Enzyme- and affinity biomolecule-mediated polymerization systems for biological signal amplification and cell screening

Understanding activity-stability tradeoffs in biocatalysts by enzyme proximity sequencing

Understanding the complex relationships between enzyme sequence, folding stability and catalytic activity is crucial for applications in industry and biomedicine. However, current enzyme assay technologies are limited by an inability to simultaneously resolve both stability and activity phenotypes and to couple these to gene sequences at large scale. Here we present the development of enzyme proximity sequencing, a deep mutational scanning method that leverages peroxidase-mediated radical labeling with single cell fidelity to dissect the effects of thousands of mutations on stability and catalytic activity of oxidoreductase enzymes in a single experiment. We use enzyme proximity sequencing to analyze how 6399 missense mutations influence folding stability and catalytic activity in a D-amino acid oxidase from Rhodotorula gracilis. The resulting datasets demonstrate activity-based constraints that limit folding stability during natural evolution, and identify hotspots distant from the active site as candidates for mutations that improve catalytic activity without sacrificing stability. Enzyme proximity sequencing can be extended to other enzyme classes and provides valuable insights into biophysical principles governing enzyme structure and function.

Device Processing Challenges for Miniaturized Sensing Systems Targeting Biological Fluids

This article presents a review of device processing technologies used in the fabrication of biomedical systems, and highlights the requirements of advanced manufacturing technology. We focus on biomedical systems that perform diagnostics of fluidic specimens, with analytes that are in the liquid phase. In the introduction, we define biomedical systems as well as their versatile applications and the essential current trends. The paper gives an overview of the most important biomolecules that typically must be detected or analyzed in several applications. The paper is structured as follows. First, the conventional architecture and construction of a biosensing system is introduced. We provide an overview of the most common biosensing methods that are currently used for the detection of biomolecules and its analysis. We present an overview of reported biochips, and explain the technology of biofunctionalization and detection principles, including their corresponding advantages and disadvantages. Next, we introduce microfluidics as a method for delivery of the specimen to the biochip sensing area. A special focus lies on material requirements and on manufacturing technology for fabricating microfluidic systems, both for niche and mass-scale production segments. We formulate requirements and constraints for integrating the biochips and microfluidic systems. The possible impacts of the conventional microassembly techniques and processing methods on the entire biomedical system and its specific parts are also described. On that basis, we explain the need for alternative microassembly technologies to enable the integration of biochips and microfluidic systems into fully functional systems.

High-throughput screening, next generation sequencing and machine learning: advanced methods in enzyme engineering

Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma. Typical enhancements sought in enzyme engineering and in vitro evolution campaigns include improved folding stability, catalytic activity, and/or substrate specificity. Despite significant progress in recent years in the areas of high-throughput screening and DNA sequencing, our ability to explore the vast space of functional enzyme sequences remains severely limited. Here, we review the currently available suite of modern methods for enzyme engineering, with a focus on novel readout systems based on enzyme cascades, and new approaches to reaction compartmentalization including single-cell hydrogel encapsulation techniques to achieve a genotype–phenotype link. We further summarize systematic scanning mutagenesis approaches and their merger with deep mutational scanning and massively parallel next-generation DNA sequencing technologies to generate mutability landscapes. Finally, we discuss the implementation of machine learning models for computational prediction of enzyme phenotypic fitness from sequence. This broad overview of current state-of-the-art approaches for enzyme engineering and evolution will aid newcomers and experienced researchers alike in identifying the important challenges that should be addressed to move the field forward.

Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma.

Dual signal amplification based on polysaccharide-initiated ring-opening polymerization and click polymerization for exosomes detection

Exosomes, as a biomarker with enhancing tumor invasion and spread, play an essential role for lung cancer diagnosis, therapy, and prognosis. In this work, a novel electrochemical sensor was fabricated for detecting exosomes secreted by lung cancer cells based on polysaccharide-initiated ring-opening polymerization (ROP) and click polymerization. First, MPA formed a self-assembled monolayer on the gold electrode surface, and then anti-EGFR was immobilized on the electrode surface by amide bond. Subsequently, a lot of phosphate groups were introduced by the specific recognition between anti-EGFR and exosomes, then sodium alginate grafted Glycidyl propargyl ether (SA-g-GPE) prepared via ROP was attached to the exosomes through PO₄^3-Zr⁴⁺-COOH coordination bond. After that, click polymerization was initiated by alkyne groups on the SA-g-GPE polymerization chain to realize highly sensitive detection of A549 exosomes. Under the optimum conditions, the fabricated sensor showed a good linear relationship between the logarithm of exosomes concentration and peak current in the range of 5 × 10³ - 5 × 10⁹ particles/mL, and the limit of detection (LOD) was as low as 1.49 × 10² particles/mL. In addition, this method had the advantages of high specificity, anti-interference, high sensitivity, simplicity, rapidity and green economy, which proposed a novel avenue for the detection of exosomes, and also had potential applications in early cancer diagnosis and biomedicine.

Rapid quantification of the malaria biomarker hemozoin by improved biocatalytically initiated precipitation atom transfer radical polymerizations

The fight against tropical diseases such as malaria requires the development of innovative biosensing techniques. Diagnostics must be rapid and robust to ensure prompt case management and to avoid further transmission. The malaria biomarker hemozoin can catalyze atom transfer radical polymerizations (ATRP), which we exploit in a polymerization-amplified biosensing assay for hemozoin based on the precipitation polymerization of N-isopropyl acrylamide (NIPAAm). The reaction conditions are systematically investigated using synthetic hemozoin to gain fundamental understanding of the involved reactions and to greatly reduce the amplification time, while maintaining the sensitivity of the assay. The use of excess ascorbate allows oxygen to be consumed in situ but leads to the formation of reactive oxygen species and to the decomposition of the initiator 2-hydroxyethyl 2-bromoisobutyrate (HEBIB). Addition of sodium dodecyl sulfate (SDS) and pyruvate results in better differentiation between the blank and hemozoin-containing samples. Optimized reaction conditions (including reagents, pH, and temperature) reduce the amplification time from 37 ± 5 min to 3 ± 0.5 min while maintaining a low limit of detection of 1.06 ng mL-1. The short amplification time brings the precipitation polymerization assay a step closer to a point-of-care diagnostic device for malaria. Future efforts will be dedicated to the isolation of hemozoin from clinical samples.

Radical polymerization reactions for amplified biodetection signals

This review summarizes various radical polymerization chemistries for amplifying biodetection signals and compares them from the practical point of view.

Biocatalytically Initiated Precipitation Atom Transfer Radical Polymerization (ATRP) as a Quantitative Method for Hemoglobin Detection in Biological Fluids

The hemoglobin content of blood is an important health indicator, and the presence of microscopic amounts of hemoglobin in places where it normally does not occur, e.g. in blood plasma or in urine, is a sign of diseases such as hemolytic anemia or urinary tract infections. Thus, methods to detect and quantify hemoglobin are important for clinical laboratories, blood banks, and for point-of-care diagnostics. The precipitation polymerization of N-isopropylacrylamide by hemoglobin-catalyzed atom transfer radical polymerization (ATRP) is used as an assay for hemoglobin quantification relying on the formation of turbidity as a simple optical read-out. Dose-response curves for pure hemoglobin and for hemoglobin in blood plasma, in urine, in erythrocytes, and in full blood are obtained. Turbidity formation increases with the concentration of hemoglobin. Concentrations of hemoglobin as low as 6.45 × 10^-3 mg mL^-1 in solution, 4.88 × 10^-1 mg mL^-1 in plasma, and 1.65 × 10^-1 mg mL^-1 in urine could be detected, which is below the clinically relevant concentrations in the respective body fluids. Total hemoglobin in full blood is also accurately determined. The reaction can be regarded as a polymerization-based signal amplification for the sensing of hemoglobin, as the analyte catalyzes the formation of radicals which add many monomer units into detectable polymer chains. While most established hemoglobin tests involve the use of highly toxic reagents such as potassium cyanide, the polymerization-based test uses simple and stable organic reagents. Thus, it is an environmentally friendlier alternative to established chemical assays for hemoglobin.

Enzyme-initiated free radical polymerizations of vinyl monomers using horseradish peroxidase

In this chapter, we highlight the use of horseradish peroxidase (HRP) as a catalyst to initiate free radical polymerizations of vinyl monomers under benign reaction conditions. A variety of vinyl monomers, including 4-acryloylmorpholine (AM), 2-hydroxyethyl methacrylate (HEMA), and poly(ethylene glycol) methyl ether acrylate (PEGA) were polymerized. The enzyme converts exogenous hydrogen peroxide into a usable radical source, which when coupled with a β-diketone, yields a radical that initiates chain growth in the presence of monomers. The resulting polymers were characterized using nuclear magnetic resonance (NMR) spectroscopy and gel permeation chromatography (GPC). By using enzymatic free radical polymerizations, polymers can be generated in a sustainable, environmentally-friendly, and scalable fashion.

Hemozoin-catalyzed precipitation polymerization as an assay for malaria diagnosis

Methods to diagnose malaria are of paramount interest to eradicate the disease. Current methods have severe limitations, as they are either costly or not sensitive enough to detect low levels of parasitemia. Here we report an ultrasensitive, yet low-resource chemical assay for the detection and quantification of hemozoin, a biomarker of all Plasmodium species. Solubilized hemozoin catalyzes the atom transfer radical polymerization of N-isopropylacrylamide above the lower critical solution temperature of poly(N-isopropylacrylamide). The solution becomes turbid, which can be observed by naked eye and quantified by UV-visible spectroscopy. The rate of turbidity increase is proportional to the concentration of hemozoin, with a detection limit of 0.85 ng mL-1. Malaria parasites in human blood can be detected down to 10 infected red blood cells μL-1. The assay could potentially be applied as a point-of-care test. The signal-amplification of an analyte by biocatalytic precipitation polymerization represents a powerful approach in biosensing.

The Role of Surface Receptor Density in Surface-Initiated Polymerizations for Cancer Cell Isolation

Fluid biopsies potentially offer a minimally invasive alternative to traditional tissue biopsies for the continual monitoring of metastatic cancer. Current established technologies for isolating circulating tumor cells (CTCs) suffer from poor purity and yield and require fixatives that preclude the collection of viable cells for longitudinal analyses of biological function. Antigen specific lysis (ASL) is a rapid, high-purity method of cell isolation based on targeted protective coatings on antigen-presenting cells and lysis depletion of unprotected antigen-negative cells. In ASL, photoinitiators are specifically labeled on cell surfaces that enable subsequent surface-initiated polymerization. Critically, the significant determinants of process yield have yet to be investigated for this emerging technology. In this work, we show that the labeling density of photoinitiators is strongly correlated with the yield of intact cells during ASL by flow cytometry analysis. Results suggest ASL is capable of delivering ∼25% of targeted cells after isolation using traditional antibody labeling approaches. Monomer formulations of two molecular weights of PEG-diacrylate (Mn ∼ 575 and 3500) are examined. The gelation response during ASL polymerization is also investigated via protein microarray analogues on planar glass. Finally, a density threshold of photoinitiator labeling required for protection during lysis is determined for both monomer formulations. These results indicate ASL is a promising technology for high yield CTC isolation for rare-cell function assays and fluid biopsies.