Assembly of Bionanostructures onto β-Cyclodextrin Molecular Printboards for Antibody Recognition and Lymphocyte Cell Counting

A supramolecular cucurbit[8]uril-based rotaxane chemosensor for the optical tryptophan detection in human serum and urine

Sensing small biomolecules in biofluids remains challenging for many optical chemosensors based on supramolecular host-guest interactions due to adverse interplays with salts, proteins, and other biofluid components. Instead of following the established strategy of developing alternative synthetic binders with improved affinities and selectivity, we report a molecular engineering approach that addresses this biofluid challenge. Here we introduce a cucurbit[8]uril-based rotaxane chemosensor feasible for sensing the health-relevant biomarker tryptophan at physiologically relevant concentrations, even in protein- and lipid-containing human blood serum and urine. Moreover, this chemosensor enables emission-based high-throughput screening in a microwell plate format and can be used for label-free enzymatic reaction monitoring and chirality sensing. Printed sensor chips with surface-immobilized rotaxane-microarrays are used for fluorescence microscopy imaging of tryptophan. Our system overcomes the limitations of current supramolecular host-guest chemosensors and will foster future applications of supramolecular sensors for molecular diagnostics.

Reversible immobilization of a protein to a gold surface through multiple host–guest interactions

Monolayers were formed by specific interactions between adamantylated proteins (transferrin, lysozyme) and a β-cyclodextrin (β-CD) monolayer on a gold surface.

Surface patterned pH-sensitive fluorescence using β-cyclodextrin functionalized poly(ethylene glycol)

This paper reports the development of a pH-responsive molecular pattern that shows specific and selective affinity for particular host-guest interactions, and its use as a pH fluorescent sensor. The pH-responsive boronate ester is formed via interactions between the diol group of β-cyclodextrin (CD) and phenylboronic acid of poly(ethylene glycol), and is strategically designed to allow reversible formation of a molecular lining pattern. Printing on a versatile substrate provides a method to monitor the positioning of different molecules by using a pH-responsive boronate ester, allowing specific host-guest interactions on any surface. Confocal laser scanning microscopy, fluorescence spectroscopy, and (1)H NMR results indicate that the assembled CD monolayer can be removed by washing with an acidic pH buffer, demonstrating the presence of a boronate ester connective bridge, which is acid labile. Therefore, visualization of the pH-responsive fluorescence sensor using a rhodamine-CD complex allows straightforward discrimination between different molecules on any substrate, thus facilitating application of this sensor in clinical diagnostics and environmental monitoring.

Functional protein micropatterning for drug design and discovery

INTRODUCTION

The past decade has witnessed tremendous progress in surface micropatterning techniques for generating arrays of various types of biomolecules. Multiplexed protein micropatterning has tremendous potential for drug discovery providing versatile means for high throughput assays required for target and lead identification as well as diagnostics and functional screening for personalized medicine. However, ensuring the functional integrity of proteins on surfaces has remained challenging, in particular in the case of membrane proteins, the most important class of drug targets. Yet, generic strategies to control functional organization of proteins into micropatterns are emerging.

AREAS COVERED

This review includes an overview introducing the most common approaches for surface modification and functional protein immobilization. The authors present the key photo and soft lithography techniques with respect to compatibility with functional protein micropatterning and multiplexing capabilities. In the second part, the authors present the key applications of protein micropatterning techniques in drug discovery with a focus on membrane protein interactions and cellular signaling.

EXPERT OPINION

With the growing importance of target discovery as well as protein-based therapeutics and personalized medicine, the application of protein arrays can play a fundamental role in drug discovery. Yet, important technical breakthroughs are still required for broad application of these approaches, which will include in vitro "copying" of proteins from cDNA arrays into micropatterns, direct protein capturing from single cells as well as protein microarrays in living cells.

Supramolecular Peptide/Surface Assembly for Monitoring Proteinase Activity and Cancer Diagnosis

Matrix metalloproteinases (MMP) are a family of proteolytic enzymes, the expression of which in a key step of tumor progression has recently been better defined. The overexpression of one or more MMPs is thus common among malignant tumors. It may characterize tumor progression and help predict its response to chemotherapy. Consequently, the development of a device for measuring MMP activities is an important challenge for diagnosis and prognosis. In this study, we describe an innovative supramolecular peptide/surface assembly for screening MMP activities. This sensor was used to discriminate various MMP activities and to distinguish between invasive and noninvasive cancerous cell suspensions. Our results confirm the proof-of-concept of a powerful tool for the determination of the tumor aggressiveness and a technical building block for future development of MMP lab-on-chip devices.

Nonfouling tunable βCD dextran polymer films for protein applications

Polymeric β-cyclodextrin (βCD) films tunable with respect to thickness and βCD content were prepared in order to develop a suitable platform, allowing for inclusion of nonpolar guest molecules in the βCD cavity, while suppressing nonspecific protein adsorption. The βCD films were synthesized from linear βCD dextran polymers, and grafted onto silicon oxide surfaces by "click" chemistry. Topographic and morphological characteristics are controllable by reaction conditions and polymer type, with average film heights from 2.5 to 12.5 nm. Reversible introduction of electrostatic charges in the βCD dextran by complex formation with 1-adamantanecarboxylic acid prior to surface grafting resulted in a thinner and denser film, presumably by decompaction of the polymers. Total internal reflection fluorescence spectroscopy (TIRF) was employed to evaluate the accessibility of βCD cavities to the fluorescent probe 2-anilinonaphthalene-6-sulfonic acid. Only a minor fraction of the βCD cavities was accessible in the thicker and less dense films; however, accessibility was largely improved with increased ionic strength using NaCl up to 1 M. Antifouling properties of the βCD dextran polymer films were assessed by TIRF real-time monitoring, using bovine serum albumin as a model protein, and showed a 5- to 10-fold reduction in nonspecific adsorption as compared to a bare quartz surface with the degree of reduction reflecting film thickness and interfacial polymer density.

Surfaces having dual affinity for plasminogen and tissue plasminogen activator: in situ plasmin generation and clot lysis

In situ activation of a surface-integrated zymogen was achieved by introducing affinity ligands for both the zymogen and its activator.

Supramolecular immobilization of bio-entities for bioelectrochemical applications

Supramolecular systems based on host-guest, electrostatic, or metal-ligand interaction and their use in bioelectrochemical applications are reviewed.

Cyclodextrin-based molecular machines

This chapter overviews molecular machines based on cyclodextrins (CDs). The categories of CD-based molecular machines, external stimuli for CD-based molecular machines, and typical examples of CD-based molecular machines are briefly described.

Chemoselective immobilization of proteins by microcontact printing and bio-orthogonal click reactions

Herein, a combination of microcontact printing of functionalized alkanethiols and site-specific modification of proteins is utilized to chemoselectively immobilize proteins onto gold surfaces, either by oxime- or copper-catalyzed alkyne-azide click chemistry. Two molecules capable of click reactions were synthesized, an aminooxy-functionalized alkanethiol and an azide-functionalized alkanethiol, and self-assembled monolayer (SAM) formation on gold was confirmed by IR spectroscopy. The alkanethiols were then individually patterned onto gold surfaces by microcontact printing. Site-specifically modified proteins-horse heart myoglobin (HHMb) containing an N-terminal α-oxoamide and a red fluorescent protein (mCherry-CVIA) with a C-terminal alkyne-were immobilized by incubation onto respective stamped functionalized alkanethiol patterns. Pattern formation was confirmed by fluorescence microscopy.

Nanoscale dynamics and protein adhesivity of alkylamine self-assembled monolayers on graphene

Atomic-scale molecular dynamics computer simulations are used to probe the structure, dynamics, and energetics of alkylamine self-assembled monolayer (SAM) films on graphene and to model the formation of molecular bilayers and protein complexes on the films. Routes toward the development and exploitation of functionalized graphene structures are detailed here, and we show that the SAM architecture can be tailored for use in emerging applications (e.g., electrically stimulated nerve fiber growth via the targeted binding of specific cell surface peptide sequences on the functionalized graphene scaffold). The simulations quantify the changes in film physisorption on graphene and the alkyl chain packing efficiency as the film surface is made more polar by changing the terminal groups from methyl (-CH3) to amine (-NH2) to hydroxyl (-OH). The mode of molecule packing dictates the orientation and spacing between terminal groups on the surface of the SAM, which determines the way in which successive layers build up on the surface, whether via the formation of bilayers of the molecule or the immobilization of other (macro)molecules (e.g., proteins) on the SAM. The simulations show the formation of ordered, stable assemblies of monolayers and bilayers of decylamine-based molecules on graphene. These films can serve as protein adsorption platforms, with a hydrophobin protein showing strong and selective adsorption by binding via its hydrophobic patch to methyl-terminated films and binding to amine-terminated films using its more hydrophilic surface regions. Design rules obtained from modeling the atomic-scale structure of the films and interfaces may provide input into experiments for the rational design of assemblies in which the electronic, physicochemical, and mechanical properties of the substrate, film, and protein layer can be tuned to provide the desired functionality.

Immobilization of Ferrocene-Modified SNAP-Fusion Proteins

The supramolecular assembly of proteins on surfaces has been investigated via the site-selective incorporation of a supramolecular moiety on proteins. To this end, fluorescent proteins have been site-selectively labeled with ferrocenes, as supramolecular guest moieties, via SNAP-tag technology. The assembly of guest-functionalized SNAP-fusion proteins on cyclodextrin- and cucurbit[7]uril-coated surfaces yielded stable monolayers. The binding of all ferrocene fusion proteins is specific as determined by surface plasmon resonance. Micropatterns of the fusion proteins, on patterned cyclodextrin and cucurbituril surfaces, have been visualized using fluorescence microscopy. The SNAP-fusion proteins were also immobilized on cyclodextrin vesicles. The supramolecular SNAP-tag labeling of proteins, thus, allows for the assembly of modified proteins via supramolecular host-guest interaction on different surfaces in a controlled manner. These findings extend the toolbox of fabricating supramolecular protein patterns on surfaces taking advantage of the high labeling efficiency of the SNAP-tag with versatile supramolecular moieties.

A supramolecular approach to enzyme immobilization in micro-channels

A supramolecular assembly scheme is developed to enable the facile in-situ immobilization of enzymes in a microfluidic channel system. A combination of orthogonal supramolecular interactions of host (β-cyclodextrin)-guest (adamantane) and biotin-Streptavidin (SAv) interactions are employed to generate reusable homogeneous enzyme layers in microchannels. The structural integrity and catalytic activity of the immobilized enzyme calf-intestine alkaline phosphatase (AlkPh) is demonstrated. From the kinetic analysis of a dephosphorylation reaction, the specificity constant k(cat)/K(M) for immobilized alkaline phosphatase in the channels is on the order of 10(5) M(-1) s(-1) and comparable to known literature values in other environments. These observations are ascribed to the good access of the substrate to favorably oriented enzymes across the microchannel. Therefore, this study demonstrates the great potential for adopting a supramolecular assembly scheme to immobilize enzymes in microfluidic devices.

Biotin-β-cyclodextrin: a new host-guest system for the immobilization of biomolecules

The formation of stable supramolecular interactions between biotin and β-cyclodextrin was studied. An association constant of 3 × 10(2) M(-1) could be determined by NMR measurements by mapping the high field shift differences of the β-cyclodextrin protons (H-3) at different biotin concentrations. With the aim to demonstrate a new alternative for the immobilization of bioreceptors, biotin and β-cyclodextrin tagged biomolecules were immobilized on transducer surfaces, which were functionalized with the correspondent host-guest partner. The reliability of this new affinity system was investigated using two enzymes (glucose oxidase and polyphenol oxidase) as biomolecule models. This supramolecular inclusion complex shows clear advantages to the classic biotin-(strept)avidin-biotin system due to a detrimental effect of the additional avidin layer reducing the transduction efficiency. A 7-fold increase in the maximum current density and an almost 20 times higher sensitivity were exhibited by the immobilized biological layer obtained using this new host-guest system.

Highly sensitive colorimetric enzyme-linked oligonucleotide assay based on cyclodextrin-modified polymeric surfaces

In this paper, we describe the development of an enzyme-linked oligonucleotide assay for the detection of a human leukocyte antigen allele associated with celiac disease based on cyclodextrin-modified polymeric surfaces. The surface of maleimide-pre-coated plates was modified with a layer of thiolated cyclodextrin polymer and used for the supramolecular capture of adamantane or ferrocene-modified carboxymethylcellulose polymers bearing DNA probes. The assay was optimised in terms of incubation time, temperature, and surface chemistry and applied to the highly sensitive and selective detection of HLA sequences with a limit of detection of 0.7 nM. A real sample analysed using this platform showed an excellent correlation with maleimide-activated plates using thiolated DNA probes.

Protein recognition by a self-assembled deep cavitand monolayer on a gold substrate

This paper details the first use of a self-folding deep cavitand on a gold surface. A sulfide-footed deep, self-folding cavitand has been synthesized, and its attachment to a cleaned gold surface studied by electrochemical and SPR methods. Complete monolayer formation is possible if the cavitand folding is templated by noncovalent binding of choline or by addition of space-filling thiols to cover any gaps in the cavitand adsorption layer. The cavitand is capable of binding trimethylammonium-tagged guests from an aqueous medium and can be deposited in 2 × 2 microarrays on the surface for characterization by SPR imaging techniques. When biotin-labeled guests are used, the cavitand:guest construct can recognize and immobilize streptavidin proteins from aqueous solution, acting as an effective supramolecular biosensor for monitoring protein recognition.

Mechanism and release rates of surface confined cyclodextrin guests

The dissociation of a cobalt bisdiphenylterpyridine, [Co(biptpy)(2)](2+), guest at mixed (γ-CD-(py)(2))-alkanethiol layers (where γ-CD-(py)(2) is di-6(A), 6(B)- deoxy-6-(4-pyridylmethyl)amino- γ-cyclodextrin) formed on platinum electrodes is reported. Cyclic voltammetry (CV) shows reversible one-electron surface confined waves consistent with the Co(2/3+) couple bound at the interface. The quantity of [Co(biptpy)(2)](3+) reduced is found to be dependent on the scan rate employed, with greater amounts at higher scan rates. This behavior is in contrast to the CD guest ferrocene, which upon oxidation to the ferrocenium ion shows little charge associated with reduction even at elevated scan rates. Chronocoulometry was conducted to systematically vary the time spent oxidizing [Co(biptpy)(2)](2+) and to measure the resulting charge associated with the reduction of [Co(biptpy)(2)](3+). It is determined experimentally that as the pulse width increases, i.e. greater time spent in the oxidizing region, the amount of charge needed to reduce [Co(biptpy)(2)](3+) decreases dramatically. This decrease, along with the CV data, suggests strongly that the [Co(biptpy)(2)](3+) dissociates from the cavity. Significantly, this dissociation of the interfacial host-guest complex occurs on a much longer timescale (the order of seconds) compared to the oxidation of [Co(biptpy)(2)](2+) to [Co(biptpy)(2)](3+), which has been measured using high speed chronoamperometry to occur with a rate contant, k(0), of approximately 10(3) s(-1). The comparison of the timescale for dissociation of the interfacial complex and for electron transfer signifies that the electron transfer step occurs before dissociation, i.e. dissociation via an EC mechanism. The dissociation mechanism of [Co(biptpy)(2)](3+) is contrasted with that of the ferrocene/ferrocenium couple.

Redox strategy for reversible attachment of biomolecules using bifunctional linkers

Soft attachment of streptavidin to β-cyclodextrin-modified pegylated SAMs was efficiently performed in a reversible and repetitive way via orthogonal bifunctional linkers involving streptavidin-biotin recognition and redox-driven multivalent host-guest (β-cyclodextrin-ferrocene) interactions.

Salt induced irreversible protein adsorption with extremely high loadings on electrospun nanofibers

LiCl is a kosmotrope that generally promotes protein salvation in aqueous solutions. Herein we report that LiCl embedded in electrospun polymeric nanofibers interestingly induced an abnormal protein adsorption and substantially augmented the adsorption capacity of the fibers. As a result, equilibrium protein loadings reached over 64% (w/w) of the dry mass of fibers, 9-fold higher than that observed in the absence of the salt. The adsorption appeared to be irreversible such that little protein loss was observed even after washing the fibers vigorously with fresh buffer solutions. We further examined the application of such intensified protein adsorption for enzyme immobilization. Proteins including bovine serum albumin (BSA) and protamine were first adsorbed, followed by covalent attachment of an outer layer of an enzyme, α-chymotrypsin. Such a multilayer-structured nanofibrous enzyme exhibited extremely high stability with no obvious activity loss even after being incubated for 8 months at 4 °C in aqueous buffer solution. The LiCl induced irreversible protein adsorption, which has been largely ignored in previous studies with electrospun materials, rendering an interesting scenario of interfacial protein-material interactions. It also reveals a new mechanism in controlling and fabricating molecular interactions at interfaces for development of a broad range of biomaterials.

Thermodynamic origin of selective binding of β-cyclodextrin derivatives with chiral chromophoric substituents toward steroids

Two β-cyclodextrin derivatives with chiral chromophoric substituents, that is, L- (1) and D-tyrosine-modified β-cyclodextrin (2), were synthesized and fully characterized. Their inclusion modes, binding abilities, and molecular selectivities with four steroid guests, that is, cholic acid sodium salt (CA), deoxycholic acid sodium salt (DCA), glycochoic acid sodium salt (GCA), and taurocholic acid sodium salt (TCA), were investigated by the circular dichroism, 2D NMR, and isothermal titration microcalorimetry (ITC). The results obtained from the circular dichroism and 2D NMR showed that two hosts adopted the different binding geometry, and these differences subsequently resulted in the significant differences of molecular binding abilities and selectivities. As compared with native β-cyclodextrin and tryptophan-modified β-cyclodextrin, host 2 showed the enhanced binding abilities for CA and DCA but the decreased binding abilities for GCA and TCA; however, host 1 showed the decreased binding abilities for all four bile salts. The best guest selectivity and the best host selectivity were K(S)(2-DCA)/K(S)(2-TCA) = 12.6 and K(S)(2-CA)/K(S)(1-CA) = 10, respectively, both exhibiting great enhancement as compared with the corresponding values of the previously reported L- and D-tryptophan-modified β-cyclodextrins. Thermodynamically, it was the favorable enthalpic gain that led to the high guest selectivity and host selectivity.

Core-shell nanosized assemblies mediated by the alpha-beta cyclodextrin dimer with a tumor-triggered targeting property

In this paper, the alpha-beta cyclodextrin dimer is designed via "click" chemistry to connect the hydrophilic and hydrophobic segments to form self-assembled noncovalently connected micelles (NCCMs) through host-guest interactions. A peptide containing the Arg-Gly-Asp (RGD) sequence was introduced to NCCMs as a target ligand to improve the cell uptake efficacy, while PEGylated technology was employed via benzoic-imine bonds to protect the ligands in normal tissues and body fluid. In addition, two fluorescent dyes were conjugated to different segments to track the formation of the micelles as well as the assemblies. It was found that the targeting property of NCCMs was switched off before reaching the tumor sites and switched on after removing the poly(ethylene glycol) (PEG) segment in the tumor sites, which was called "tumor-triggered targeting". With deshielding of the PEG segment, the drugs loaded in NCCMs could be released rapidly due to the thermoinduced phase transition. The new concept of "tumor-triggered targeting" proposed here has great potential for cancer treatment.

PM-IRRAS assessment of the compression-mediated orientation of the nanocavity of a monoacylated beta-cyclodextrin in monolayers at the air-water interface

The structural orientation adopted along the compression-decompression isotherm by a monoacylated beta-cyclodextrin (C16-betaCD) at the air-water interface was assessed by polarization-modulation infrared reflection-adsorption spectroscopy (PM-IRRAS). The adoption of different orientations of the cyclic oligosaccharide unit, relative to the interfacial plane, was interpreted analyzing the PM-IRRAS band intensity ratios of specific vibrations corresponding to the cyclodextrin moiety as a function of the surface pressure for successive compression/decompression cycles. The spectroscopic analysis revealed that the cyclic oligosaccharide modifies its position under compression from one in which the plane of the cavity of the monoacylated beta-cyclodextrin lies almost parallel to the interface to another in which the plane of the cavity is perpendicular to the interface. Through the PM-IRRAS analysis, it was also possible to evidence the establishment of an intermolecular hydrogen bonding network that may play an important role in the dynamic properties of the monolayer packing. The hydrogen bonding network becomes more important with the increases of surface pressure, up to a molecular packing limit, and it imparts the surface properties of the film for future compression-decompression cycles.

Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'

Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.

Fabrication and luminescence of designer surface patterns with beta-cyclodextrin functionalized quantum dots via multivalent supramolecular coupling

Supramolecular microcontact printing was used to obtain controlled patterns consisting of quantum dots (QDs) functionalized at their periphery with beta-cyclodextrin (beta-CD) in combination with adamantyl terminated dendrimeric "glues". Functionalization of core--shell CdSe/ZnS QDs was achieved by surface ligation. Immobilization of the QDs from solution onto glass substrates printed with (a) adamantyl-terminated poly(propylene imine) dendrimers and (b) via direct microcontact printing of QDs onto the dendrimer layer both yielded stable and robust multilayer structures. The stability of the patterns was primarily due to multivalent supramolecular host--guest interactions between beta-CD located at the QD surface and adamantyl groups at the dendrimer periphery as the dendrimers acted as a "supramolecular glue". The surface-immobilized QDs were capable of forming host--guest complexes with other molecules of interest at binding cavities not occupied by adamantyl groups. Complex formation with ferrocene-functionalized molecules at these sites led to partial quenching of the luminescence emission of QDs demonstrating the principle for sensing using the QD multilayer structures.