Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry

The COVID-19 pandemic has highlighted the necessity to develop fast, highly sensitive and selective virus detection methods. Surface-based DNA-biosensors are interesting candidates for this purpose. Functionalization of solid substrates with DNA must be precisely controlled to achieve the required accuracy and sensitivity. In particular, achieving high hybridization density at the sensing surface is a prerequisite to reach a low limit of detection. We herein describe a strategy based on peptides as anchoring units to immobilize DNA probes at the surface of borosilicate slides. While the coating pathway involves copper-catalyzed click chemistry, a copper-free variation is also reported. The resulting biochips display a high hybridization density (2.9 pmol per cm2) with their targeted gene sequences.

Switchable Separation Strategy via Host-Guest Locks

Universal separation strategies are the ultimate goal in separation science. However, there is always a tradeoff between universality and selectivity due to the negative influence among different recognition domains. With the goal of universal separation in mind, an unprecedented, switchable, and versatile separation strategy using reversible supramolecular host-guest interactions has been developed. These adjustable separation mediums were prepared using surface-grafted cationic cyclodextrin to firmly bind negatively charged adamantane derivatives. By changing guest structures, the surface functionality of the separation medium can be precisely regulated to be selective for a variety of substrates including chiral or achiral molecules, thus producing satisfactory single-column universality. This method offers a new approach to move beyond conventional separation methodologies and should stimulate the design of switchable functional materials.

UV- and Visible-Light Photopatterning of Molecular Gradients Using the Thiol-yne Click Reaction

The rational design of chemical coatings is used to control surface interactions with small molecules, biomolecules, nanoparticles, and liquids as well as optical and other properties. Specifically, micropatterned surface coatings have been used in a wide variety of applications, including biosensing, cell growth assays, multiplexed biomolecule interaction arrays, and responsive surfaces. Here, a maskless photopatterning process is studied, using the photocatalyzed thiol-yne "click" reaction to create both binary and gradient patterns on thiolated surfaces. Nearly defect-free patterns are produced by first coating glass surfaces with mercaptopropylsilatrane, a silanizing agent that forms smoother self-assembled monolayers than the commonly used 3-mercaptopropyltrimethoxysilane. Photopatterning is then performed using UV (365 nm) or visible (405 nm) light to graft molecules onto the surface in tunable concentrations based on the local exposure. The technique is demonstrated for multiple types of molecular grafts, including fluorescent dyes, poly(ethylene glycol), and biotin, the latter allowing subsequent deposition of biomolecules via biotin-avidin binding. Patterning is demonstrated in water and dimethylformamide, and the process is repeated to combine molecules soluble in different phases. The combination of arbitrary gradient formation, broad applicability, a low defect rate, and fast prototyping thanks to the maskless nature of the process creates a particularly powerful technique for molecular surface patterning that could be used for a wide variety of micropatterned applications.

3D-Printed Drug Capture Materials Based on Genomic DNA Coatings

The toxic side effects of chemotherapy have long limited its efficacy, prompting expensive and long-drawn efforts to develop more targeted cancer therapeutics. An alternative approach to mitigate off-target toxicity is to develop a device that can sequester chemotherapeutic agents from the veins that drain the target organ before they enter systemic circulation. This effectively localizes the chemotherapy to the target organ, minimizing any hazardous side effects. 3D printing is ideal for fabricating these devices, as the geometric control afforded allows us to precisely dictate its hemodynamic performance in vivo. However, the existing materials compatible with 3D printing do not have drug-binding capabilities. Here, we report the stable coating of genomic DNA on a 3D-printed structure for the capture of doxorubicin. Genomic DNA is an effective chemotherapeutic-agent capture material due to the intrinsic DNA-targeting mechanism of action of these drugs. Stable DNA coatings were achieved through a combination of electrostatic interactions and ultraviolet C (UVC, 254 nm) cross-linking. These UVC cross-linked DNA coatings were extremely stable-leaching on average 100 pg of genomic DNA per mm2 of 3D-printed structure over a period of 30 min. In vitro studies of these materials in phosphate buffered saline and human serum demonstrated that they were able to capture, on average, 72 and 60 ng of doxorubicin per mm2 of structure, respectively. The stability and efficacy of these genomic DNA-coated 3D-printed materials represent a significant step forward towards the translation of these devices to clinical applications for the potential improvement of chemotherapy treatment.

Highly Transparent Cyclic Olefin Copolymer Film with a Nanotextured Surface Prepared by One-Step Photografting for High-Density DNA Immobilization

Compared with conventional glass slides and two-dimensional (2D) planar microarrays, polymer-based support materials and three-dimensional (3D) surface structures have attracted increasing attention in the field of biochips because of their good processability in microfabrication and low cost in mass production, as well as their improved sensitivity and specificity for the detection of biomolecules. In the present study, UV-induced emulsion graft polymerization was carried out on a cyclic olefin copolymer (COC) surface to generate 3D nanotextures composed of loosely stacked nanoparticles with a diameter of approximately 50 nm. The introduction of a hierarchical nanostructure on a COC surface only resulted in a 5% decrease in its transparency at a wavelength of 550 nm but significantly increased the surface area, which markedly improved immobilization density and efficiency of an oligonucleotide probe compared with the functional group and polymer brush-modified substrates. The highest immobilization efficiency of the probes reached 93%, and a limit of detection of 75 pM could be obtained. The hybridization experiment demonstrated that the 3D gene chip exhibited excellent sensitivity for target DNA detection and single-nucleotide polymorphism discrimination. This one-step approach to the construction of nanotextured surfaces on the COC has promising applications in the fields of biochips and immunoassays.

Real Time Monitoring of a UV Light-Assisted Biofunctionalization Protocol Using a Nanophotonic Biosensor

A protocol for the covalent biofunctionalization of silicon-based biosensors using a UV light-induced thiol–ene coupling (TEC) reaction has been developed. This biofunctionalization approach has been used to immobilize half antibodies (hIgG), which have been obtained by means of a tris(2-carboxyethyl)phosphine (TCEP) reduction at the hinge region, to the surface of a vinyl-activated silicon-on-insulator (SOI) nanophotonic sensing chip. The response of the sensing structures within the nanophotonic chip was monitored in real time during the biofunctionalization process, which has allowed us to confirm that the bioconjugation of the thiol-terminated bioreceptors onto the vinyl-activated sensing surface is only initiated upon UV light photocatalysis.

Evaporation-Induced Biomolecule Detection on Versatile Superhydrophilic Patterned Surfaces: Glucose and DNA Assay

We introduce a droplet-based biomolecular detection platform using robust, versatile, and low-cost superhydrophilic patterned superhydrophobic surfaces. Benefitting from confinement and evaporation-induced shrinkage of droplets on wetted patterns, we show enrichment-based biomolecular detection using very low sample volumes. First, we developed a glucose assay using fluorescent polydopamine (PDA) based on enhancement of PDA emission by hydrogen peroxide (H₂O₂) produced in enzyme-mediated glucose oxidation reaction. Incubation in evaporating droplets resulted in brighter fluorescence compared to that in bulk solutions. Droplet assay was highly sensitive toward increasing glucose concentration while that in milliliter-volume solutions resulted in no fluorescence enhancement at similar time scales. This is due to droplet evaporation that increased the reaction rate by causing enrichment of PDA and glucose/glucose oxidase as well as increased concentration of H₂O₂ generated in shrinking droplet. Second, we chemically functionalized wetted patterns with single-stranded DNA and developed fluorescence-based DNA detection to demonstrate the adaptability of the patterned surfaces for a different class of assay. We achieved detection of glucose and DNA with concentration down to 130 μM and 200 fM, respectively. Patterned superhydrophobic surfaces with their simple production, sensitive response, and versatility present potential for bioanalysis from low sample volumes.

Decoration of trastuzumab with short oligonucleotides: synthesis and detailed characterization

Trastuzumab (Herceptin®) is an FDA-approved therapeutic antibody currently employed in the treatment of metastatic stages of breast cancer. Herein, we propose a simple, fast and cost-effective methodology to conjugate trastuzumab with 22-mer 5' thiol-modified oligonucleotides using a bifunctional crosslinker. The conjugates were successfully characterized by MALDI-ToF MS and SDS-PAGE, obviating the need for enzymatic digestion and difficult chromatographic separations. Furthermore, ELISA was performed to ensure that trastuzumab activity is not affected by oligonucleotide conjugation.

Thiol–ene click chemistry towards easy microarraying of half-antibodies

UV light catalyses in a few seconds the thiol–ene coupling reaction between half-antibodies and vinyl functionalized surfaces, providing high performance microarrays.

Approach Matters: The Kinetics of Interfacial Inverse-Electron Demand Diels-Alder Reactions

Rapid and quantitative click functionalization of surfaces remains an interesting challenge in surface chemistry. In this regard, inverse electron demand Diels-Alder (IEDDA) reactions represent a promising metal-free candidate. Herein, we reveal quantitative surface functionalization within 15 min. Furthermore, we report the comprehensive effects of substrate stereochemistry, surrounding microenvironment and substrate order on the reaction kinetics as obtained by surface-bound mass spectrometry (DART-HRMS).

Rapid and Complete Surface Modification with Strain-Promoted Oxidation-Controlled Cyclooctyne-1,2-Quinone Cycloaddition (SPOCQ)

Strain-promoted oxidation-controlled cyclooctyne-1,2-quinone cycloaddition (SPOCQ) between functionalized bicyclo[6.1.0]non-4-yne (BCN) and surface-bound quinones revealed an unprecedented 100 % conjugation efficiency. In addition, monitoring by direct analysis in real time mass spectrometry (DART-MS) revealed the underlying kinetics and activation parameters of this immobilization process in dependence on its microenvironment.

Organic Monolayers by B(C6F5)3-Catalyzed Siloxanation of Oxidized Silicon Surfaces

Inspired by the homogeneous catalyst tris(pentafluorophenyl) borane [B(C6F5)3], which acts as a promotor of Si-H bond activation, we developed and studied a method of modifying silicon oxide surfaces using hydrosilanes with B(C6F5)3 as the catalyst. This dedihydrosiloxanation reaction yields complete surface coverage within 10 min at room temperature. Organic monolayers derived from hydrosilanes with varying carbon chain lengths (C8-C18) were prepared on oxidized Si(111) surfaces, and the thermal and hydrolytic stabilities of the obtained monolayers were investigated in acidic (pH 3) medium, basic (pH 11) medium, phosphate-buffered saline (PBS), and deionized water (neutral conditions) for up to 30 days. DFT calculations were carried out to gain insight into the mechanism, and the computational results support a mechanism involving silane activation with B(C6F5)3. This catalyzed reaction path proceeds through a low-barrier-height transition state compared to the noncatalyzed reaction path.

Improved Performance of DNA Microarray Multiplex Hybridization Using Probes Anchored at Several Points by Thiol-Ene or Thiol-Yne Coupling Chemistry

Nucleic acid microarray-based assay technology has shown lacks in reproducibility, reliability, and analytical sensitivity. Here, a new strategy of probe attachment modes for silicon-based materials is built up. Thus, hybridization ability is enhanced by combining thiol-ene or thiol-yne click chemistry reactions with a multipoint attachment of polythiolated probes. The viability and performance of this approach was demonstrated by specifically determining Salmonella PCR products up to a 20 pM sensitivity level.

Imaging and spectroscopic comparison of multi-step methods to form DNA arrays based on the biotin-streptavidin system

Three multi-step multi-molecular approaches using the biotin-streptavidin system to contact-print DNA arrays on SiO2 surfaces modified with (3-glycidoxypropyl)trimethoxysilane are examined after each deposition/reaction step by atomic force microscopy, X-ray photoelectron spectroscopy and time of flight secondary ion mass spectrometry. Surface modification involves the spotting of preformed conjugates of biotinylated oligonucleotides with streptavidin onto surfaces coated with biotinylated bovine serum albumin b-BSA (approach I) or the spotting of biotinylated oligonucleotides onto a streptavidin coating, the latter prepared through a reaction with immobilized b-BSA (approach II) or direct adsorption (approach III). AFM micrographs, quantified by autocorrelation and height histogram parameters (e.g. roughness), reveal uniform coverage after each modification step with distinct nanostructures after the reaction of biotinylated BSA with streptavidin or of a streptavidin conjugate with biotinylated oligonucleotides. XPS relates the immobilization of biomolecules with covalent binding to the epoxy-silanized surface. Protein coverage, estimated from photoelectron attenuation, shows that regarding streptavidin the highest and the lowest immobilization efficiency is achieved by following approaches I and III, respectively, as confirmed by TOF-SIMS microanalysis. The size of the DNA spot reflects the contact radius of the printed droplet and increases with protein coverage (and roughness) prior to the spotting, as epoxy-silanized surfaces are hardly hydrophilic. Representative TOF-SIMS images show sub-millimeter spots: uniform for approach I, doughnut-like (with a small non-zero minimum) for approach II, both with coffee-rings or peak-shaped for approach III. Spot features, originating from pinned contact lines and DNA surface binding and revealed by complementary molecular distributions (all material, DNA, streptavidin, BSA, epoxy, SiO2), indicate two modes of droplet evaporation depending on the details of each applied approach.

DNA molecules site-specific immobilization and their applications

In addition to its role as a carrier of genetic information, DNA has been recognized as a construction material for the assembly of different objects and structural arrangements with nanoscale features. As a result of DNA’s self-recognition properties (based on the specific base-pairing of G-C and T-A), monolayer films of nucleic acids on solid supports have attracted an escalating attentions. Recently, numerous novel materials based on two-dimensional (2D) and three-dimensional (3D) DNA structures have been reported, which extends their utility to a large number of appliations. This review paper intends to be a new and comprehensive overview of recent strategies to site-specifically immobilized DNA on various materials, including carbonaceous substances, gold, and silica substrate, emphasizing the applications of site-specific DNA nanostructure-based devices for diagnostic, bioanalytical, food safety and environmental monitoring. Additionally, an up-to-date perspective is proposed at the end of this review.

Multicolor and erasable DNA photolithography

The immobilization of DNA molecules onto a solid support is a crucial step in biochip research and related applications. In this work, we report a DNA photolithography method based on photocleavage of 2-nitrobenzyl linker-modified DNA strands. These strands were subjected to ultraviolet light irradiation to generate multiple short DNA strands in a programmable manner. Coupling the toehold-mediated DNA strand-displacement reaction with DNA photolithography enabled the fabrication of a DNA chip surface with multifunctional DNA patterns having complex geometrical structures at the microscale level. The erasable DNA photolithography strategy was developed to allow different paintings on the same chip. Furthermore, the asymmetrical modification of colloidal particles was carried out by using this photolithography strategy. This strategy has broad applications in biosensors, nanodevices, and DNA-nanostructure fabrication.

Surface-functionalized silica gel adsorbents for efficient remediation of cationic dyes

The toxic and non-biodegradable nature of organic dyes necessitates the design and synthesis of novel adsorbents for their effective removal from the environment. This study reports an effective remediation behavior of surface-functionalized silica gel against water-soluble cationic dyes (up to 98 % removal). Thiol groups were functionalized at the surface of silica gel (SiO2–SH). The surface-tethered –SH groups were further oxidized to sulfonic acid groups to generate the negatively charged moieties at the surface of silica gel (SiO2–SO3 H). The morphology of the developed adsorbents and the surface modifications were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS). Uptake study of three cationic dyes, namely, rhodamine B (Rh B), rhodamine 6G (Rh 6G), and crystal violet (CV) with SiO2–SH and SiO2–SO3 H adsorbents was performed by varying the adsorbent amount, contact time, pH of solution, and temperature. The presence of negatively charged species at the surface of SiO2–SO3 H results in an increased electrostatic interaction with the cationic dyes, which leads to better remediation characteristics for SiO2–SO3 H as compared to SiO2–SH. The reusability of the developed adsorbents was also assessed by investigating adsorption/desorption of dyes. The simple fabrication process provides a facile avenue to the adsorbents with efficient remediation towards cationic dyes.

Streptavidin binding as a model to characterize thiol-ene chemistry-based polyamine surfaces for reversible photonic protein biosensing

Biotin- and iminobiotin-bonded surfaces obtained by thiol-ene chemistry and subsequent modification with polyamines were characterized with respect to streptavidin-binding capacity and reversibility for photonic biosensing using X-ray photoelectron spectroscopy and Mach-Zehnder-interferometric sensors. The streptavidin-iminobiotin system was exploited for reversible multilayer deposition and determination of affinity constants on each layer.

Construction of DNA microarrays on cyclic olefin copolymer surfaces using confined photocatalytic oxidation

A novel strategy for DNA immobilization on cyclic olefin copolymer surfaces.

Site-specific immobilization of DNA on silicon surfaces by using the thiol–yne reaction

Covalent immobilization of ssDNA fragments onto silicon-based materials was performed using the thiol–yne reaction.

Thiol–ene “click” reactions and recent applications in polymer and materials synthesis: a first update

This contribution serves as an update to a previous review (Polym. Chem.2010,1, 17–36) and highlights recent applications of thiol–ene ‘click’ chemistry as an efficient tool for both polymer/materials synthesis as well as modification.

Poly(acrylic acid)-grafted fluoropolymer films for highly sensitive fluorescent bioassays

In this study, a facile and effective method for the surface functionalization of inert fluoropolymer substrates using surface grafting was demonstrated for the preparation of a new platform for fluorescence-based bioassays. The surface of perfluorinated poly(ethylene-co-propylene) (FEP) films was functionalized using a 150 keV ion implantation, followed by the graft polymerization of acrylic acid, to generate a high density of carboxylic acid groups on the implanted surface. The resulting functionalized surface was investigated in terms of the surface density of carboxylic acid, wettability, chemical structure, surface morphology, and surface chemical composition. These results revealed that poly(acrylic acid) (PAA) was successfully grafted onto the implanted FEP surface and its relative amount depended on the fluence. To demonstrate the usefulness of this method for the fabrication of bioassays, the PAA-grafted FEP films were utilized for the immobilization of probe DNA for anthrax toxin, followed by hybridization with Cy3-labeled target DNA. Liver cancer-specific α-feto-protein (AFP) antigen was also immobilized on the PAA-grafted FEP films. Texas Red-labeled secondary antibody was reacted with AFP-specific primary antibody prebound to the AFP antigen using an immunoassay method. The results revealed that the fluorescence intensity clearly depended on the concentration of the target DNA hybridized to the probe DNA and the AFP antigen immobilized on the FEP films. The lowest detectable concentrations of the target DNA and the AFP antigen were 10 fg/mL and 10 pg/mL, respectively, with the FEP films prepared at a fluence of 3 × 10(14) ions/cm(2).

Chemical surface modifications for the development of silicon-based label-free integrated optical (IO) biosensors: a review

Increasing interest has been paid to label-free biosensors in recent years. Among them, refractive index (RI) optical biosensors enable high density and the chip-scale integration of optical components. This makes them more appealing to help develop lab-on-a-chip devices. Today, many RI integrated optical (IO) devices are made using silicon-based materials. A key issue in their development is the biofunctionalization of sensing surfaces because they provide a specific, sensitive response to the analyte of interest. This review critically discusses the biofunctionalization procedures, assay formats and characterization techniques employed in setting up IO biosensors. In addition, it provides the most relevant results obtained from using these devices for real sample biosensing. Finally, an overview of the most promising future developments in the fields of chemical surface modification and capture agent attachment for IO biosensors follows.