak, J.-W.; Park, J. W. Sensors 2010, 10(1), 428–455. (3) Liu, Z.; Chen, K.; Davis, C.; Sherlock, S.; Cao, Q.; Chen, X.; Dai, H. Cancer Res. 2008, 68(16), 6652–6660. (4) Z. W. Ulissi, J. Zhang, V. Sresht, D. Blankschtein, M. S. Strano, Langmuir 2015, 31(1), 628–636.

Development of high performance and facile to pack molecularly imprinted particles for aqueous applications

Different kinds of molecularly imprinted particles were synthesized and compared, aiming at the development of materials combining high molecular recognition capabilities and facile use as column packing materials for chromatographic aqueous applications. Solution, inverse-suspension and precipitation polymerization were considered and two different model molecules (5-fluorouracil and caffeine) were used to highlight the effect of the interaction between the template molecule and the functional monomer on imprinting efficiency. Particles synthesized through the proposed inverse-suspension process exhibit facile use for packing columns, allow the stable running of chromatographic systems and present a high performance in drug uptake and release in aqueous media. Frontal analysis measurements highlight these key features of the synthesized particles. Drug sorption capabilities of 0.890μmol/g and 5.774μmol/g were measured for 5-fluorouracil and caffeine, respectively, using frontal analysis with eluents containing the target molecules at concentration 0.1mM. Due to the lower amount of solvent required than with precipitation polymerization, the developed inverse-suspension process presents high synthesis yields, which can be exploited for the large-scale manufacture and commercialization of molecularly imprinted materials. The combined features of the particles makes possible their direct use in bioseparations or in the development of assays and pharmacokinetic studies concerning the presence of drugs in biological fluids.

Review—Engineering the Selectivity of the DNA-SWCNT Sensor

Single-walled carbon nanotubes (SWCNTs) demonstrate a unique combination of optical, chemical, and physical properties that render them suitable for a variety of sensing applications. Their photostable near-infrared (nIR) fluorescence emissions are highly sensitive to perturbations in the surrounding SWCNT environment, enabling optical sensors with single-molecule detection limits. Despite these immanent advantages, SWCNTs lack the inherent molecular recognition capabilities required for selective sensing applications. One approach to tuning sensor selectivity is to engineer synthetic and biological wrappings that cover the nanotube's surface in a manner that limits chemical access to the surface to specific target analytes. Among the numerous possible wrappings, deoxyribonucleic acid (DNA) has emerged as the most studied polymeric wrapping. In addition to the sequence-dependent tunability DNA offers in engineering selectivity, DNA assumes a peculiar helical wrapping conformation along the SWCNT surface that has been the focus of many experimental and computational studies. In this review, we summarize some of the major findings in the field, focusing on the underlying molecular interactions responsible for the conformational and molecular recognition elements of the wrapping. Special focus is given to characterizing the nucleotide binding affinity, DNA sequence dependency, DNA length variation, SWCNT chirality, and sugar backbone (RNA vs. DNA) contributions to the wrapping conformation and SWCNT fluorescence. This article concludes with an assessment of the latest DNA-SWCNT-based sensing platforms used for the selective, single- and multi-modal detection of target analytes.

Incorporation of Cobalt-Cyclen Complexes into Templated Nanogels Results in Enhanced Activity.

Recent advances in nanomaterials have identified nanogels as an excellent matrix for novel biomimetic catalysts using the molecular imprinting approach. Polymerisable Co‐cyclen complexes with phosphonate and carbonate templates have been prepared, fully characterised and used to obtain nanogels that show high activity and turnover with low catalytic load, compared to the free complex, in the hydrolysis of 4‐nitrophenyl phosphate, a nerve agent simulant. This work demonstrates that the chemical structure of the template has an impact on the coordination geometry and oxidation state of the metal centre in the polymerisable complex resulting in very significant changes in the catalytic properties of the polymeric matrix. Both pseudo‐octahedral cobalt(III) and trigonal‐bipyramidal cobalt(II) structures have been used for the synthesis of imprinted nanogels, and the catalytic data demonstrate that: i) the imprinted nanogels can be used in 15 % load and show turnover; ii) the structural differences in the polymeric matrices resulting from the imprinting approach with different templates are responsible for the molecular recognition capabilities and the catalytic activity. Nanogel P1, imprinted with the carbonate template, shows >50 % higher catalytic activity than P2 imprinted with the phosphonate.

A novel photoelectrochemical sensor for bilirubin based on porous transparent TiO2 and molecularly imprinted polypyrrole

Transparent photocatalytic surfaces are of ever increasing importance for the enhancement of the photocatalytic efficiency. Here, the porous transparent TiO2 (PTT) was conveniently fabricated on the glass substrate by a sol-gel process, and a novel photoelectrochemical sensing platform with excellent photochemical catalysis and molecular recognition capabilities was established for bilirubin detection based on the modification of molecularly imprinted polypyrrole (MIPPy) onto PTT surface by the molecular imprinting technique. The performance of the fabricated sensor was evaluated and the results indicated that the sensor exhibited high sensitivity in bilirubin detection, with a linear range from 0.03 to 28μM and a limit of detection of 0.001μM. Moreover, the sensor exhibited outstanding selectivity while used in coexisting systems containing various interferents with high concentration. The practical application of the sensor was also realized in the selective detection of bilirubin in real samples. The favorable performance of the developed bilirubin sensor can be mainly attributed to the high transparency and photoelectric activity of PTT and selective recognition and excellent conductivity of MIPPy.

Synthesis, Structural Characterization, and Host–Guest Studies of Aminoquinonato-Bridged Re(I) Supramolecular Rectangles

Aminoquinonato bridged Re(I)-based metallarectangles have been constructed via an orthogonal bonding approach. Self-assembly of Re2(CO)10 and aminoquinone ligands in the presence of ditopic linear pyridyl ligands has resulted in the formation of metallarectangles of the general formula [{(CO)3Re(μ-η(4)-L)Re(CO)3}2(μ-N-L'-N)2] (1-4), wherein 1, L = 2,5-bis(n-butylamino)-1,4-benzoquinonato (bbbq) and N-L'-N = 4,4'-bipyridine (bpy); 2, L = 2,5-bis(phenethylamino)-1,4-benzoquinonato (bpbq) and N-L'-N = 4,4'-bipyridine; 3, L = 2,5-bis(n-butylamino)-1,4-benzoquinonato (bbbq) and N-L'-N = trans-1,2-bis(4-pyridyl)ethylene (bpe) and 4, L = 2,5-bis(phenethylamino)-1,4-benzoquinonato (bpbq) and N-L'-N = trans-1,2-bis(4-pyridyl)ethylene (bpe). Metallarectangles 1-4 have been characterized by elemental analysis, IR, NMR, and UV-vis absorption spectroscopic techniques. The molecular structures of 1 and 4 were determined by single-crystal X-ray diffraction methods. The molecular recognition capability of 1 and 3 with pyrene and triphenylene has been investigated using UV-vis absorption and emission spectroscopic techniques. The formation of host-guest complex has been further corroborated by the single-crystal X-ray structural evidence of carceplex system (3⊃pyrene)·(DMF).

Simple and Rapid Functionalization of Gold Nanorods with Oligonucleotides Using an mPEG-SH/Tween 20-Assisted Approach.

DNA conjugated gold nanorods (AuNRs) are widely applied for nanostructure assembly, gene therapy, biosensing, and drug delivery. However, it is still a great challenge to attach thiolated DNA on AuNRs, because the positively charged AuNRs readily aggregate in the presence of negatively charged DNA. This article reports an mPEG-SH/Tween 20-assisted method to load thiolated DNA on AuNRs in 1 h. Tween 20 and mPEG-SH are used to synergistically displace CTAB on the surface of AuNRs by repeated centrifugation and resuspension, and thiolated DNA are attached to AuNRs in the presence of 1 M NaCl, 100 mM MgCl2, or 100 mM citrate. AuNRs with different sizes and aspect ratios can be functionalized with DNA by this method. The number of DNA loaded on each AuNR can be easily controlled by the concentrations of mPEG-SH and Tween 20 or the ratio between DNA and AuNR. Functionalized AuNRs were used for nanoparticle assembly and cancer cell imaging to confirm that DNA anchored on the surface of AuNRs retains its hybridization and molecular recognition capability. The new method is easy, rapid, and robust for the preparation of DNA functionalized AuNRs for a variety of applications such as cancer therapy, drug delivery, self-assembly, and imaging.

Coordination-mediated programmable assembly of unmodified oligonucleotides on plasmonic silver nanoparticles.

DNA-decorated metal nanoparticles have found numerous applications, most of which rely on thiolated DNA (SH-DNA)-modified gold nanoparticles (AuNPs). Whereas silver nanoparticles (AgNPs) are known to have stronger plasmonic properties than AuNPs, modification of AgNPs with SH-DNA is technically challenging, partially due to the instability of Ag-S bonding. Here we demonstrate a facile approach to self-assemble unmodified DNA on AgNPs by exploiting intrinsic silver-cytosine (Ag-C) coordination. The strong Ag-C coordination allows for the ready formation of DNA-AgNP conjugates, which show favorable stability under conditions of high ionic strength and high temperature. These nanoconjugates possess much higher efficient molecular recognition capability and faster hybridization kinetics than thiolated DNA-modified AgNPs. More importantly, we could programmably tune the DNA density on AgNPs with the regulation of silver-cytosine coordination numbers, which in turn modulated their hybridizability. We further demonstrated that these DNA-AgNP conjugates could serve as excellent building blocks for assembling silver and hybrid silver-gold nanostructures with superior plasmonic properties.

Implementation of molecularly imprinted polymer beads for surface enhanced Raman detection.

Molecularly imprinted polymers (MIPs) have a predesigned molecular recognition capability that can be used to build robust chemical sensors. MIP-based chemical sensors allow label-free detection and are particularly interesting due to their simple operation. In this work we report the use of thiol-terminated MIP microspheres to construct surfaces for detection of a model organic analyte, nicotine, by surface enhanced Raman scattering (SERS). The nicotine-imprinted microspheres are synthesized by RAFT precipitation polymerization and converted into thiol-terminated microspheres through aminolysis. The thiol groups on the MIP surface allow the microspheres to be immobilized on a gold-coated substrate. Three different strategies are investigated to achieve surface enhanced Raman scattering in the vicinity of the imprinted sites: (1) direct sputtering of gold nanoparticles, (2) immobilization of gold colloids through the MIP's thiol groups, and (3) trapping of the MIP microspheres in a patterned SERS substrate. For the first time we show that large MIP microspheres can be turned into selective SERS surfaces through the three different approaches of assembly. The MIP-based sensing surfaces are used to detect nicotine to demonstrate the proof of concept. As synthesis and surface functionalization of MIP microspheres and nanoparticles are well established, the methods reported in this work are handy and efficient for constructing label-free chemical sensors, in particular for those based on SERS detection.

Attainment of unstable β nucleation of glycine in presence of l-tyrosine and its analytical interpretation—A combined approach

The ability of l-tyrosine molecules to act as a template and to facilitate the nucleation of unstable β polymorph in the solution has been revealed through in-situ nucleation study. This nucleation of β occurs along with the existing α nucleation at the critical concentration of additive in the solution. The presence of l-tyrosine molecules lowers the inherent barrier that exists for β nucleation in the solution. No nucleation of γ was observed over the entire range of concentrations studied. The molecular recognition capability and stereo selective inhibitory action of the added l-tyrosine molecules towards glycine molecule have been successfully revealed in terms of habit modification observed in the nucleated polymorphs. In the case of α polymorph, l-tyrosine induces a change in the morphology along the enantiopolar −b direction while in the case of β polymorph, habit modification from needle to plate like structure is observed. With the increase in time span, solution mediated phase transformation from β to α polymorph has been observed in the solution. Analytically the nucleation parameters of α and β polymorphs were estimated based on Classical Nucleation Theory. Form of crystallization of the nucleated polymorphs of glycine was confirmed by a powder x-ray diffraction analysis.

Modification of carbon aerogel electrode with molecularly imprinted polypyrrole for electrochemical determination of dopamine

Carbon aerogel (CA) was prepared by sol–gel process at ambient pressure drying. A novel electrochemical sensing platform with electrocatalytical activity and molecular recognition capabilities was developed for the detection of dopamine (DA), based on the modification of molecularly imprinted polypyrrole (MIPPy) onto a CA surface by electropolymerization and molecular imprinting techniques. The optimum sensing conditions could be provided with pyrrole-DA molar ratio of 1.5:1. The performance of the fabricated sensor was evaluated and the results indicated that the sensor exhibited high sensitivity in DA detection, with a linear range from 0.007 to 35μM and a limit of detection of 0.0004μM. Moreover, the sensor showed high selectivity towards DA in comparison to other interferents. The practical application of the sensor was also realized in the selective detection of DA in real samples.

Design of molecularly imprinted TiO2/carbon aerogel electrode for the photoelectrochemical determination of atrazine

Carbon aerogel (CA) was prepared by sol–gel process at ambient pressure drying. A novel photoelectrochemical sensing platform with excellent photochemical catalysis and molecular recognition capabilities was fabricated on the CA with a convenient surface modification of molecularly imprinted TiO2 (MIT) (denoted as MIT/CA) for the atrazine monitoring. Under the optimal experimental conditions, the designed MIT/CA electrode presented high sensitivity in atrazine determination, with a linear range from 0.12 to 93μM and a limit of detection of 0.008μM. Moreover, the electrode exhibited outstanding selectivity while used in coexisting systems containing various interferents with high concentration, 25 times that of atrazine. The practical application of the electrode was also realized in the selective determination of atrazine in water samples. The favourable performance of the as-prepared electrode can be mainly attributed to the selective recognition and high photoelectric activity of MIT and excellent conductivity of CA that promotes the charge transfer.

Electrochemical simultaneous determination of hydroquinone and p-nitrophenol based on host–guest molecular recognition capability of dual β-cyclodextrin functionalized Au@graphene nanohybrids

Cyclodextrins (CDs) are extensively used in nanoscale electrochemical devices because of their outstanding host–guest molecular recognition capability. In this study, uniform, monodispersed 4.5nm gold nanoparticles (Au NPs) were anchored onto carboxylic graphene nanosheets (CGS) using a green approach performed under mild conditions and without using any additional surfactant or reductant. A dual β-CD (SH/NH2-β-CD)-functionalized Au@CGS (β-CD–Au@CGS) nanohybrid was successfully fabricated by subsequent conjugation of β-CD with the aid of thiol and carboxyl groups. Simultaneous electrochemical determination of hydroquinone (HQ) and p-nitrophenol (PNP) using a β-CD–Au@CGS nanohybrid-modified glassy carbon electrode was conducted. Differential pulse voltammetry was used to simultaneously quantify HQ and PNP within the concentration range of 0.01–200μM under optimal conditions. The limits of quantification for both HQ and PNP were 0.01μM. The detection limits (S/N=3) of the β-CD–Au@CGS-nanohybrid electrode for HQ and PNP were 6.5 and 3.8nM, respectively. Interference study results demonstrated that several similar aromatic compounds did not interfere during the determination of HQ and PNP, indicating the high selectivity of the β-CD–Au@CGS-nanohybrid electrode. The low detection limit and high selectivity of the proposed electrochemical sensor were caused by the high surface area, the excellent conductivity, and the high host–guest molecular recognition capability of the β-CD–Au@CGS nanohybrids.

Controlling self-assembly of DNA-polymer conjugates for applications in imaging and drug delivery.

Amphiphilic supramolecular structures such as micelles and vesicles can be formed through phase-driven self-assembly of monomer units having discrete hydrophilic and hydrophobic blocks. These structures show great promise for use in medical and biological applications, and incorporating DNA as the hydrophilic block of the amphiphilic monomers enables the creation of assemblies that also take advantage of the unique information storage and molecular recognition capabilities of DNA. Recently, significant advances have been made in the synthesis of DNA-polymer conjugates (DPCs), controlling the morphology of DPC assemblies by altering monomer structure, and probing the effect of assembly on DNA stability and hybridization. Together, these investigations have laid the framework for using DPCs in drug delivery, cellular imaging, and other applications in materials science and chemistry.