large-area-scanning-probe-nanolithography-facilitated-automated

Large-area Scanning Probe Nanolithography Facilitated by Automated Alignment and Its Application to Substrate Fabrication for Cell Culture Studies

Scanning probe microscopy has enabled the creation of a variety of methods for the constructive (&#39;additive&#39;) top-down fabrication of ...

University of Manchester

Natural products have evolved, at least in part, to bind to biological macromolecules, particularly proteins. As a result, natural products are able to interact with many specific targets within the cell. Indeed for many years this has been central in the drug development process. Today, however, natural products are finding increasing use as probes to interrogate biological systems as part of chemical genomics and related research. In order to demonstrate the utility of natural products in these efforts, the biological activities of many of the major classes of natural products is discussed, according to the cellular organelle and localisation of their specific molecular targets. Emphasis is given to newly discovered compounds and activities that either provide interesting insights into a specific biological function, or that form the basis for potentially new therapeutic approaches.

Cellular targets of natural products.

Immobilization of proteins onto solid supports is important in the preparation of functional protein microarrays and in the development of bead-based bioassays, biosensors, and industrial biocatalysts. In order to generate the stable, functional, and homogeneous materials required for these applications, attention has focused on methods that enable the efficient and site-specific covalent immobilization of recombinant proteins onto a wide range of platforms. To this end, the phosphopantetheinyl transferase Sfp was employed to catalyze the direct immobilization of recombinant proteins bearing the small, genetically encoded ybbR tag onto surfaces functionalized with CoA. Using mass spectrometry, it was shown that the Sfp catalyzes immobilization of a model acyl carrier protein (ACP) onto CoA-derivatized PEGA resin beads through specific covalent bond formation. Luciferase (Luc) and glutathione-S-transferase (GST) ybbR-fusion proteins were similarly immobilized onto PEGA resin retaining high levels of enzyme activity. This strategy was also successfully applied for the immobilization of the ACP, as well as ybbR-Luc, -GST, and -thioredoxin fusion proteins, on hydrogel microarray slides. Overall, the Sfp-catalyzed surface ligation is mild, quantitative, and rapid, occurring in a single step without prior chemical modification of the target protein. Immobilization of the target proteins directly from a cell lysate mixture was also demonstrated.

Direct site-selective covalent protein immobilization catalyzed by a phosphopantetheinyl transferase.

Selective covalent protein immobilization: strategies and applications.

The immobilisation of proteins on to nanoparticles has a number of applications ranging from biocatalysis through to cellular delivery of biopharmaceuticals. Here we describe a phosphopantetheinyl transferase (Sfp)-catalysed method for immobilising proteins bearing a small 12-mer "ybbR" tag on to nanoparticles functionalised with coenzyme A. The Sfp-catalysed immobilisation of proteins on to nanoparticles is a highly efficient, single step reaction that proceeds under mild conditions and results in a homogeneous population of proteins that are covalently and site-specifically attached to the surface of the nanoparticles. Several enzymes of interest for biocatalysis, including an arylmalonate decarboxylase (AMDase) and a glutamate racemase (GluR), were immobilised on to nanoparticles using this approach. These enzymes retained their activity and showed high operational stability upon immobilisation.

Site-selective immobilisation of functional enzymes on to polystyrene nanoparticles.

A solid-phase synthetic strategy was developed that uses modular building blocks to prepare symmetric oligo(ethylene glycol)-terminated disulfides with a variety of lengths and terminal functionalities. The modular disulfides, composed of alkyl amino groups linked by an amide group to oligoethylene chains were used to generate self-assembled monolayers (SAMs), which were characterised to determine their applicability for biomolecular applications. X-ray photoelectron spectroscopy (XPS) of the SAMs obtained from these molecules demonstrated improved stability towards displacement by 16-hexadecanethiol, while surface plasmon resonance (SPR) analyses of SAMs prepared with the hydroxy-terminated oligoethylene disulfide showed equal resistance to non-specific protein adsorption in comparison to 11-mercaptoundecyl tri(ethylene glycol). SAMs made from these adsorbates were amenable to nanoscale patterning by scanning near-field photolithography (SNP), facilitating the fabrication of nanopatterned, protein-functionalised surfaces. Such SAMs may be further developed for bionanotechnology applications such as the fabrication of nanoscale biological arrays and sensor devices.

Nanoscale biomolecular structures on self-assembled monolayers generated from modular pegylated disulfides.

S-adenosyl methionine (SAM) is a universal biological cofactor that is found in all branches of life where it plays a critical role in the transfer of methyl groups to various biomolecules, including DNA, proteins and small-molecule secondary metabolites. The methylation process thus has important implications in various disease processes and applications in industrial chemical processing. This methyl transfer is catalysed by SAM-dependent methyltransferases (MTases), which are by far the largest groups of SAM-dependent enzymes. A significant amount is now known regarding the structural biology and enzymology of these enzymes, and, consequently, there is now significant scope for the development of new MTases and SAM analogues for applications from biomolecular imaging to biocatalytic industrial processes. This review will focus on current efforts in the manipulation of class I and V SAM-dependent MTases and the use of synthetic SAM analogues, which together offer the best prospects for rational redesign towards biotechnological applications. Firstly, metabolic engineering of organisms incorporating small-molecule MTases is discussed; this can be applied in a variety of areas from the industrial bioprocessing of flavourants and antibiotics to frontier research in biofuel production and bioremediation. Secondly, the application of MTases in combination with SAM analogues is reviewed; this allows the tagging of proteins and oligonucleotides with moieties other than the methyl group. Such tagging allows the isolation of the tagged biomolecule and aids its visualisation by a range of analytical methods. The review then summarises the potential advantages of MTase-mediated chemistry and offers some future perspectives on downstream applications.

S-adenosyl-methionine-dependent methyltransferases: highly versatile enzymes in biocatalysis, biosynthesis and other biotechnological applications.

The use of scanning probes bearing catalysts to perform surface nanolithography combines the exquisite spatial precision of scanning probe microscopy with the synthetic capabilities of (bio)chemical catalysis. The ability to use these probes to direct a variety of localised chemical reactions enables the generation of nanoscale features with a high degree of chemical complexity in a "direct-write" manner. This article surveys the range of reactions that have been employed and the key factors necessary for the successful use of such catalytic scanning probes. These factors include the experimental parameters such as write speed, force applied to the probes and temperature; as well as the processes involved in the preparation of the catalysts on the probes and the surface that is to be fabricated. Where possible, the various reactions are also compared and contrasted; and future perspectives are discussed. 

Harnessing catalysis to enhance scanning probe nanolithography.

Arylhalides are important building blocks in many fine chemicals, pharmaceuticals and agrochemicals, and there has been increasing interest in the development of more "green" halogenation methods based on enzyme catalysis. However, the screening and development of new enzymes for biohalogenation has been hampered by a lack of high-throughput screening methods. Described herein is the development of a colorimetric assay for detecting both chemical and enzymatic arylamine halogenation reactions in an aqueous environment. The assay is based on the unique UV/Vis spectrum created by the formation of an ortho-benzoquinone-amine adduct, which is produced by the peroxidase-catalysed benzoquinone generation, followed by Michael addition of either a halogenated or non-halogenated arylamine. This assay is sensitive, rapid and amenable to high-throughput screening platforms. We have also shown this assay to be easily coupled to a flavin-dependent halogenase, which currently lacks any convenient colorimetric assay, in a "one-pot" workflow. 

A high-throughput assay for arylamine halogenation based on a peroxidase-mediated quinone-amine coupling with applications in the screening of enzymatic halogenations.

Bioorthogonal chemistry enables a specific moiety in a complex biomolecule to be selectively modified in the presence of many reactive functional groups and other cellular entities. Such selectivity has become indispensable in biology, enabling biomolecules to be derivatized, conjugated, labeled, or immobilized for imaging, biochemical assays, or therapeutic applications. Methyltransferase enzymes (MTase) that accept analogues of the cofactor S-adenosyl methionine have been widely deployed for alkyl-diversification and bioorthogonal labeling. However, MTases typically possess tight substrate specificity. Here we introduce a more flexible methodology for selective derivatization of phenolic moieties in complex biomolecules. Our approach relies on the tandem enzymatic reaction of a fungal tyrosinase and the mammalian catechol-O-methyltransferase (COMT), which can effect the sequential hydroxylation of the phenolic group to give an intermediate catechol moiety that is subsequently O-alkylated. When used in this combination, the alkoxylation is highly selective for tyrosine residues in peptides and proteins, yet remarkably tolerant to changes in the peptide sequence. Tyrosinase-COMT are shown to provide highly versatile and regioselective modification of a diverse range of substrates including peptide antitumor agents, hormones, cyclic peptide antibiotics, and model proteins. 

An Enzyme Cascade for Selective Modification of Tyrosine Residues in Structurally Diverse Peptides and Proteins.

The family of silicatein enzymes from marine sponges (phylum Porifera) is unique in nature for catalyzing the formation of inorganic silica structures, which the organisms incorporate into their skeleton. However, the synthesis of organosiloxanes catalyzed by these enzymes has thus far remained largely unexplored. To investigate the reactivity of these enzymes in relation to this important class of compounds, their catalysis of Si-O bond hydrolysis and condensation was investigated with a range of model organosilanols and silyl ethers. The enzymes' kinetic parameters were obtained by a high-throughput colorimetric assay based on the hydrolysis of 4-nitrophenyl silyl ethers. These assays showed unambiguous catalysis with / values on the order of 2-50 min μM Condensation reactions were also demonstrated by the generation of silyl ethers from their corresponding silanols and alcohols. Notably, when presented with a substrate bearing both aliphatic and aromatic hydroxy groups the enzyme preferentially silylates the latter group, in clear contrast to nonenzymatic silylations. Furthermore, the silicateins are able to catalyze transetherifications, where the silyl group from one silyl ether may be transferred to a recipient alcohol. Despite close sequence homology to the protease cathepsin L, the silicateins seem to exhibit no significant protease or esterase activity when tested against analogous substrates. Overall, these results suggest the silicateins are promising candidates for future elaboration into efficient and selective biocatalysts for organosiloxane chemistry.

Recombinant silicateins as model biocatalysts in organosiloxane chemistry.

As cell function and phenotype can be directed by the mechanical characteristics of the surrounding matrix, hydrogels have become important platforms for cell culture systems, with properties that can be tuned by external stimuli, such as divalent cations, enzymatic treatment, and pH. However, many of these stimuli can directly affect cell behavior, making it difficult to distinguish purely mechanical signaling events. This study reports on the development of a hydrogel that incorporates photoswitchable cross-linkers, which can reversibly alter their stiffness upon irradiation with the appropriate wavelength of light. Furthermore, this study reports the response of bone-marrow-derived mesenchymal stem cells (MSCs) on these hydrogels that were stiffened systematically by irradiation with blue light. The substrates were shown to be noncytotoxic, and crucially MSCs were not affected by blue-light exposure. Time-resolved analysis of cell morphology showed characteristic cell spreading and increased aspect ratios in response to greater substrate stiffness. This hydrogel provides a platform to study mechanosignaling in cells responding to dynamic changes in stiffness, offering a new way to study mechanotransduction signaling pathways and biological processes, with implicit changes to tissue mechanics, such as development, ageing, and fibrosis.

Photoresponsive Hydrogels with Photoswitchable Mechanical Properties Allow Time-Resolved Analysis of Cellular Responses to Matrix Stiffening.

Scanning probe lithography (SPL) offers a more accessible alternative to conventional photolithography as a route to surface nanofabrication. In principle, the synthetic scope of SPL could be greatly enhanced by combining the precision of scanning probe systems with the chemoselectivity offered by biocatalysis. This report describes the development of multiplexed SPL employing probes functionalized with horseradish peroxidase, and its subsequent use for the constructive fabrication of polyaniline features on both silicon oxide and gold substrates. This polymer is of particular interest due to its potential applications in organic electronics, but its use is hindered by its poor processability, which could be circumvented by the direct in situ synthesis at the desired locations. Using parallelized arrays of probes, the lithography of polymer features over 1 cm2 areas was achieved with individual feature widths as small as 162 ± 24 nm. The nature of the deposited materials was confirmed by Raman spectroscopy, and it was further shown that the features could be chemically derivatized postlithographically by Huisgen [2 + 3] "click" chemistry, when 2-propargyloxyaniline was used as the monomer in the initial lithography step.

Article	Year
Cellular targets of natural products. Natural product reports\| PubMed ID: 18033580	2007
Direct site-selective covalent protein immobilization catalyzed by a phosphopantetheinyl transferase. Journal of the American Chemical Society\| PubMed ID: 18722432	2008
Selective covalent protein immobilization: strategies and applications. Chemical reviews\| PubMed ID: 19572643	2009
Site-selective immobilisation of functional enzymes on to polystyrene nanoparticles. Organic & biomolecular chemistry\| PubMed ID: 20135034	2010
Nanoscale biomolecular structures on self-assembled monolayers generated from modular pegylated disulfides. Chemistry (Weinheim an der Bergstrasse, Germany)\| PubMed ID: 20839371	2010
S-adenosyl-methionine-dependent methyltransferases: highly versatile enzymes in biocatalysis, biosynthesis and other biotechnological applications. Chembiochem : a European journal of chemical biology\| PubMed ID: 23180741	2012
Harnessing catalysis to enhance scanning probe nanolithography. Nanoscale\| PubMed ID: 24710746	2014
A high-throughput assay for arylamine halogenation based on a peroxidase-mediated quinone-amine coupling with applications in the screening of enzymatic halogenations. Chemistry (Weinheim an der Bergstrasse, Germany)\| PubMed ID: 25319801	2014
An Enzyme Cascade for Selective Modification of Tyrosine Residues in Structurally Diverse Peptides and Proteins. Journal of the American Chemical Society\| PubMed ID: 26867114	2016
Recombinant silicateins as model biocatalysts in organosiloxane chemistry. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 28630316	2017
Photoresponsive Hydrogels with Photoswitchable Mechanical Properties Allow Time-Resolved Analysis of Cellular Responses to Matrix Stiffening. ACS applied materials & interfaces\| PubMed ID: 29430919	2018
Parallelized biocatalytic scanning probe lithography for the additive fabrication of conjugated polymer structures. Nanoscale\| PubMed ID: 29620786	2018

Lu Shin Wong

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