Automated Purification of DNA Origami with SPRI Beads

DNA origami synthesis is a well-established technique with wide-ranging applications. In most cases, the synthesized origami must be purified to remove excess materials such as DNA oligos and other functional molecules. While several purification techniques are routinely used, all have limitations, and cannot be integrated with robotic systems. Here the use of solid-phase reversible immobilization (SPRI) beads as a scalable, high-throughput, and automatable method to purify DNA origami is demonstrated. Not only can this method remove unreacted oligos and biomolecules with yields comparable to existing methods while maintaining the high structural integrity of the origami, but it can also be integrated into an automated workflow to purify simultaneously large numbers and quantities of samples. It is envisioned that the SPRI beads purification method will improve the scalability of DNA nanostructures synthesis both for research and commercial applications.

Therapeutic drug monitoring of immunotherapies with novel Affimer-NanoBiT sensor construct

Concentration-therapeutic efficacy relationships have been observed for several therapeutic monoclonal antibodies (TmAb), where low circulating levels can result in ineffective treatment and high concentrations can cause adverse reactions. Rapid therapeutic drug monitoring (TDM) of TmAb drugs would provide the opportunity to adjust an individual patient's dosing regimen to improve treatment results. However, TDM for immunotherapies is currently limited to centralised testing methods with long sample-collection to result timeframes. Here, we show four point-of-care (PoC) TmAb biosensors by combining anti-idiotypic Affimer proteins and NanoBiT split luciferase technology at a molecular level to provide a platform for rapid quantification (<10 minutes) for four clinically relevant TmAb (rituximab, adalimumab, ipilimumab and trastuzumab). The rituximab sensor performed best with 4 pM limit of detection (LoD) and a quantifiable range between 8 pM-2 nM with neglectable matrix effects in serum up to 1%. After dilution of serum samples, the resulting quantifiable range for all four sensors falls within the clinically relevant range and compares favourably with the sensitivity and/or time-to-result of current ELISA standards. Further development of these sensors into a PoC test may improve treatment outcome and quality of life for patients receiving immunotherapy.

Next-Generation Nanopore Sensors Based on Conductive Pulse Sensing for Enhanced Detection of Nanoparticles

Nanopore sensing has been successfully used to characterize biological molecules with single-molecule resolution based on the resistive pulse sensing approach. However, its use in nanoparticle characterization has been constrained by the need to tailor the nanopore aperture size to the size of the analyte, precluding the analysis of heterogeneous samples. Additionally, nanopore sensors often require the use of high salt concentrations to improve the signal-to-noise ratio, which further limits their ability to study a wide range of nanoparticles that are unstable at high ionic strength. Here, a new paradigm in nanopore research that takes advantage of a polymer electrolyte system to comprise a conductive pulse sensing approach is presented. A finite element model is developed to explain the conductive pulse signals observed and compare these results with experiments. This system enables the analytical characterization of heterogeneous nanoparticle mixtures at low ionic strength . Furthermore, the wide applicability of the method is demonstrated by characterizing metallic nanospheres of varied sizes, plasmonic nanostars with various degrees of branching, and protein-based spherical nucleic acids with different oligonucleotide loadings. This system will complement the toolbox of nanomaterials characterization techniques to enable real-time optimization workflow for engineering a wide range of nanomaterials.

Enzyme - Switch sensors for therapeutic drug monitoring of immunotherapies

Therapeutic monoclonal antibodies (TmAb) have emerged as effective treatments for a number of cancers and autoimmune diseases. However, large interpatient disparities in the pharmacokinetics of TmAb treatment requires close therapeutic drug monitoring (TDM) to optimise dosage for individual patients. Here we demonstrate an approach for achieving rapid, sensitive quantification of two monoclonal antibody therapies using a previously described enzyme switch sensor platform. The enzyme switch sensor consists of a β-lactamase - β-lactamase inhibitor protein (BLA-BLIP) complex with two anti-idiotype binding proteins (Affimer proteins) as recognition elements. The BLA-BLIP sensor was engineered to detect two TmAbs (trastuzumab and ipilimumab) by developing constructs incorporating novel synthetic binding reagents to each of these mAbs. Trastuzumab and ipilimumab were successfully monitored with sub nM sensitivity in up to 1% serum, thus covering the relevant therapeutic range. Despite the modular design, the BLA-BLIP sensor was unsuccessful in detecting two further TmAbs (rituximab and adalimumab), an explanation for which was explored. In conclusion, the BLA-BLIP sensors provide a rapid biosensor for TDM of trastuzumab and ipilimumab with the potential to improve therapy. The sensitivity of this platform alongside its rapid action would be suitable for bedside monitoring in a point-of-care (PoC) setting.

Nanopore fingerprinting of supramolecular DNA nanostructures

DNA nanotechnology has paved the way for new generations of programmable nanomaterials. Utilizing the DNA origami technique, various DNA constructs can be designed, ranging from single tiles to the self-assembly of large-scale, complex, multi-tile arrays. This technique relies on the binding of hundreds of short DNA staple strands to a long single-stranded DNA scaffold that drives the folding of well-defined nanostructures. Such DNA nanostructures have enabled new applications in biosensing, drug delivery, and other multifunctional materials. In this study, we take advantage of the enhanced sensitivity of a solid-state nanopore that employs a poly-ethylene glycol enriched electrolyte to deliver real-time, non-destructive, and label-free fingerprinting of higher-order assemblies of DNA origami nanostructures with single-entity resolution. This approach enables the quantification of the assembly yields for complex DNA origami nanostructures using the nanostructure-induced equivalent charge surplus as a discriminant. We compare the assembly yield of four supramolecular DNA nanostructures obtained with the nanopore with agarose gel electrophoresis and atomic force microscopy imaging. We demonstrate that the nanopore system can provide analytical quantification of the complex supramolecular nanostructures within minutes, without any need for labeling and with single-molecule resolution. We envision that the nanopore detection platform can be applied to a range of nanomaterial designs and enable the analysis and manipulation of large DNA assemblies in real time.

A Systematic Review of the Effect of Therapeutic Drug Monitoring on Patient Health Outcomes during Treatment with Carbapenems

Adjusting dosing regimens based on measurements of carbapenem levels may improve carbapenem exposure in patients. This systematic review aims to describe the effect carbapenem therapeutic drug monitoring (TDM) has on health outcomes, including the emergence of antimicrobial resistance (AMR). Four databases were searched for studies that reported health outcomes following adjustment to dosing regimens, according to measurements of carbapenem concentration. Bias in the studies was assessed with risk of bias analysis tools. Study characteristics and outcomes were tabulated and a narrative synthesis was performed. In total, 2 randomised controlled trials (RCTs), 17 non-randomised studies, and 19 clinical case studies were included. Significant variation in TDM practice was seen; consequently, a meta-analysis was unsuitable. Few studies assessed impacts on AMR. No significant improvement on health outcomes and no detrimental effects of carbapenem TDM were observed. Five cohort studies showed significant associations between achieving target concentrations and clinical success, including suppression of resistance. Studies in this review showed no obvious improvement in clinical outcomes when TDM is implemented. Optimisation and standardisation of carbapenem TDM practice are needed to improve intervention success and enable study synthesis. Further suitably powered studies of standardised TDM are required to assess the impact of TMD on clinical outcomes and AMR.

O04 A systematic review of the effect of therapeutic drug monitoring on patient health outcomes during treatment with penicillins

Background

Dosing regimens guided by therapeutic drug monitoring (TDM) may be able to improve penicillin exposure in patients. Improved penicillin exposure could result in improved patient health outcomes. This systematic review aims to describe the impact TDM in penicillin treatment has on health outcomes, including the emergence of antimicrobial resistance (AMR).

Methods

A search of four databases was conducted and supplemented with a hand search of the literature. Studies that measured concentrations of penicillins in patients, adjusted dosing regimens according to the result and reported health outcomes were selected. The risk of bias was assessed according to study type: randomized controlled trials (RCTs) were assessed with the revised Cochrane risk-of-bias tool for randomized trials (RoB2) assessment tool, the risk of bias in non-randomized studies (ROBINS-1) assessment tool was used to assess observational studies, and the Office of Health Assessment and Translation (OHAT) tool was used to assess case studies. The study characteristics were tabulated and described using a narrative synthesis.

Results

Three RCTs, 16 observational cohort studies and 9 case studies were included. None of the studies showed statistically significant improvements in health outcomes, when comparing groups receiving TDM and standard care. Five observational studies showed improvement in at least one health outcome statistically significantly associated with target attainment: mortality,^1–5 bacterial persistence,^1,4,5 ICU length of stay,⁴ treatment efficacy,^1,4,6 and suppression of AMR.⁴ However there was a high risk of bias in all of these studies for health outcomes. Most had pharmacological primary outcomes and were underpowered to detect health outcomes. All three RCTs and four (25%) observational studies found that the use of penicillin TDM was associated with improved pharmacological target attainment. Only one study was found that assessed the impact of β-lactams TDM on AMR and found that target attainment of 100% ƒT>_4×MIC was significantly associated with suppression of resistance. No studies found a detrimental effect of penicillin TDM on health outcomes. A meta-analysis was not performed due to the heterogeneity of the included studies.

Conclusions

There is little evidence to suggest that TDM improves health outcomes, however neither health outcomes nor reductions in emergence of AMR were adequately addressed by currently published studies. The evaluation of health outcomes was not the primary aim of the majority of the included studies, consequently those that did include these outcomes were underpowered to detect a difference. Observational studies often did not take into account co-interventions, or confounding factors, resulting in a high risk of bias. Large variations in how TDM of penicillins was implemented and the different populations used meant that a quantitative synthesis of results was not suitable. Recommendations to standardize penicillin TDM are a challenge currently, as there is no clear evidence of optimal conditions. Suitably powered studies designed to assess clinical outcomes are required to resolve the ambiguity surrounding the impacts of TDM on clinical outcomes, and to address the gap of the impacts on AMR. Further, appropriate standardized protocols and concentration targets for penicillin TDM in humans need to be identified for it to be implemented successfully.

OUP accepted manuscript

Background

Dosing regimens guided by therapeutic drug monitoring (TDM) may be able to improve penicillin exposure in patients, which could result in improved patient health outcomes.

Objectives

This systematic review aims to describe the impact penicillin TDM has on health outcomes, including antimicrobial resistance (AMR).

Methods

Studies measuring penicillins in patient samples that adjusted regimens according to the result, and reported health outcomes were selected. Study bias was assessed according to study type. Included study characteristics were tabulated and described by narrative synthesis.

Results

Three randomized controlled trials (RCTs), 16 cohort studies, and 9 case studies were included. No RCTs showed statistically significant improvements in health outcomes. Five cohort studies showed improvement in at least one health outcome associated with target attainment. However, there was a high risk of bias in all studies for health outcomes. One study assessed the impact of penicillin TDM on AMR and found that improved target attainment was associated with suppression of resistance. No studies found a detrimental effect of penicillin TDM.

Conclusions

There is little evidence to suggest that TDM improves health outcomes, however neither health outcomes nor impact on AMR were adequately addressed. Variations in TDM implementation meant that a meta-analysis was not suitable. Penicillin TDM needs standardization, however there is currently no clear evidence of optimal conditions. Suitably powered studies are required to resolve the ambiguity surrounding the impact of TDM on clinical outcomes, including AMR. Further, standardized protocols and concentration targets need to be identified for TDM to be implemented successfully.

Micro-homology intermediates: RecA's transient sampling revealed at the single molecule level

Recombinase A (RecA) is central to homologous recombination. However, despite significant advances, the mechanism with which RecA is able to orchestrate a search for homology remains elusive. DNA nanostructure-augmented high-speed AFM offers the spatial and temporal resolutions required to study the RecA recombination mechanism directly and at the single molecule level. We present the direct in situ observation of RecA-orchestrated alignment of homologous DNA strands to form a stable recombination product within a supporting DNA nanostructure. We show the existence of subtle and short-lived states in the interaction landscape, which suggests that RecA transiently samples micro-homology at the single RecA monomer-level throughout the search for sequence alignment. These transient interactions form the early steps in the search for sequence homology, prior to the formation of stable pairings at >8 nucleotide seeds. The removal of sequence micro-homology results in the loss of the associated transient sampling at that location.

DNA nanostructures: A versatile lab-bench for interrogating biological reactions

At its inception DNA nanotechnology was conceived as a tool for spatially arranging biological molecules in a programmable and deterministic way to improve their interrogation. To date, DNA nanotechnology has provided a versatile toolset of nanostructures and functional devices to augment traditional single molecule investigation approaches - including atomic force microscopy - by isolating, arranging and contextualising biological systems at the single molecule level. This review explores the state-of-the-art of DNA-based nanoscale tools employed to enhance and tune the interrogation of biological reactions, the study of spatially distributed pathways, the visualisation of enzyme interactions, the application and detection of forces to biological systems, and biosensing platforms.

Direct Single-Molecule Observation of Mode and Geometry of RecA-Mediated Homology Search

Genomic integrity, when compromised by accrued DNA lesions, is maintained through efficient repair via homologous recombination. For this process the ubiquitous recombinase A (RecA), and its homologues such as the human Rad51, are of central importance, able to align and exchange homologous sequences within single-stranded and double-stranded DNA in order to swap out defective regions. Here, we directly observe the widely debated mechanism of RecA homology searching at a single-molecule level using high-speed atomic force microscopy (HS-AFM) in combination with tailored DNA origami frames to present the reaction targets in a way suitable for AFM-imaging. We show that RecA nucleoprotein filaments move along DNA substrates via short-distance facilitated diffusions, or slides, interspersed with longer-distance random moves, or hops. Importantly, from the specific interaction geometry, we find that the double-stranded substrate DNA resides in the secondary DNA binding-site within the RecA nucleoprotein filament helical groove during the homology search. This work demonstrates that tailored DNA origami, in conjunction with HS-AFM, can be employed to reveal directly conformational and geometrical information on dynamic protein-DNA interactions which was previously inaccessible at an individual single-molecule level.

Cooperative RecA clustering: the key to efficient homology searching

The mechanism by which pre-synaptic RecA nucleoprotein filaments efficiently locate sequence homology across genomic DNA remains unclear. Here, using atomic force microscopy, we directly investigate the intermediates of the RecA-mediated homologous recombination process and find it to be highly cooperative, involving multiple phases. Initially, the process is dominated by a rapid ‘association’ phase, where multiple filaments interact on the same dsDNA simultaneously. This cooperative nature is reconciled by the observation of localized dense clusters of pre-synaptic filaments interacting with the observed dsDNA molecules. This confinement of reactive species within the vicinity of the dsDNA, is likely to play an important role in ensuring that a high interaction rate between the nucleoprotein filaments and the dsDNA can be achieved. This is followed by a slower ‘resolution’ phase, where the synaptic joints either locate sequence homology and progress to a post-synaptic joint, or dissociate from the dsDNA. Surprisingly, the number of simultaneous synaptic joints decreases rapidly after saturation of the dsDNA population, suggesting a reduction in interaction activity of the RecA filaments. We find that the time-scale of this decay is in line with the time-scale of the dispersion of the RecA filament clusters, further emphasising the important role this cooperative phenomena may play in the RecA-facilitated homology search.

Soft Ultraviolet (UV) Photopatterning and Metallization of Self-Assembled Monolayers (SAMs) Formed from the Lipoic Acid Ester of α-Hydroxy-1-acetylpyrene: The Generality of Acid-Catalyzed Removal of Thiol-on-Gold SAMs using Soft UV Light

Under a layer of 0.1 M HCl in isopropanol, soft ultraviolet (UV) (365 nm) photolysis of the thiol-on-gold self-assembled monolayer (SAM) derived from the lipoic acid ester of α-hydroxy-1-acetylpyrene results in the expected removal of the acetylpyrene protecting group. When photolyzing through a mask, this can be used to produce a patterned surface and, at a controlled electrochemical potential, it is then possible to selectively and reversibly electrodeposit copper on the photolyzed regions. Rather surprisingly, under these photolysis conditions, there is not only the expected photodeprotection of the ester but also partial removal of the lipoic acid layer which has been formed. In further studies, it is shown that this type of acid-catalyzed photoremoval of SAM layers by soft UV is a rather general phenomenon and results in the partial removal of the thiol-on-gold SAM layers derived from other ω-thiolated carboxylic acids. However, this phenomenon is chain-length dependent. Under conditions in which there is a ∼60% reduction in the thickness of the SAM derived from dithiobutyric acid, the SAM derived from mercaptoundecanoic acid is almost unaffected. The process by which the shorter-chain SAM layers are partially removed is not fully understood because these compounds do not absorb significantly in the 365 nm region of the spectrum! Significantly, this study shows that acid catalysis photolysis of thiol-on-gold SAMs needs to be used with caution.

DNA self-assembly-driven positioning of molecular components on nanopatterned surfaces

We present a method for the specific, spatially targeted attachment of DNA molecules to lithographically patterned gold surfaces-demonstrated by bridging DNA strands across nanogap electrode structures. An alkanethiol self-assembled monolayer was employed as a molecular resist, which could be selectively removed via electrochemical desorption, allowing the binding of thiolated DNA anchoring oligonucleotides to each electrode. After introducing a bridging DNA molecule with single-stranded ends complementary to the electrode-tethered anchoring oligonucleotides, the positioning of the DNA molecule across the electrode gap, driven by self-assembly, occurred autonomously. This demonstrates control of molecule positioning with resolution limited only by the underlying patterned structure, does not require any alignment, is carried out entirely under biologically compatible conditions, and is scalable.

Label-free electrochemical impedance biosensor to detect human interleukin-8 in serum with sub-pg/ml sensitivity

Biosensors with high sensitivity and short time-to-result that are capable of detecting biomarkers in body fluids such as serum are an important prerequisite for early diagnostics in modern healthcare provision. Here, we report the development of an electrochemical impedance-based sensor for the detection in serum of human interleukin-8 (IL-8), a pro-angiogenic chemokine implicated in a wide range of inflammatory diseases. The sensor employs a small and robust synthetic non-antibody capture protein based on a cystatin scaffold that displays high affinity for human IL-8 with a K_D of 35±10 nM and excellent ligand specificity. The change in the phase of the electrochemical impedance from the serum baseline, ∆θ(ƒ), measured at 0.1 Hz, was used as the measure for quantifying IL-8 concentration in the fluid. Optimal sensor signal was observed after 15 min incubation, and the sensor exhibited a linear response versus logarithm of IL-8 concentration from 900 fg/ml to 900 ng/ml. A detection limit of around 90 fg/ml, which is significantly lower than the basal clinical levels of 5–10 pg/ml, was observed. Our results are significant for the development of point-of-care and early diagnostics where high sensitivity and short time-to-results are essential.

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A label-free electrochemical impedance-based sensor for the detection of human interleukin-8 (IL-8) in full serum was developed.

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Detection limit of 90 fg/ml and time-to-result of 15 min was found.

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A large dynamic range of the sensor was observed, with sensor response linear vs logarithm of IL-8 concentration from 900 fg/ml to 900 ng/ml.

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The sensor employs a small and robust synthetic non-antibody capture protein, with high stability and excellent ligand specificity.

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Findings are particularly relevant for the development of point-of-care and early diagnosis sensors where high sensitivity and short time-to-results are essential.

Antibody mimetic receptor proteins for label-free biosensors

Small synthetic antibody mimetic receptor proteins which offer high stability, specificity and affinity are presented as capture molecules in solid-state electro-chemical biosensors.

The influence of two-dimensional organization on peptide conformation

Molecular crowding plays a significant role in regulating molecular conformation in cellular environments. It is also likely to be important wherever high molecular densities are required, for example in surface-phase studies, in which molecular densities generally far exceed those observed in solution. Using on-surface circular dichroism (CD) spectroscopy, we have investigated the structure of a synthetic peptide assembled into a highly packed monolayer. The immobilized peptide undergoes a structural transition between α-helical and random coil conformation upon changes in pH and ionic concentration, but critically the threshold for conformational change is altered dramatically by molecular crowding within the peptide monolayer. This study highlights the often overlooked role molecular crowding plays in regulating molecular structure and function in surface-phase studies of biological molecules.

Directed assembly of 3-nm-long RecA nucleoprotein filaments on double-stranded DNA with nanometer resolution

Protein-mediated self-assembly is arguably one of the most promising routes for building complex molecular nanostructures. Here, we report a molecular self-assembly technique that allows programmable, site-specific patterning of double-stranded DNA scaffolds, at a single-base resolution, by 3-nm-long RecA-based nucleoprotein filaments. RecA proteins bind to single-stranded DNA to form nucleoprotein filaments. These can self-assemble onto a double-stranded DNA scaffold at a region homologous to the nucleoprotein's single-stranded DNA sequence. We demonstrate that nucleoprotein filaments can be formed from single-stranded DNA molecules ranging in length from 60 nucleotides down to just 6 nucleotides, and these can be assembled site-specifically onto a model DNA scaffold both at the end of the scaffold and away from the end. In both cases, successful site-specific self-assembly is demonstrated even for the smallest nucleoprotein filaments, which are just 3 nm long, comprise only two monomers of RecA, and cover less than one helical turn of the double-stranded DNA scaffold. Finally, we demonstrate that the RecA-mediated assembly process is highly site-specific and that the filaments indeed bind only to the homologous region of the DNA scaffold, leaving the neighboring scaffold exposed.

Improving the dielectric properties of ethylene-glycol alkanethiol self-assembled monolayers

Self-assembled monolayers (SAMs) can be formed at the interface between solids and fluids, and are often used to modify the surface properties of the solid. One of the most widely employed SAM systems is exploiting thiol-gold chemistry, which, together with alkane-chain-based molecules, provides a reliable way of SAM formation to modify the surface properties of electrodes. Oligo ethylene-glycol (OEG) terminated alkanethiol monolayers have shown excellent antifouling properties and have been used extensively for the coating of biosensor electrodes to minimize nonspecific binding. Here, we report the investigation of the dielectric properties of COOH-capped OEG monolayers and demonstrate a strategy to improve the dielectric properties significantly by mixing the OEG SAM with small concentrations of 11-mercaptoundecanol (MUD). The monolayer properties and composition were characterized by means of impedance spectroscopy, water contact angle, ellipsometry and X-ray photoelectron spectroscopy. An equivalent circuit model is proposed to interpret the EIS data and to determine the conductivity of the monolayer. We find that for increasing MUD concentrations up to about 5% the resistivity of the SAM steadily increases, which together with a considerable decrease of the phase of the impedance, demonstrates significantly improved dielectric properties of the monolayer. Such monolayers will find widespread use in applications which depend critically on good dielectric properties such as capacitive biosensor.

Solid phase synthesis of functionalised SAM-forming alkanethiol-oligoethyleneglycols

We present an efficient solid phase synthesis methodology that provides easy access to a range of functionalised long-chain alkanethiol-oligoethyleneglycols that form well-defined self-assembled monolayers on gold and are compatible with pre- or post-assembly conjugation of (bio)molecules. We demonstrate the versatility of our synthetic route by synthesising LCAT-OEGs with a range of functional moieties, including peptides, electro-active redox groups, chemical handles for post-assembly conjugation of (bio)molecules, and demonstrate the application of our LCAT-OEG monolayers in immunosensing, where they show good biocompatibility with minimal biofouling.

Discovery of novel biomarkers and phenotypes by semantic technologies

BACKGROUND

Biomarkers and target-specific phenotypes are important to targeted drug design and individualized medicine, thus constituting an important aspect of modern pharmaceutical research and development. More and more, the discovery of relevant biomarkers is aided by in silico techniques based on applying data mining and computational chemistry on large molecular databases. However, there is an even larger source of valuable information available that can potentially be tapped for such discoveries: repositories constituted by research documents.

RESULTS

This paper reports on a pilot experiment to discover potential novel biomarkers and phenotypes for diabetes and obesity by self-organized text mining of about 120,000 PubMed abstracts, public clinical trial summaries, and internal Merck research documents. These documents were directly analyzed by the InfoCodex semantic engine, without prior human manipulations such as parsing. Recall and precision against established, but different benchmarks lie in ranges up to 30% and 50% respectively. Retrieval of known entities missed by other traditional approaches could be demonstrated. Finally, the InfoCodex semantic engine was shown to discover new diabetes and obesity biomarkers and phenotypes. Amongst these were many interesting candidates with a high potential, although noticeable noise (uninteresting or obvious terms) was generated.

CONCLUSIONS

The reported approach of employing autonomous self-organising semantic engines to aid biomarker discovery, supplemented by appropriate manual curation processes, shows promise and has potential to impact, conservatively, a faster alternative to vocabulary processes dependent on humans having to read and analyze all the texts. More optimistically, it could impact pharmaceutical research, for example to shorten time-to-market of novel drugs, or speed up early recognition of dead ends and adverse reactions.

Fabrication and characterization of gold nano-wires templated on virus-like arrays of tobacco mosaic virus coat proteins

The rod-shaped plant virus tobacco mosaic virus (TMV) is widely used as a nano-fabrication template, and chimeric peptide expression on its major coat protein has extended its potential applications. Here we describe a simple bacterial expression system for production and rapid purification of recombinant chimeric TMV coat protein carrying C-terminal peptide tags. These proteins do not bind TMV RNA or form disks at pH 7. However, they retain the ability to self-assemble into virus-like arrays at acidic pH. C-terminal peptide tags in such arrays are exposed on the protein surface, allowing interaction with target species. We have utilized a C-terminal His-tag to create virus coat protein-templated nano-rods able to bind gold nanoparticles uniformly. These can be transformed into gold nano-wires by deposition of additional gold atoms from solution, followed by thermal annealing. The resistivity of a typical annealed wire created by this approach is significantly less than values reported for other nano-wires made using different bio-templates. This expression construct is therefore a useful additional tool for the creation of chimeric TMV-like nano-rods for bio-templating.

Directed surface attachment of nanomaterials via coiled-coil-driven self-assembly

Numerous nanoscale devices and materials have been fabricated in recent years using a variety of biological scaffolds. However, the interfacing of these devices and materials into existing circuits and ordered arrays has proved problematic. Here, we describe a simple solution to this problem using self-assembly of the peptide coiled-coil heterodimer ACID:BASE to immobilize M13 bacteriophage particles to specific locations on a patterned gold surface. Surface plasmon resonance demonstrated that free ACID peptides will assemble onto a surface derivatized with BASE. We then displayed the ACID peptide on the pIX coat protein of M13 and showed that these phage particles permit formation of the coiled-coil resulting in specific surface attachment. The ACID:immobilized BASE affinities appear to be similar for free peptide and phage-displayed ACID. Finally, we fabricated two gold electrodes, separated by a 200 nm gap, coated one of them with BASE and showed that this allows localization of the M13:ACID onto the functionalized electrode.

On-surface assembly of coiled-coil heterodimers

The coiled coil is a widespread protein motif responsible for directing the assembly of a wide range of protein complexes. To date, research has focused largely on the solution phase assembly of coiled-coil complexes. Here, we describe an investigation into coiled-coil heterodimer assembly where one of the peptides is immobilized directly onto a gold electrode. Immobilization is achieved by the introduction of a unique cysteine residue at the C terminus, allowing for covalent and orientated attachment to a thiol-reactive surface, here the gold electrode. We show an electrochemical impedance of the resulting self-assembled polypeptide monolayer around |Z| = 4 × 10(4) Ω cm(2) at 100 mHz with a minimum phase angle of -84°, consistent with the formation of a densely packed, insulating layer. The thickness of the peptide monolayer, as measured using ellipsometry, is around 3 nm, close to that expected for a self-assembled monolayer assembled from helical peptides. Crucially, we find that the efficiency of dimerization between a peptide in solution and its coiled-coil partner peptide immobilized on a surface is strongly dependent upon the density of the immobilized peptide layer, with dimer assembly being strongly suppressed by high-density peptide monolayers. We thus develop an approach for controlling the density of the immobilized peptide by diluting the monolayer with a thiolated, random-coil peptide to modulate dimerization efficiency and demonstrate electrochemical detection of highly specific, coiled-coil heterodimer on-surface assembly.

Nanoscale programmable sequence-specific patterning of DNA scaffolds using RecA protein

Molecular self-assembly inherent to many biological molecules, in conjunction with suitable molecular scaffolds to facilitate programmable positioning of nanoscale objects, offers a promising approach for the integration of functional nanoscale complexes into macroscopic host devices. Here, we report the use of the protein RecA as a means of highly efficient programmable patterning of double-stranded (ds)DNA molecules with molecular-scale precision at specific locations along the DNA strand. RecA proteins form nucleoprotein filaments with single-stranded (ss)DNA molecules, which are chosen to be of sequence homologous to the desired binding region on the dsDNA scaffold. We show that the patterning yield can be in excess of 85% and we demonstrate that concurrent patterning of multiple locations on the same dsDNA scaffold can be achieved with separation between the assembled nucleoprotein filaments of less than 4 nm. This is an important prerequisite for this programmable and flexible DNA scaffold patterning technique to be employed in molecular- and nanoscale assembly applications.

Redox-induced conformational change in mercaptoalkanoic acid multilayer films

We discuss the assembly, structure, and stability of multilayer molecular films formed from multiple mercaptoalkanoic acid monolayers ligated via carboxyl and thiol interactions with divalent copper ions. Using dual-polarization interferometry to study the assembly of multilayer films in real time, we observe a clear linear relationship between the number of layers within a film and the overall average film thickness. Unexpectedly, however, we find a restructuring of the lower monolayer upon association of the Cu(2+) ions to form the Cu carboxylate surface. In particular, the thickness of the lower monolayer was found to decrease significantly, accompanied by an increase in the film density. The conformation of the monolayer subsequently recovered to that observed originally following the reduction of the Cu ion to Cu(+) upon chemisorption of the adlayer. Comparable restructuring was also observed in molecular dynamics simulations of a bilayer film assembled on a gold surface. Our combined experimental and theoretical study suggests that the observed restructuring is a result of charge-charge interactions between adjacent Cu ions that exist in the +2 oxidation state in the copper carboxylate surface and in the +1 oxidation state following chemisorption of the adlayer.

RecA protein mediated nano-scale patterning of DNA scaffolds

Molecular lock-and-key functionality inherent to a large number of biological molecules is arguably one of the most promising potential routes for building complex nanostructures and eventually nano-electronic devices by self-assembly. Here, we report the use of the DNA-binding protein RecA as a tool for patterning DNA scaffolds site-specifically and in a programmable way at the nanometre-scale. This is demonstrated by patterning a 3 kilo-base-pair double-stranded DNA molecule at ten different locations with nanometre-sized RecA-based nucleoprotein filaments. This protein-based molecular patterning technique, which is site-specific, programmable, and scalable, offers a potential basis for molecular lithography applications, and opens previously inaccessible routes towards the fabrication of complex functional nano-electronic devices by self-assembly.

Effect of chain length on the assembly of mercaptoalkanoic acid multilayer films ligated through divalent Cu ions

The structural stability of alkenthiolate monolayers assembled on gold surfaces is a result of the well-defined organization of the individual molecules within the film. The formation of three-dimensional films assembled by stacking multiple molecular monolayers is substantially more challenging because the correct organization of the molecular components is required not only within the individual monolayers but also between the monolayers of the film. In this paper we examine the structure of multilayer films based on mercaptoalkanoic acid monolayers in which ligation between adjacent monolayers is achieved using the interaction of carboxylic acid and thiol groups with a divalent Cu ion. Using contact angle analysis and atomic force microscopy, we show that the use of Cu(2+) has profound implications on the properties and structure of the multilayer film. In particular, the divalent ions effectively prohibit the complete assembly of the next monolayer. For multilayer SAMs assembled from short alkane chains with six methylene groups, we find that molecules in the incomplete adlayer organize themselves randomly over the underlying monolayer. However, as the number of methylene groups increases (11 and 16 methylene groups), the upper layer tends to fracture into discrete islands which cover around 50% of the surface. The height of these islands is found to be equal to that expected for a complete, well-ordered monolayer assembled from the equivalent mercaptoalkanoic acid molecules. This relationship between chain length and island growth results from the migration of molecules into ordered aggregates driven by the reduction of free energy associated with maximizing intermolecular interactions.

Controlling liquid crystal alignment using photocleavable cyanobiphenyl self-assembled monolayers

We report on the development of novel cyano-biphenyl-based thiolate self-assembled monolayers designed to promote homeotropic alignment of calamitic liquid crystals. The molecules developed contain an ortho-nitrobenzyl protected carboxylic acid group that on irradiation by soft UV (365 nm) is cleaved to yield carboxylic acid groups exposed at the surface that promote planar alignment. Using a combination of wetting, X-ray photoelectron spectroscopy, Fourier transform-infrared reflection absorption spectroscopy, and ellipsometry we show that high photolysis yields (>90%) can be achieved and that the patterned SAMs are suitable for the controlled alignment of calamitic liquid crystals. This study further shows that such photo-patterned SAMs can be used to control the formation of focal conic domains (FCDs) in the smectic-A phase in terms of positioning and size confinement on surfaces.

Synthesis of core-shell gold coated magnetic nanoparticles and their interaction with thiolated DNA

Core-shell magnetic nanoparticles have received significant attention recently and are actively investigated owing to their large potential for a variety of applications. Here, the synthesis and characterization of bimetallic nanoparticles containing a magnetic core and a gold shell are discussed. The gold shell facilitates, for example, the conjugation of thiolated biological molecules to the surface of the nanoparticles. The composite nanoparticles were produced by the reduction of a gold salt on the surface of pre-formed cobalt or magnetite nanoparticles. The synthesized nanoparticles were characterized using ultraviolet-visible absorption spectroscopy, transmission electron microscopy, energy dispersion X-ray spectroscopy, X-ray diffraction and super-conducting quantum interference device magnetometry. The spectrographic data revealed the simultaneous presence of cobalt and gold in 5.6±0.8 nm alloy nanoparticles, and demonstrated the presence of distinct magnetite and gold phases in 9.2±1.3 nm core-shell magnetic nanoparticles. The cobalt-gold nanoparticles were of similar size to the cobalt seed, while the magnetite-gold nanoparticles were significantly larger than the magnetic seeds, indicating that different processes are responsible for the addition of the gold shell. The effect on the magnetic properties by adding a layer of gold to the cobalt and magnetite nanoparticles was studied. The functionalization of the magnetic nanoparticles is demonstrated through the conjugation of thiolated DNA to the gold shell.

Flip-chip fabrication of nanoscale co-planar embedded electrodes with controlled exposed areas

We discuss the fabrication of closely spaced nanoscale embedded co-planar electrodes with concealed contact wires, using a GaAs-based flip-chip technology. The co-planarity of the electrodes with the substrate and the low roughness of the exposed surface are achieved by templating the deposition of both the dielectric and electrode metal onto a smooth GaAs substrate. The resulting electrodes, with sizes of around 300 nm and separations as low as 25 nm, have RMS roughnesses of less than 0.2 nm and a co-planarity of around 1 nm.

The fabrication of embedded co-planar electrodes using a self-assembled monolayer molecular resist

We demonstrate a new process for fabricating embedded co-planar electrodes which combines top-down with bottom-up approaches to nanofabrication. The co-planarity of the electrodes with the substrate surface is achieved by deposition of a dielectric filling layer around a set of lithographically defined metallic electrodes. In order to prevent adhesion of the dielectric to the pre-defined electrodes, an adhesion inhibiting layer, based on a self-assembled monolayer, is formed specifically on the electrode surface prior to deposition of the dielectric. For monolayers with an acid functional group, this adhesion inhibitor yields almost complete non-adhesion of the dielectric filling layer.

Electrical protein detection in cell lysates using high-density peptide-aptamer microarrays

BACKGROUND

The dissection of biological pathways and of the molecular basis of disease requires devices to analyze simultaneously a staggering number of protein isoforms in a given cell under given conditions. Such devices face significant challenges, including the identification of probe molecules specific for each protein isoform, protein immobilization techniques with micrometer or submicrometer resolution, and the development of a sensing mechanism capable of very high-density, highly multiplexed detection.

RESULTS

We present a novel strategy that offers practical solutions to these challenges, featuring peptide aptamers as artificial protein detectors arrayed on gold electrodes with feature sizes one order of magnitude smaller than existing formats. We describe a method to immobilize specific peptide aptamers on individual electrodes at the micrometer scale, together with a robust and label-free electronic sensing system. As a proving proof of principle experiment, we demonstrate the specific recognition of cyclin-dependent protein kinases in whole-cell lysates using arrays of ten electrodes functionalized with individual peptide aptamers, with no measurable cross-talk between electrodes. The sensitivity is within the clinically relevant range and can detect proteins against the high, whole-cell lysate background.

CONCLUSION

The use of peptide aptamers selected in vivo to recognize specific protein isoforms, the ability to functionalize each microelectrode individually, the electronic nature and scalability of the label-free detection and the scalability of the array fabrication combine to yield the potential for highly multiplexed devices with increasingly small detection areas and higher sensitivities that may ultimately allow the simultaneous monitoring of tens or hundreds of thousands of protein isoforms.

Generic technique to generate large branched DNA complexes

The inherent self-recognition properties of DNA have led to its use as a scaffold for various nanotechnology self-assembly applications, with macromolecular complexes, metallic and semiconducting nanoparticles, proteins, inter alia, being assembled onto a designed DNA scaffold. Such structures may typically comprise a number of DNA molecules organized into macromolecules. Many studies have used synthetic methods to produce the constituent DNA molecules, but this typically constrains the molecules to be no longer than around 100 base pairs (30 nm). However, applications that require larger self-assembling DNA complexes, several tens of nanometers or more, need to be generated by other techniques. Here, we present a generic technique to generate large linear, branched, and/or circular DNA macromolecular complexes. The effectiveness of this technique is demonstrated here by the use of Lambda Bacteriophage DNA as a template to generate single- and double-branched DNA structures approximately 120 nm in size.

The implementation of the 'International Classification of Functioning, Disability and Health' (ICF) in daily practice of neurorehabilitation: an interdisciplinary project at the Kantonsspital of Lucerne, Switzerland

PURPOSE

The current paper describes the implementation of ICF as a standard language and framework for description of human functioning and disability for common use in every day work by the multiprofessional team.

METHOD

An interdisciplinary project team involving all rehabilitation specialities was constituted. The extensive original document of ICF was broken down to a simplified raster for body functions and structures, activities and participation, as well as for contextual factors. These rasters had to cover the most important aspects concerning the patients treated on our unit. Checklists on the basis of these rasters were worked out for use by the different specialized teams. Using these checklists, rehabilitation conferences, form and language of interdisciplinary communication, goal setting and documentation were introduced newly in every day work for the interdisciplinary rehabilitation team, structured strictly based on the ICF-criteria.

RESULTS

Since April 2002 the ICF-based processes are implemented in routine work for all members of the rehabilitation staff. First experiences show good acceptance by the team members, improvements in communication and documentation as well as substantial gains in content and handling of rehabilitation conferences. As a result of the implementation we observed, that participation, context and domiciliary interventions gained quite more influence in every day work at the unit.

CONCLUSION

Implementation improved considerably the quality of interdisciplinary work processes and contributed to a more systematic approach to rehabilitation tasks by the team members.