Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device.

Studies of the proteome would benefit greatly from methods to directly sequence and digitally quantify proteins and detect posttranslational modifications with single-molecule sensitivity. Here, we demonstrate single-molecule protein sequencing using a dynamic approach in which single peptides are probed in real time by a mixture of dye-labeled N-terminal amino acid recognizers and simultaneously cleaved by aminopeptidases. We annotate amino acids and identify the peptide sequence by measuring fluorescence intensity, lifetime, and binding kinetics on an integrated semiconductor chip. Our results demonstrate the kinetic principles that allow recognizers to identify multiple amino acids in an information-rich manner that enables discrimination of single amino acid substitutions and posttranslational modifications. With further development, we anticipate that this approach will offer a sensitive, scalable, and accessible platform for single-molecule proteomic studies and applications.

Analytical Comparison of Methods for Extraction of Short Cell-Free DNA from Urine.

Urine cell-free DNA (cfDNA) is a valuable noninvasive biomarker for cancer mutation detection, infectious disease diagnosis (eg, tuberculosis), organ transplantation monitoring, and prenatal screening. Conventional silica DNA extraction does not efficiently capture urine cfDNA, which is dilute (ng/mL) and highly fragmented [30 to 100 nucleotides (nt)]. The clinical sensitivity of urine cfDNA detection increases with decreasing target length, motivating use of sample preparation methods designed for short fragments. We compared the analytical performance of two published protocols (Wizard resin/guanidinium thiocyanate and Q Sepharose), three commercial kits (Norgen, QIAamp, and MagMAX), and an in-house sequence-specific hybridization capture technique. Dependence on fragment length (25 to 150 nt), performance at low concentrations (10 copies/mL), tolerance to variable urine conditions, and susceptibility to PCR inhibition were characterized. Hybridization capture and Q Sepharose performed best overall (60% to 90% recovery), although Q Sepharose had reduced recovery (<10%) of the shortest 25-nt fragment. Wizard resin/guanidinium thiocyanate recovery was dependent on pH and background DNA concentration and was limited to <35%, even under optimal conditions. The Norgen kit led to consistent PCR inhibition but had high recovery of short fragments. The QIAamp and MagMAX kits had minimal recovery of fragments <150 and <80 nt, respectively. Urine cfDNA extraction methods differ widely in ability to capture short, dilute cfDNA in urine; using suboptimal methods may profoundly impair clinical results.

Separation and dual detection of prostate cancer cells and protein biomarkers using a microchip device.

Current efforts for the detection of prostate cancer using only prostate specific antigen are not ideal and indicate a need to develop new assays - using multiple targets - that can more accurately stratify disease states. We previously introduced a device capable of the concurrent detection of cellular and molecular markers from a single sample fluid. Here, an improved design, which achieves affinity as well as size-based separation of captured targets using antibody-conjugated magnetic beads and a silicon chip containing micro-apertures, is presented. Upon injection of the sample, the integration of magnetic attraction with the micro-aperture chip permits larger cell-bead complexes to be isolated in an upper chamber with the smaller protein-bead complexes and remaining beads passing through the micro-apertures into the lower chamber. This enhances captured cell purity for on chip quantification, allows the separate retrieval of captured cells and proteins for downstream analysis, and enables higher bead concentrations for improved multiplexed ligand targeting. Using LNCaP cells and prostate specific membrane antigen (PSMA) to model prostate cancer, the device was able to detect 34 pM of spiked PSMA and achieve a cell capture efficiency of 93% from culture media. LNCaP cells and PSMA were then spiked into diluted healthy human blood to mimic a cancer patient. The device enabled the detection of spiked PSMA (relative to endogenous PSMA) while recovering 85-90% of LNCaP cells which illustrated the potential of new assays for the diagnosis of prostate cancer.

Cellulose paper sensors modified with zwitterionic poly(carboxybetaine) for sensing and detection in complex media.

Poly(carboxybetaine) (PCB) functionalized cellulose paper was used as a paper-based microfluidic device. The results showed that the PCB modified paper sensor was able to achieve (a) more rapid and sensitive glucose detection from undiluted human serum compared to bare cellulose and (b) specific antigen detection via covalently immobilized antibodies.

Achieving One-step Surface Coating of Highly Hydrophilic Poly(Carboxybetaine Methacrylate) Polymers on Hydrophobic and Hydrophilic Surfaces.

It is highly desirable to develop a universal nonfouling coating via a simple one-step dip-coating method. Developing such a universal coating method for a hydrophilic polymer onto a variety of surfaces with hydrophobic and hydrophilic properties is very challenging. This work demonstrates a versatile and simple method to attach zwitterionic poly(carboxybetaine methacrylate) (PCB), one of the most hydrophilic polymers, onto both hydrophobic and hydrophilic surfaces to render them nonfouling. This is achieved by the coating of a catechol chain end carboxybetaine methacrylate polymer (DOPA-PCB) assisted by dopamine. The coating process was carried out in water. Water miscible solvents such as methanol and tetrahydrofuran (THF) are added to the coatings if surface wettability is an issue, as for certain hydrophobic surfaces. This versatile coating method was applied to several types of surfaces such as polypropylene (PP), polydimethyl siloxane (PDMS), Teflon, polystyrene (PS), polymethylmethacrylate (PMMA), polyvinyl chloride (PVC) and also on metal oxides such as silicon dioxide.

Directly functionalizable surface platform for protein arrays in undiluted human blood plasma.

Protein arrays are a high-throughput approach for proteomic profiling, vital for achieving a greater understanding of biological systems, in addition to disease diagnostics and monitoring therapeutic treatments. In this work, zwitterionic carboxybetaine polymer (pCB) coated substrates were investigated as an array surface platform to enable convenient amino-coupling chemistry on a single directly functionalizable and unblocked film for the sensitive detection of target analytes from undiluted human blood plasma. Using a surface plasmon resonance (SPR) imaging sensor, the antibody immobilization conditions which provided excellent spot morphology and the largest antigen response were determined. It was found that pCB functionalization and the corresponding antigen detection both increased with pH and antibody concentration. Additionally, immobilization only required an aqueous buffer without the need for additives to improve spot quality. The nonspecific protein adsorption to undiluted human plasma on both the antibody immobilized pCB spots and the background were found to be about 9 and 6 ng/cm(2), respectively. A subsequent array consisting of three antibodies spotted onto pCB revealed little cross-reactivity for antigens spiked into the undiluted plasma. The low postfunctionalized nonfouling properties combined with antibody amplification showed similar sensitivities achievable with conventional spectroscopic SPR sensors and the same pCB films, but now with high-throughput capabilities. This represents the first demonstration of low fouling properties following antibody functionalization on protein arrays from undiluted human plasma and indicates the great potential of the pCB platform for high-throughput protein analysis.

Zwitterionic polymer-modified silicon microring resonators for label-free biosensing in undiluted human plasma.

A widely acknowledged goal in personalized medicine is to radically reduce the costs of highly parallelized, small fluid volume, point-of-care and home-based diagnostics. Recently, there has been a surge of interest in using complementary metal-oxide-semiconductor (CMOS)-compatible silicon photonic circuits for biosensing, with the promise of producing chip-scale integrated devices containing thousands of orthogonal sensors, at minimal cost on a per-chip basis. A central challenge in biosensor translation is to engineer devices that are both sensitive and specific to a target analyte within unprocessed biological fluids. Despite advances in the sensitivity of silicon photonic biosensors, poor biological specificity at the sensor surface remains a significant factor limiting assay performance in complex media (i.e. whole blood, plasma, serum) due to the non-specific adsorption of proteins and other biomolecules. Here, we chemically modify the surface of silicon microring resonator biosensors for the label-free detection of an analyte in undiluted human plasma. This work highlights the first application of a non-fouling zwitterionic surface coating to enable silicon photonic-based label-free detection of a protein analyte at clinically relevant sensitivities in undiluted human plasma.

Two-layer architecture using atom transfer radical polymerization for enhanced sensing and detection in complex media.

A novel, two-layer hierarchical architecture based on surface-initiated atom transfer radical polymerization was investigated. It combines a thin and highly dense first layer, for nonfouling properties, with a loose second layer for high immobilization levels of active biomolecules. Sodium azide treatment, to reduce the concentration of macroinitiators on the first layer for reinitiation, and by controlling the polydispersity allowed one to achieve three polymer architectures with low, moderate, or high azide substitution. Moderate substitution enabled the highest immobilization levels with a nonfouling background. Integration with dual-functional zwitterionic poly(carboxybetaine) made this platform suitable for applications in undiluted complex media such as blood. It was demonstrated via a surface plasmon resonance biosensor that antigen accessibility and antibody loading were greatly improved. These results indicate the two-layer strategy as a generic concept suitable for applications from diagnostics to medical coatings in order to maximize and minimize specific and nonspecific responses, respectively.

Simple and robust approach for passivating and functionalizing surfaces for use in complex media.

Pluronic is a popular triblock copolymer used as a surfactant to introduce hydrophilic coatings onto many different types of material surfaces, from engineering to biomedical applications. Unfortunately, this is limited in its ability to resist fouling from complex media (i.e., blood) and leaves the surface hard for further modification. Herein, we report a simple, yet robust approach for passivating and functionalizing surfaces based on zwitterionic poly(carboxybetaine) (PCB) based triblock copolymer, which can be directly applied to surfaces to prevent nonspecific protein adsorption from undiluted blood plasma, and to provide additional functionalities needed for the attachment of biomolecules. Several hydrophobic surfaces including polydimethylsiloxane, silanized silica, and self-assembled monolayers are tested to demonstrate its applicability to a wide range of systems. This approach provides a robust, convenient, and effective surface modification method for real-world applications from simple surface passivation to specific targeting in complex media.

Suppressing surface reconstruction of superhydrophobic PDMS using a superhydrophilic zwitterionic polymer.

Poly(dimethyl siloxane) (PDMS) is extensively used for biomedical applications due to its low cost, ease of fabrication, high durability and flexibility, oxygen permeability, and self-healing properties. PDMS, however, has some significant drawbacks. PDMS endures unacceptably high levels of nonspecific protein fouling when used with biological samples due to its superhydrophobic characteristics. Unfortunately, conventional surface modification methods do not work for PDMS due to its low glass transition temperature. This phenomenon has been well-known for years as "hydrophobic regeneration". For the same reason, it is also very difficult to bring functionalities onto PDMS surfaces. Herein, we demonstrate how a superhydrophilic zwitterionic material, poly(carboxybetaine methacrylate) (pCBMA), can provide a highly stable coating with long-term stabilty due to the sharp contrast in hydrophobicity between pCBMA and PDMS. This material is able to suppress nonspecific protein adsorption in complex media and functionalize desired biomolecules needed in applications, such as diagnostics, without sacrificing its nonfouling characteristics.

Controlled hierarchical architecture in surface-initiated zwitterionic polymer brushes with structurally regulated functionalities.

Hierarchical polymer films with structurally regulated functionalities are achieved by integrating 2D and 3D structures to enable ultralow nonspecific protein binding and high loading of molecular recognition elements, such as antibodies.

Dry film refractive index as an important parameter for ultra-low fouling surface coatings.

Here we demonstrate that the film refractive index (RI) can be an even more important parameter than film thickness for identifying nonfouling polymer films to undiluted human blood plasma and serum. The film thickness and RI are two parameters obtained from ellipsometry. Previously, film thickness has been correlated to ultra-low fouling properties. Practically, the film RI can be used to characterize polymer density but is often overlooked. By varying the water content in the surface-initiated atom transfer radical polymerization of zwitterionic carboxybetaine, a minimum of ∼1.5 RI units was necessary to achieve <5 ng/cm(2) of adsorption from undiluted human serum. A model of the film structure versus water content was also developed. These results point to an important parameter and simple approach for identifying surface coatings suitable for real-world applications involving complex media. Therefore, ultra-low fouling using a thin film is possible if it is densely packed.

Internal architecture of zwitterionic polymer brushes regulates nonfouling properties.

In this work, we study how film thickness and chain packing density affect the protein-resistant properties of polymer brushes in complex media. Polymer brushes based on dual-functional poly(carboxybetaine acrylamide) (pCB) were prepared via surface-initiated photoiniferter-mediated polymerization. By adjusting UV radiation time and solvent polarity, pCB films with different thicknesses can be achieved and characterized using an ellipsometer. The packing density of pCB polymer chains is directly related to the swelling ratio of swollen to collapsed film thicknesses. Results showed that the dry film thickness alone, used often in the literature, is not sufficient to correlate with nonfouling properties and the chain packing density must be considered for the design of nonfouling surface coatings.

Ultra-low fouling and functionalizable zwitterionic coatings grafted onto SiO2 via a biomimetic adhesive group for sensing and detection in complex media.

Non-specific protein binding from human plasma and serum has severely hindered the full capabilities of biosensors concerned with cancer biomarker detection. Currently, there is a strong desire for developing new materials which allow for the convenient attachment of an ultra-low fouling and functionalizable surface coating which can be used for highly sensitive and label-free detection of target analytes directly from complex media. In this work, a short 20 min in situ "graft to" protocol using Tris pH 8.5 buffer was developed for zwitterionic carboxybetaine methacrylate (CBMA) polymer conjugates containing the adhesive biomimetic moiety, 3,4-dihydroxy-L-phenylalanine (DOPA), on SiO(2) substrates. Using a surface plasmon resonance (SPR) biosensor, different buffers, pH values, salt concentrations, and temperatures were investigated for determining the "graft to" conditions that yield dense polymer films which both minimize non-specific protein adsorption and maximize antibody immobilization. The optimized surface coatings were shown to be highly protein resistant to 100% human blood plasma and serum. Subsequent antibody functionalized surfaces without any blocking agents enabled the specific detection of the cancer biomarker ALCAM directly from undiluted human serum down to 64 ng/mL. The successful use of this zwitterionic surface coating for detection from complex media on SiO(2) surfaces indicates its potential for broad impacts in the development of implantable medical devices, in vivo diagnostics, and nano-scale biosensors.

Label-free biomarker sensing in undiluted serum with suspended microchannel resonators.

Improved methods are needed for routine, inexpensive monitoring of biomarkers that could facilitate earlier detection and characterization of cancer. Suspended microchannel resonators (SMRs) are highly sensitive, batch-fabricated microcantilevers with embedded microchannels that can directly quantify adsorbed mass via changes in resonant frequency. As in other label-free detection methods, biomolecular measurements in complex media such as serum are challenging due to high background signals from nonspecific binding. In this report, we demonstrate that carboxybetaine-derived polymers developed to adsorb directly onto SMR SiO(2) surfaces act as ultralow fouling and functionalizable surface coatings. Coupled with a reference microcantilever, this approach enables detection of activated leukocyte cell adhesion molecule (ALCAM), a model cancer biomarker, in undiluted serum with a limit of detection of 10 ng/mL.