Synthetic multifunctional pores: lessons from rigid-rod beta-barrels

In this account, studies on synthetic multifunctional pores formed by rigid-rod beta-barrels are summarized comprehensively. The first section outlines the evolution of synthetic multifunctional pores from the introduction of rigid-rod molecules in bioorganic chemistry and the discovery of synthetic beta-barrels in comparison with pertinent developments in related areas of research. Design strategies to position active sites at the inner surface of rigid-rod beta-barrel pores are described in the second section. The third section focuses on the characteristics of transmembrane barrel-stave pores, emphasizing the dynamic nature of supramolecular oligomers with the aid of notional phase and energy diagrams. Section four introduces multifunctionality with the use of synthetic pores as hosts of a rich collection of guests, reaching from inorganic cations to organic macromolecules like peptides, oligonucleotides, polysaccharides and polyacetylenes. In section five, practical applicability of molecular recognition by synthetic multifunctional pores is documented with non-invasive fluorometric enzyme sensing. The application of host-guest chemistry within synthetic pores to couple molecular recognition and translocation with molecular transformation is the topic of section six. The last section mentions some perspectives and challenges with synthetic multifunctional pores.     

Sugar sensing with synthetic multifunctional pores

Recently, synthetic multifunctional pores have been identified as "universal" detectors of chemical reactions. In this report, we show that with the assistance of enzymes as variable co-sensors, synthetic multifunctional pores can serve as similar universal sensors of variable components in mixed analytes. Sugar sensing in soft drinks is used to exemplify this new concept. This is achieved using invertase and hexokinase as co-sensors and a new synthetic multifunctional pore capable of discriminating between ATP and ADP in an "on-off" manner as sensor. The on-off discrimination between ATP as good and ADP as poor pore blocker is shown to be reasonably tolerant of changing experimental conditions. These results identify universal sensing with synthetic multifunctional pores as a robust, sensitive, and noninvasive method with appreciable promise for practical applications.     

Versatile logic devices based on programmable DNA-regulated silver-nanocluster signal transducers

A DNA-encoding strategy is reported for the programmable regulation of the fluorescence properties of silver nanoclusters (AgNCs). By taking advantage of the DNA-encoding strategy, aqueous AgNCs were used as signal transducers to convert DNA inputs into fluorescence outputs for the construction of various DNA-based logic gates (AND, OR, INHIBIT, XOR, NOR, XNOR, NAND, and a sequential logic gate). Moreover, a biomolecular keypad that was capable of constructing crossword puzzles was also fabricated. These AgNC-based logic systems showed several advantages, including a simple transducer-introduction strategy, universal design, and biocompatible operation. In addition, this proof of concept opens the door to a new generation of signal transducer materials and provides a general route to versatile biomolecular logic devices for practical applications.     

Versatile Logic Devices Based on Programmable DNA‐Regulated Silver‐Nanocluster Signal Transducers

A DNA‐encoding strategy is reported for the programmable regulation of the fluorescence properties of silver nanoclusters (AgNCs). By taking advantage of the DNA‐encoding strategy, aqueous AgNCs were used as signal transducers to convert DNA inputs into fluorescence outputs for the construction of various DNA‐based logic gates (AND, OR, INHIBIT, XOR, NOR, XNOR, NAND, and a sequential logic gate). Moreover, a biomolecular keypad that was capable of constructing crossword puzzles was also fabricated. These AgNC‐based logic systems showed several advantages, including a simple transducer‐introduction strategy, universal design, and biocompatible operation. In addition, this proof of concept opens the door to a new generation of signal transducer materials and provides a general route to versatile biomolecular logic devices for practical applications.     

Molecular recognition: Supramolecular, polymeric and biomimetic coatings for chemical sensors and chromatographic columns

Complete control of the selective and reversible interaction of molecules from the gas or liquid phase at complementary recognition sites is of increasing interest for both basic science and practical applications. This recognition may occur at the surface or in the bulk of optimized chemically sensitive coatings. It is either monitored discontinuously by chromatography or continuously by a suitable sensor. The latter contains the optimized coating and converts the chemical information about concentrations of certain molecules by means of a certain transducer into an electronic signal. Generally speaking, these transducers form the essential part of ‘chemical sensors’; they monitor the molecular interactions at the chemically sensitive layer by changes in resistivity, impedance, mass, capacitance, work function, heat, electrochemical potential, optical thickness, or optical absorption in a certain spectral range. Three selected case studies of such molecular recognition devices which utilize supramolecular, polymeric, and biomimetic coatings are presented. Examples are given for both gas and liquid sensing devices. For simplification, because of its general applicability and its easy absolute calibration, particular emphasis is put on signal transduction via quartz crystal oscillators. The measurement principle is based on frequency changes which are directly correlated with mass changes and thus provide a particularly suitable signal transduction. The examples presented here concern systematic variations in the design of supramolecular cages, of selective interaction sites in polymeric matrices, and of covalently attached biomimetic recognition sites to monitor antibodies or enzyme interactions. Received: 11 August 1997 / Revised: 3 March 1998 / Accepted: 3 March 1998     

Molecular recognition: Supramolecular, polymeric and biomimetic coatings for chemical sensors and chromatographic columns

Complete control of the selective and reversible interaction of molecules from the gas or liquid phase at complementary recognition sites is of increasing interest for both basic science and practical applications. This recognition may occur at the surface or in the bulk of optimized chemically sensitive coatings. It is either monitored discontinuously by chromatography or continuously by a suitable sensor. The latter contains the optimized coating and converts the chemical information about concentrations of certain molecules by means of a certain transducer into an electronic signal. Generally speaking, these transducers form the essential part of ‘chemical sensors’; they monitor the molecular interactions at the chemically sensitive layer by changes in resistivity, impedance, mass, capacitance, work function, heat, electrochemical potential, optical thickness, or optical absorption in a certain spectral range. Three selected case studies of such molecular recognition devices which utilize supramolecular, polymeric, and biomimetic coatings are presented. Examples are given for both gas and liquid sensing devices. For simplification, because of its general applicability and its easy absolute calibration, particular emphasis is put on signal transduction via quartz crystal oscillators. The measurement principle is based on frequency changes which are directly correlated with mass changes and thus provide a particularly suitable signal transduction. The examples presented here concern systematic variations in the design of supramolecular cages, of selective interaction sites in polymeric matrices, and of covalently attached biomimetic recognition sites to monitor antibodies or enzyme interactions. Received: 11 August 1997 / Revised: 3 March 1998 / Accepted: 3 March 1998     

Adhesive pi-clamping within synthetic multifunctional pores

We report the design, synthesis, and evaluation of synthetic multifunctional pores with adhesive, that is, electron-deficient naphthalenediimide (NDI) pi-clamps at their inner surface. We find that, in lipid bilayer membranes, comparable synthetic pores with and without pi-clamps have similar, nanomolar activity. Functional relevance of adhesive pi-clamping within synthetic pores is demonstrated by means of an innovative in situ blocker screening method. The obtained line of experimental evidence includes (a) different blockage efficiency with and without pi-clamps (quantified as clamping factors), (b) increasing clamping factors with increasing blocker charge (supportive ion pairing), and, most importantly, (c) increasing clamping factors with increasing aromatic electron donor-acceptor interactions. The availability of advanced synthetic multifunctional pores with refined active sites is important for practical applications in domains such as drug discovery (enzyme inhibitor screening) and diagnostics (multianalyte sensing).     

Electrochemical sensors based on metal and semiconductor nanoparticles

Metal and semiconductor nanoparticles exhibit unique optical, electrical, thermal and catalytic properties. Therefore, they have attracted considerable interest and have been employed for construction of various electrochemical sensors. This minireview gives a general view of recent advances in electrochemical sensor development based on metal and semiconductor nanoparticles covering genosensors, protein and enzyme-based sensors, gas sensors and sensor for other organic and inorganic substances. Different assay strategies based on metal and semiconductor nanoparticles for biosensor and bioelectronic applications are presented, including electrochemical, electrical, and magnetic signal transduction techniques. Electrochemical transduction principles provide signal changes in conductance, charge, potential and current. We have paid much attention to the potential-based and current-based sensors herein. Lastly, a brief introduction is given into advances concerning the role of nanoparticles, quantum dots and nanowires for nanomedicine, such as drug delivery and discovery.     

Biomolecular Assemblies Combining Two Orthogonal Copper‐Mediated Ligations in a One‐Pot Reaction

The access to multifunctional biomolecular compounds involves multistep reactions usually with a complicated protection scheme and lengthy separation processes. The development of a strategy combining several orthogonal ligations is highly desirable. Herein, we introduce a new method that involves two orthogonal copper‐mediated ligations of azide with alkyne, and amine with thioacid. We established compatible conditions to carry out molecular assemblies of three different chemical components in a single one‐pot reaction. The effectiveness of the method was demonstrated in the synthesis of biomolecular compounds that are known to target tumor tissue. The simple reaction conditions suggest that this strategy of combining several orthogonal ligations could have wide potential for the chemical synthesis of complex macromolecules.     

Harnessing host–guest chemistry for electrochemical sensing in complex matrices

Amid increasing demands for modernizing cumbersome and laboratory-bound analytical approaches, researchers are developing generalizable electrochemical sensing alternatives for point-of-need applications that are analogous to the glucometer. For this, integrating host–guest chemistry in electrochemical sensors represents an increasingly attractive strategy due to the vast library of host molecules and the ease with which they could be substituted for measuring different guest molecules. In response, we briefly explore the different signal transduction mechanisms (i.e., non-faradaic and faradaic) that enable electrochemical host–guest sensing. We describe the various advantages and shortcomings of the different approaches with hopes that this review will stimulate innovation toward the development of commercialized electrochemical devices relying on host–guest chemistry amenable at the point-of-need.     

Piezoelectric Genosensor Based on PCR Amplification and Application to Detection of Human Papillomavirus Oncogene

This report presents a new concept of genosensor based on polymerase chain reaction (PCR) amplification with in-situ piezoelectric micro-mass measurement. Though there are increasing reports on DNA hybridization sensors based on electrochemical, optical and piezoelectric transducers with advantages such as simplicity and cost-effectiveness, the sensitivity of genosensors developed so far could not match with the PCR technique, which is well-known to be generated in abundance.     

Multi‐Level Logic Gate Operation Based on Amplified Aptasensor Performance

Conventional electronic circuits can perform multi‐level logic operations; however, this capability is rarely realized by biological logic gates. In addition, the question of how to close the gap between biomolecular computation and silicon‐based electrical circuitry is still a key issue in the bioelectronics field. Here we explore a novel split aptamer‐based multi‐level logic gate built from INHIBIT and AND gates that performs a net XOR analysis, with electrochemical signal as output. Based on the aptamer–target interaction and a novel concept of electrochemical rectification, a relayed charge transfer occurs upon target binding between aptamer‐linked redox probes and solution‐phase probes, which amplifies the sensor signal and facilitates a straightforward and reliable diagnosis. This work reveals a new route for the design of bioelectronic logic circuits that can realize multi‐level logic operation, which has the potential to simplify an otherwise complex diagnosis to a “yes” or “no” decision.     

Electrochemical Monitoring of DNA Hybridization by Multiwalled Carbon Nanotube Based Screen Printed Electrodes

The application of multiwalled carbon nanotube (MWCNT) based screen printed graphite electrodes (SPEs) was explored in this study for the electrochemical monitoring of DNA hybridization related to specific sequences on Hepatitis B virus (HBV) DNA. After the microscopic characterization of bare MWCNT‐SPEs and DNA immobilized ones was performed, the optimization of assay has been studied. The development of screen printing process combined with nanomaterial based disposable sensor technology leads herein a great opportunity for DNA detection using differential pulse voltammetry (DPV) by measuring the guanine oxidation signal observed at +1.00 V in the presence of DNA hybridization between HBV probe and its complementary, target. The detection limit estimated for signal to noise ratios =3 corresponds to 96.33 nM target concentration in the 40 μL samples. The advantages of carbon nanotube based screen printed electrode used for electrochemical monitoring of DNA hybridization are discussed with sensitivity, selectivity and reproducibility in comparison with previous nanomaterial based electrochemical transducers developed for DNA or other biomolecular recognitions.     

Boronic acid converters for reactive hydrazide amplifiers: polyphenol sensing in green tea with synthetic pores

Multicomponent sensing in complex matrices with synthetic pores became feasible with the introduction of amplifiers. Amplifiers are defined as molecules that can covalently capture undetectable analytes after enzymatic signal generation and drag them into the pore for transduction. Here, we introduce converters as molecules that can shift the reactivity of amplifiers in situ to capture chemoorthogonal analytes. For this purpose, a series of dialkoxynaphthalene (DAN) and dialkoxyanthracene (DAA) hydrazinoboronic acids was prepared in situ from DAN and DAA hydrazides and formylphenylboronic acids. These converted amplifiers efficiently inactivate synthetic pores with internal naphthalenediimide clamps. This pore inactivation by DAN and DAA hydrazinoboronic acids vanishes in the presence of catechols such as (+)-catechin, presumably because the obtained boronate esters are too large to bind within the synthetic beta-barrel pore or because they prefer to partition into the bilayer membrane. The resulting increase in pore activity with increasing catechol concentration at constant amplifier concentration is shown to be compatible with the sensing of polyphenols in green tea.     

Homogeneous Oligomeric Ligands Prepared via Radical Polymerization that Recognize and Neutralize a Target Peptide

Abiotic ligands that bind to specific biomolecules have attracted attention as substitutes for biomolecular ligands, such as antibodies and aptamers. Radical polymerization enables the production of robust polymeric ligands from inexpensive functional monomers. However, little has been reported about the production of monodispersed polymeric ligands. Herein, we present homogeneous ligands prepared via radical polymerization that recognize epitope sequences on a target peptide and neutralize the toxicity of the peptide. Taking advantage of controlled radical polymerization and separation, a library of multifunctional oligomers with discrete numbers of functional groups was prepared. Affinity screening revealed that the sequence specificity of the oligomer ligands strongly depended on the number of functional groups. The process reported here will become a general step for the development of abiotic ligands that recognize specific peptide sequences.     

The depth of molecular recognition: voltage-sensitive blockage of synthetic multifunctional pores with refined architecture

Voltage-sensitive blockage by ADP, ATP and phytate (IP6) demonstrates that active-site contraction toward the middle of newly synthesized rigid-rod beta-barrels provides a general strategy to rationally create and modulate the voltage sensitivity (and to increase the efficiency) of molecular recognition by synthetic multifunctional pores.     

Synthetic pores with sticky pi-clamps

In this report, we describe design, synthesis, evaluation and molecular dynamics simulations of synthetic multifunctional pores with pi-acidic naphthalenediimide clamps. Experimental evidence is provided for the formation of unstable but inert, heterogeneous and acid-insensitive dynamic tetrameric pores that are sensitive to base and ionic strength. Blockage experiments reveal that the introduction of aromatic electron donor-acceptor interactions provides access to the selective recognition of pi-basic intercalators within the pore. This breakthrough is important for the application of synthetic pores as multianalyte sensors.     

Multifunctionalization of dendrimers through orthogonal transformations

A straightforward methodology for the synthesis of multifunctionalized dendrimers that is based on an orthogonal functionalization strategy has been developed. Polyamide-based dendrimers that possess both a single aldehyde and a single azide moiety on their periphery have been synthesized by using a convergent synthetic strategy. These dendrimers can be functionalized quantitatively with small organic and biological molecules that contain hydrazide and/or alkyne groups in which each functional moiety is completely specific for its complementary motif. This orthogonal functionalization strategy has the potential to be used to synthesize multifunctional dendrimers for a variety of applications, which range from targeted biological delivery vehicles to optical materials.     

Sensing A Paradigm Shift in the Field of Molecular Recognition: From Selective to Differential Receptors

Molecular recognition has evolved from a science designed to understand biological systems into a much more diverse area of research. While work continues to elucidate “nature's tricks” with respect to intermolecular interactions, much attention has turned to the perspective that molecular recognition, by design, can lead to new technologies. Applications ranging from molecular sensing to information storage and even working molecular machines have been envisioned. This review will highlight a few historical hallmarks of molecular recognition oriented at studying the basic science of intermolecular interactions, but then detail recent advances in molecular recognition aimed towards applications in the field of molecular sensing. Rational design can be used to create synthetic receptors with a good deal of predictability and selectivity, and many signal transduction mechanisms exist for converting these receptors into sensors. This is the first topic discussed. The concept of “differential” or “generalized” sensing is then presented, where one uses an array of sensors that do not necessarily conform to the “lock and key” principle. This approach to sensing is inspired by the mammalian senses of taste and smell, which we briefly describe. To mimic senses of taste and smell, one is naturally led to the use of combinatorial libraries, a direction of research that has seen continued growth over the past few years. We summarize the current state of the art in synthetic combinatorial receptors/sensors, and then predict a future direction that the field of molecular recognition will possibly take. The review is not meant for the specialist, but instead for a general audience. It does not present a highly detailed analysis of each individual topic: synthetic receptors, sensors, olfaction/gustation, and combinatorial receptors/sensors. Instead, this review shows how all these fields complement each other and fit together to create sensing devices. Our conclusion is that specific analyte sensing, differential sensing, and combinatorial chemistry can and will be combined to create sensor arrays, and give the subfield of molecular recognition that uses synthetic systems a bright future in this type of sensing scenario.     

Multifunctional polymers as multi-role materials for photonics

Multifunctional polymers can play multi-roles such as laser light source, passive interconnects, optical signal processing and optical data storage in the development of photonics technology. In this paper, two approaches to achieve nanostructure control to introduce multifunctionality at both molecular and bulk levels are presented. A novel concept of multiphasic nanostructured composites is discussed. Various applications of a specific multifunctional property introduced by strong two-photon absorption and efficient fluorescence are presented. The combined action of these two functions produces upconverted emission. Specific applications discussed are upconversion lasing, optical data storage, confocal microscopy, and photodynamic therapy.