Immobilization of acrylamide-modified oligonucleotides by co-polymerization

Hydrogel-Encapsulated Beads Enable Proximity-Driven Encoded Library Synthesis and Screening

Encoded combinatorial library technologies have dramatically expanded the chemical space for screening but are usually only analyzed by affinity selection binding. It would be highly advantageous to reformat selection outputs to "one-bead-one-compound" solid-phase libraries, unlocking activity-based and cellular screening capabilities. Here, we describe hydrogel-encapsulated magnetic beads that enable such a transformation. Bulk emulsion polymerization of polyacrylamide hydrogel shells around magnetic microbeads yielded uniform particles (7 ± 2 μm diameter) that are compatible with diverse in-gel functionalization (amine, alkyne, oligonucleotides) and transformations associated with DNA-encoded library synthesis (acylation, enzymatic DNA ligation). In a case study of reformatting mRNA display libraries, transcription from DNA-templated magnetic beads encapsulated in gel particles colocalized both RNA synthesis via hybridization with copolymerized complementary DNA and translation via puromycin labeling. Two control epitope templates (V5, HA) were successfully enriched (50- and 99-fold, respectively) from an NNK5 library bead screen via FACS. Proximity-driven library synthesis in concert with magnetic sample manipulation provides a plausible means for reformatting encoded combinatorial libraries at scale.

Plasma Activation of Microplates Optimized for One-Step Reagent-Free Immobilization of DNA and Protein

Activated microplates are widely used in biological assays and cell culture to immobilize biomolecules, either through passive physical adsorption or covalent cross-linking. Covalent attachment gives greater stability in complex biological mixtures. However, current multistep chemical activation methods add complexity and cost, require specific functional groups, and can introduce cytotoxic chemicals that affect downstream cellular applications. Here, we show a method for one-step linker-free activation of microplates by energetic ions from plasma for covalent immobilization of DNA and protein. Two types of energetic ion plasma treatment were shown to be effective: plasma immersion ion implantation (PIII) and plasma-activated coating (PAC). This is the first time that PIII and PAC have been reported in microwell plates with nonflat geometry. We confirm that the plasma treatment generates radical-activated surfaces at the bottom of wells despite potential shadowing from the walls. Comprehensive surface characterization studies were used to compare the PIII and PAC microplate surface composition, wettability, radical density, optical properties, stability, and biomolecule immobilization density. PAC plates were found to have more nitrogen and lower radical density and were more hydrophobic and more stable over 3 months than PIII plates. Optimal conditions were obtained for high-density DNA (PAC, 0 or 21% nitrogen, pH 3-4) and streptavidin (PAC, 21% nitrogen, pH 5-7) binding while retaining optical properties required for typical high-throughput biochemical microplate assays, such as low autofluorescence and high transparency. DNA hybridization and protein activity of immobilized molecules were confirmed. We show that PAC activation allows for high-density covalent immobilization of functional DNA and protein in a single step on both 96- and 384-well plates without specific linker chemistry. These microplates could be used in the future to bind other user-selected ligands in a wide range of applications, for example, for solid phase polymerase chain reaction and stem cell culture and differentiation.

Fueling DNA Self-Assembly via Gel-Released Regulators

The development of responsive, multicomponent molecular materials requires means to physically separate yet easily couple distinct processes. Here we demonstrate methods to use molecules and reactions loaded into microliter-sized polyacrylamide hydrogels (mini-gels) to control the dynamic self-assembly of DNA nanotubes. We first characterize the UV-mediated release of DNA molecules from mini-gels, changing diffusion rates and minimizing spontaneous leakage of DNA. We then demonstrate that mini-gels can be used as compartments for storage and release of DNA that mediates the assembly or disassembly of DNA nanotubes in a one-pot process and that the speed of DNA release is controlled by the mini-gel porosity. With this approach, we achieve control of assembly and disassembly of nanotubes with distinct kinetics, including a finite delay that is obtained by loading distinct DNA regulators into distinct mini-gels. We finally show that mini-gels can also host and localize enzymatic reactions, by transcribing RNA regulators from synthetic genes loaded in the mini-gels, with diffusion of RNA to the aqueous phase resulting in the activation of self-assembly. Our experimental data are recapitulated by a mathematical model that describes the diffusion of DNA molecules from the gel phase to the aqueous phase in which they control self-assembly of nanotubes. Looking forward, DNA-loaded mini-gels may be further miniaturized and patterned to build more sophisticated storage compartments for use within multicomponent, complex biomolecular materials relevant for biomedical applications and artificial life.

DNA-Crosslinked 2D Photonic Crystal Hydrogels for Detection of Adenosine Actuated by an Adenosine-Binding Aptamer

There is a need to develop versatile sensing motifs that can be used to detect a variety of chemical targets in resource-limited settings, for example, at the point of care. While numerous sensing technologies have been developed toward this effort, these technologies can be overly complex and require a skilled technician, extensive sample preparation, or sophisticated instrumentation to use, limiting their generalizability and application in resource-limited settings. Here, we report a novel sensing motif that utilizes DNA-crosslinked two-dimensional photonic crystal (2DPC) hydrogels. These hydrogel sensors contain a DNA aptamer recognition group that binds a target analyte. As proof of concept, we fabricated 2DPC hydrogels using a well-studied adenosine-binding aptamer. This adenosine aptamer is duplexed with a partially complementary strand and forms responsive crosslinks in the hydrogel polymer network. When adenosine is introduced, aptamer-adenosine binding occurs, breaking the DNA crosslinks and causing the hydrogel to swell. This in turn increases the particle spacing of an embedded 2DPC array, shifting the 2DPC Bragg diffraction. Thus, adenosine concentration can be monitored through 2DPC Bragg diffraction measurements. A linear range of 20 μM to 2 mM was observed. The detection limits were calculated to be 13.9 μM in adenosine-binding buffer and 26.7 μM in fetal bovine serum. This reported sensing motif has a readout that is simple and rapid and requires minimal equipment. We hypothesize that this sensing motif is generalizable and that other sensors can be easily fabricated by simply exchanging the aptamer that serves as a molecular recognition group.

Reactive Acrylamide-Modified DNA Traps for Accurate Cross-Linking with Cysteine Residues in DNA–Protein Complexes Using Mismatch Repair Protein MutS as a Model

Covalent protein capture (cross-linking) by reactive DNA derivatives makes it possible to investigate structural features by fixing complexes at different stages of DNA–protein recognition. The most common cross-linking methods are based on reactive groups that interact with native or engineered cysteine residues. Nonetheless, high reactivity of most of such groups leads to preferential fixation of early-stage complexes or even non-selective cross-linking. We synthesised a set of DNA reagents carrying an acrylamide group attached to the C5 atom of a 2′-deoxyuridine moiety via various linkers and studied cross-linking with MutS as a model protein. MutS scans DNA for mismatches and damaged nucleobases and can form multiple non-specific complexes with DNA that may cause non-selective cross-linking. By varying the length of the linker between DNA and the acrylamide group and by changing the distance between the reactive nucleotide and a mismatch in the duplex, we showed that cross-linking occurs only if the distance between the acrylamide group and cysteine is optimal within the DNA–protein complex. Thus, acrylamide-modified DNA duplexes are excellent tools for studying DNA–protein interactions because of high selectivity of cysteine trapping.

DNA-Controlled Spatiotemporal Patterning of a Cytoskeletal Active Gel

Living cells move and change their shape because signaling chemical reactions modify the state of their cytoskeleton, an active gel that converts chemical energy into mechanical forces. To create life-like materials, it is thus key to engineer chemical pathways that drive active gels. Here we describe the preparation of DNA-responsive surfaces that control the activity of a cytoskeletal active gel composed of microtubules: A DNA signal triggers the release of molecular motors from the surface into the gel bulk, generating forces that structure the gel. Depending on the DNA sequence and concentration, the gel forms a periodic band pattern or contracts globally. Finally, we show that the structuration of the active gel can be spatially controlled in the presence of a gradient of DNA concentration. We anticipate that such DNA-controlled active matter will contribute to the development of life-like materials with self-shaping properties.

DNA Aptamer Functionalized Hydrogels for Interferometric Fiber-Optic Based Continuous Monitoring of Potassium Ions

In the present paper, we describe a potassium sensor based on DNA-aptamer functionalized hydrogel, that is capable of continuous label-free potassium ion (K+) monitoring with potential for in situ application. A hydrogel attached to the end of an optical fiber is designed with di-oligonucleotides grafted to the polymer network that may serve as network junctions in addition to the covalent crosslinks. Specific affinity toward K+ is based on exploiting a particular aptamer that exhibits conformational transition from single-stranded DNA to G-quadruplex formed by the di-oligonucleotide in the presence of K+. Integration of this aptamer into the hydrogel transforms the K+ specific conformational transition to a K+ concentration dependent deswelling of the hydrogel. High-resolution interferometry monitors changes in extent of swelling at 1 Hz and 2 nm resolution for the hydrogel matrix of 50 µm. The developed hydrogel-based biosensor displayed high selectivity for K+ ions in the concentration range up to 10 mM, in the presence of physiological concentrations of Na+. Additionally, the concentration dependent and selective K+ detection demonstrated in the artificial blood buffer environment, both at room and physiological temperatures, suggests substantial potential for practical applications such as monitoring of potassium ion concentration in blood levels in intensive care medicine.

Freezing-Assisted Conjugation of Unmodified Diblock DNA to Hydrogel Nanoparticles and Monoliths for DNA and Hg2+ Sensing

Acrydite-modified DNA is the most frequently used reagent to prepare DNA-functionalized hydrogels. Herein, we show that unmodified penta-adenine (A₅ ) can reach up to 75 % conjugation efficiency in 8 h under a freezing polymerization condition in polyacrylamide hydrogels. DNA incorporation efficiency was reduced by forming duplex or other folded structures and by removing the freezing condition. By designing diblock DNA containing an A₅ block, various functional DNA sequences were attached. Such hydrogels were designed for ultrasensitive DNA hybridization and Hg²⁺ detection, with detection limits of 50 pM and 10 nM, respectively, demonstrating the feasibility of using unmodified DNA to replace acrydite-DNA. The same method worked for both gel nanoparticles and monoliths. This work revealed interesting reaction products by exploiting freezing and has provided a cost-effective way to attach DNA to hydrogels.

Mini review: Enzyme-based DNA synthesis and selective retrieval for data storage

The market for using and storing digital data is growing, with DNA synthesis emerging as an efficient way to store massive amounts of data. Storing information in DNA mainly consists of two steps: data writing and reading. The writing step requires encoding data in DNA, building one nucleotide at a time as a form of single-stranded DNA (ssDNA). Once the data needs to be read, the target DNA is selectively retrieved and sequenced, which will also be in the form of an ssDNA. Recently, enzyme-based DNA synthesis is emerging as a new method to be a breakthrough on behalf of decades-old chemical synthesis. A few enzymatic methods have been presented for data memory, including the use of terminal deoxynucleotidyl transferase. Besides, enzyme-based amplification or denaturation of the target strand into ssDNA provides selective access to the desired dataset. In this review, we summarize diverse enzymatic methods for either synthesizing ssDNA or retrieving the data-containing DNA.

3× multiplexed detection of antibiotic resistant plasmids with single molecule sensitivity

Bacterial pathogens resistant to antibiotics have become a serious health threat. Those species which have developed resistance against multiple drugs such as the carbapenems, are more lethal as these are last line therapy antibiotics. Current diagnostic tests for these resistance traits are based on singleplex target amplification techniques which can be time consuming and prone to errors. Here, we demonstrate a chip based optofluidic system with single molecule sensitivity for amplification-free, multiplexed detection of plasmids with genes corresponding to antibiotic resistance, within one hour. Rotating disks and microfluidic chips with functionalized polymer monoliths provided the upstream sample preparation steps to selectively extract these plasmids from blood spiked with E. coli DH5α cells. Waveguide-based spatial multiplexing using a multi-mode interference waveguide on an optofluidic chip was used for parallel detection of three different carbapenem resistance genes. These results point the way towards rapid, amplification-free, multiplex analysis of antibiotic-resistant pathogens.

DNA-based long-lived reaction-diffusion patterning in a host hydrogel

The development of living organisms is a source of inspiration for the creation of synthetic life-like materials. Embryo development is divided into three stages that are inextricably linked: patterning, differentiation and growth. During patterning, sustained out-of-equilibrium molecular programs interpret underlying molecular cues to create well-defined concentration profiles. Implementing this patterning stage in an autonomous synthetic material is a challenge that at least requires a programmable and long-lasting out-of-equilibrium chemistry compatible with a host material. Here, we show that DNA/enzyme reactions can create reaction-diffusion patterns that are extraordinarily long-lasting both in solution and inside an autonomous hydrogel. The life-time and stability of these patterns - here, traveling fronts and two-band patterns - are significantly increased by blocking parasitic side reactions and by dramatically reducing the diffusion coefficient of specific DNA strands. Immersed in oil, hydrogels pattern autonomously with limited evaporation, but can also exchange chemical information with other gels when brought into contact. Providing a certain degree of autonomy and being capable of interacting with each other, we believe these out-of-equilibrium hydrogels open the way for the rational design of primitive metabolic materials.

Engineering functional hydrogel microparticle interfaces by controlled oxygen-inhibited photopolymerization

Functional poly(ethylene glycol) diacrylate (PEGDA) hydrogel microparticles for the detection of bioactive macromolecules were fabricated via oxygen-inhibited photopolymerization in a droplet microfluidic device. Hydrogel network functionalization and architecture were characterized using a biotin-avidin binding assay, which revealed radial network inhomogeneities dependent on exposure conditions. Empirical results were corroborated using a reaction-diffusion model, describing the effects of exposure intensity on the spatial photopolymerization kinetics and resulting polymeric mesh network. The combination of finely controlled exposure conditions and predictive simulations enables the generation of tailored particles with microengineered interfaces and gradients in crosslinking density, which dictate solute diffusivity and elasticity, augmenting the utility of this approach in engineering multifunctional, size-excluding hydrogel particles for multiplexed biomolecular sensing.

A variant of GRK5 is associated with the therapeutic efficacy of repaglinide in Chinese Han patients with type 2 diabetes mellitus

Post-Market Research We aimed to investigate the impact of G protein-coupled receptor kinase 5 (GRK5) rs10886471 polymorphism on repaglinide efficacy in Chinese patients with type 2 diabetes mellitus (T2DM). A total of 300 T2DM patients and 210 healthy controls were genotyped for GRK5 rs10886471 on a three-dimensional polyacrylamide gel-based DNA microarray. Eighty-five patients with the same genotypes of cytochrome P450 (CYP) 2C8*3 139Arg and organic anion-transporting polypeptide 1B1 (OATP1B1) 521TT were randomly selected to orally take repaglinide for eight consecutive weeks. Then, the biochemical indicators and pharmacodynamic parameters were measured before and after repaglinide treatment. The T allelic frequency of GRK5 rs10886471 was higher in T2DM patients than in healthy subjects (p < .01). T2DM patients with genotypes CC and CT at GRK5 rs10886471 had a significant reduction in terms of fasting plasma glucose (FPG) compared with those with genotype TT (p < .01). In addition, the carriers of genotypes CC and CT at GRK5 rs10886471 had higher differential values of postprandial serum insulin (PINS) compared with genotype TT carriers (p < .05). These findings suggest that GRK5 rs10886471 polymorphism may influence the therapeutic efficacy of repaglinide in Chinese Han T2DM patients.

Rapid Capture and Release of Nucleic Acids through a Reversible Photo-Cycloaddition Reaction in a Psoralen-Functionalized Hydrogel

Reversible immobilization of DNA and RNA is of great interest to researchers who seek to manipulate DNA or RNA in applications such as microarrays, DNA hydrogels, and gene therapeutics. However, there is no existing system that can rapidly capture and release intact nucleic acids. To meet this unmet need, we developed a functional hydrogel for rapid DNA/RNA capture and release based on the reversible photo-cycloaddition of psoralen and pyrimidines. The functional hydrogel can be easily fabricated through copolymerization of acrylamide with the synthesized allylated psoralen. The psoralen-functionalized hydrogel exhibits effective capture and release of nucleic acids spanning a wide range of lengths in a rapid fashion; over 90 % of the capture process is completed within 1 min, and circa 100 % of the release process is completed within 2 min. We observe no deleterious effects on the hybridization to the captured targets.

Selective Nascent Polymer Catch-and-Release Enables Scalable Isolation of Multi-Kilobase Single-Stranded DNA

Scalable methods currently are lacking for isolation of long ssDNA, an important material for numerous biotechnological applications. Conventional biomolecule purification strategies achieve target capture using solid supports, which are limited in scale and susceptible to contamination owing to nonspecific adsorption and desorption on the substrate surface. We herein disclose selective nascent polymer catch and release (SNAPCAR), a method that utilizes the reactivity of growing poly(acrylamide-co-acrylate) chains to capture acrylamide-labeled molecules in free solution. The copolymer acts as a stimuli-responsive anchor that can be precipitated on demand to pull down the target from solution. SNAPCAR enabled scalable isolation of multi-kilobase ssDNA with high purity and 50-70 % yield. The ssDNA products were used to fold various DNA origami. SNAPCAR-produced ssDNA will expand the scope of applications in nanotechnology, gene editing, and DNA library construction.

Surface isoelectric focusing (sIEF) with carrier ampholyte pH gradient

Isoelectric focusing (IEF) is a powerful tool for amphoteric protein separations because of high sensitivity, bio-compatibility, and reduced complexity compared to chromatography or mechanical separation techniques. IEF miniaturization is attractive because it enables rapid analysis, easier adaptation to point of care applications, and smaller sample demands. However, existing small-scale IEF tools have not yet been able to analyze single protein spots from array libraries, which are ubiquitous in many pharmaceutical discovery and screening protocols. Thus, we introduce an in situ, novel, miniaturized protein analysis approach that we have termed surface isoelectric focusing (sIEF). Low volume printed sIEF gels can be run at length scales of ∼300 μm, utilize ∼0.9 ng of protein with voltages below 10 V. Further, the sIEF device platform is so simple that it can be integrated with protein library arrays to reduce cost; devices demonstrate reusability above 50 uses. An acrylamide monomer solution containing broad-range carrier ampholytes was microprinted with a Nano eNabler^TM between micropatterned gold electrodes spaced 300 μm apart on a glass slide. The acrylamide gel was polymerized in situ followed by protein loading via printed diffusional exchange. A pH gradient formed via carrier ampholyte stacking when electrodes were energized; the gradient was verified using ratiometric pH-sensitive FITC/TRITC dyes. Green fluorescent protein (GFP) and R-phycoerythrin (R-PE) were utilized both as pI markers and to test sIEF performance as a function of electric field strength and ampholyte concentration. Factors hampering sIEF included cathodic drift and pH gradient compression, but were reduced by co-printing non-ionic Synperonic® F-108 surfactant to reduce protein-gel interactions. sIEF gels achieved protein separations in <10 min yielding bands < 50 μm wide with peak capacities of ∼8 and minimum pI differences from 0.12 to 0.14. This new sIEF technique demonstrated comparable focusing at ∼100 times smaller dimensions than any previous IEF. Further, sample volumes required were reduced four orders of magnitude from 20 μL for slab gel IEF to 0.002 μL for sIEF. In summary, sIEF advantages include smaller volumes, reduced power consumption, and microchip surface accessibility to focused bands along with equivalent separation resolutions to prior IEF tools. These attributes position this new technology for rapid, in situ protein library analysis in clinical and pharmaceutical settings.

Unzipping and shearing DNA with electrophoresed nanoparticles in hydrogels

We show electric control of unzipping and shearing dehybridization of a DNA duplex anchored to a hydrogel. Tensile force is applied by electrophoresing (25 V cm^-1) gold nanoparticles pulling the DNA duplex. The pulled DNA strand is gradually released from the hydrogel. The unzipping release rate is faster than shearing; for example, 3-fold for a 15 base pair duplex, which helps to design electrically driven DNA devices.

Chemoselective Coupling Preserves the Substrate Integrity of Surface-Immobilized Oligonucleotides for Emulsion PCR-Based Gene Library Construction

Combinatorial bead libraries figure prominently in next-generation sequencing and are also important tools for in vitro evolution. The most common methodology for generating such bead libraries, emulsion PCR (emPCR), enzymatically extends bead-immobilized oligonucleotide PCR primers in emulsion droplets containing a single progenitor library member. Primers are almost always immobilized on beads via noncovalent biotin-streptavidin binding. Here, we describe covalent bead functionalization with primers (∼10⁶ primers/2.8-μm-diameter bead) via either azide-alkyne click chemistry or Michael addition. The primers are viable polymerase substrates (4-7% bead-immobilized enzymatic extension product yield from one thermal cycle). Carbodiimide-activated carboxylic acid beads only react with oligonucleotides under conditions that promote nonspecific interactions (low salt, low pH, no detergent), comparably immobilizing primers on beads, but yielding no detectable enzymatic extension product. Click-functionalized beads perform satisfactorily in emPCR of a site-saturation mutagenesis library, generating monoclonal templated beads (10⁴-10⁵ copies/bead, 1.4-kb amplicons). This simpler, chemical approach to primer immobilization may spur more economical library preparation for high-throughput sequencing and enable more complex surface elaboration for in vitro evolution.

On-Flow Synthesis of Co-Polymerizable Oligo-Microspheres and Application in ssDNA Amplification

We fabricated droplet-based microfluidic platform for copolymerizable microspheres with acrydite modified DNA probe. The copolymerizable 3-D polyacrylamide microspheres were successfully produced from microcontinuous-flow synthesis with on-channel solidification. DNA copolymerization activity, surface presentation and thermostability were assessed by using fluorescent labeled complementary probe. The binding performance was only visible on the surface area of oligo-microspheres. We show that the resulting oligo-microspheres can be directly integrated into a streamlined microsphere-PCR protocol for amplifying ssDNA. Our microspheres could be utilized as a potential material for ssDNA analysis such as DNA microarray and automatic DNA SELEX process.

Molecularly Imprinted Polymers with DNA Aptamer Fragments as Macromonomers

Molecularly imprinted polymers (MIPs) are produced in the presence of a template molecule. After removing the template, the cavity can selectively rebind the template. MIPs are attractive functional materials with a low cost and high stability, but traditional MIPs often suffer from low binding affinity. This study employs DNA aptamer fragments as macromonomers to improve MIPs. The DNA aptamer for adenosine was first split into two halves, fluorescently labeled, and copolymerized into MIPs. With a fluorescence quenching assay, the importance of imprinting was confirmed. Further studies were carried out using isothermal titration calorimetry (ITC). Compared to the mixture of the free aptamer fragments, their MIPs doubled the binding affinity. Each free aptamer fragment alone cannot bind adenosine, whereas MIPs containing each fragment are effective binders. We further shortened one of the aptamer fragments, and the DNA length was pushed to as short as six nucleotides, yielding MIPs with a dissociation constant of 27 μM adenosine. This study provides a new method for preparing functional MIP materials by combining high-affinity biopolymer fragments with low-cost synthetic monomers, allowing higher binding affinity and providing a method for signaling binding based on DNA chemistry.

Three-dimensional polyacrylamide gel-based DNA microarray method effectively identifies UDP-glucuronosyltransferase 1A1 gene polymorphisms for the correct diagnosis of Gilbert's syndrome

Gilbert's syndrome is a mild genetic liver disorder characterized by unconjugated hyperbilirubinemia due to defects in the UDP-glucuronosyltransferase 1A1 (UGT1A1) gene. The T-3279G mutation in the phenobarbital responsive enhancer module (PBREM), the TA-insertion in the TATA box, creating the A(TA)7TAA motif instead of A(TA)6TAA and the G211A mutation in coding exon 1, particularly in Asian populations, of the human UGT1A1 gene are the three common genotypes found in patients with Gilbert's syndrome. Different approaches for detecting the T-3279G, A(TA)6/7TAA and G211A mutations of the UGT1A1 gene have been described. In this study, to the best of our knowledge, we established a three-dimensional polyacrylamide gel-based DNA microarray method for the first time, in order to study UGT1A1 gene polymorphisms. This method, based on a step-by-step three-dimensional polyacrylamide gel-based DNA microarray protocol, successfully identified all possible genotypes of T-3279G, A(TA)6/7TAA and G211A in 20 patients with hyperbilirubinemia. In addition, sequencing was performed to confirm these results. The data from the current study demonstrate that the three-dimensional polyacrylamide gel microarray method has the potential to be applied as a useful, reliable and cost-effective tool to detect the T-3279G, the A(TA)6/7TAA and the G211A mutations of the UGT1A1 gene in patients with hyperbilirubinemia and thereby aid in the diagnosis of Gilbert's syndrome.

Detection of human genome mutations associated with pregnancy complications using 3-D microarray based on macroporous polymer monoliths

Analysis of variations in DNA structure using a low-density microarray technology for routine diagnostic in evidence-based medicine is still relevant. In this work the applicability of 3-D macroporous monolithic methacrylate-based platforms for detection of different pathogenic genomic substitutions was studied. The detection of nucleotide replacements in F5 (Leiden G/A, rs6025), MTHFR (C/T, rs1801133) and ITGB3 (T/C, rs5918), involved in coagulation, and COMT (C/G, rs4818), TPH2 (T/A, rs11178997), PON1 (T/A rs854560), AGTR2 (C/A, rs11091046) and SERPINE1 (5G/4G, rs1799889), associated with pregnancy complications, was performed. The effect of such parameters as amount and type of oligonucleotide probe, amount of PCR product on signal-to-noise ratio, as well as mismatch discrimination was analyzed. Sensitivity and specificity of mutation detections were coincided and equal to 98.6%. The analysis of SERPINE1 and MTHFR genotypes by both NGS and developed microarray was performed and compared.

Open source and DIY hardware for DNA nanotechnology labs

A set of instruments and specialized equipment is necessary to equip a laboratory to work with DNA. Reducing the barrier to entry for DNA manipulation should enable and encourage new labs to enter the field. We present three examples of open source/DIY technology with significantly reduced costs relative to commercial equipment. This includes a gel scanner, a horizontal PAGE gel mold, and a homogenizer for generating DNA-coated particles. The overall cost savings obtained by using open source/DIY equipment was between 50 and 90%.

Easy daylight fabricated hydrogel array for colorimetric DNA analysis

The fabrication of 3D hydrogel microarrays for DNA analytics that allow simple visual signal readout for on-site applications is described. A convenient one-step polymerization of the hydrogel including in situ capture oligonucleotide immobilization is accomplished by using N,N'-dimethylacrylamide/polyethylene glycol (PEG1900 )-bisacrylamide monomers. The implementation of an acylphosphine-oxide photoinitiator even allows polymerization at daylight, whereas other approaches require exposure with light in the UV-range. This minimizes the risk of UV-caused DNA damages within the capture DNA-strand that could adversely affect the subsequent hybridization step. The porous network of these gel segments allows DNA as well as protein penetration. Thus, the successful in-gel DNA hybridization is monitored by the deposition of silver nanoparticles. These metal particles allow naked eye signal readout.

Responsive DNA-based hydrogels and their applications

The term hydrogel describes a type of soft and wet material formed by cross-linked hydrophilic polymers. The distinct feature of hydrogels is their ability to absorb a large amount of water and swell. The properties of a hydrogel are usually determined by the chemical properties of their constituent polymer(s). However, a group of hydrogels, called "smart hydrogels," changes properties in response to environmental changes or external stimuli. Recently, DNA or DNA-inspired responsive hydrogels have attracted considerable attention in construction of smart hydrogels because of the intrinsic advantages of DNA. As a biological polymer, DNA is hydrophilic, biocompatible, and highly programmable by Watson-Crick base pairing. DNA can form a hydrogel by itself under certain conditions, and it can also be incorporated into synthetic polymers to form DNA-hybrid hydrogels. Functional DNAs, such as aptamers and DNAzymes, provide additional molecular recognition capabilities and versatility. In this Review, DNA-based hydrogels are discussed in terms of their stimulus response, as well as their applications.

Spatial control of DNA reaction networks by DNA sequence

We have developed a set of DNA circuits that execute during gel electrophoresis to yield immobile, fluorescent features in the gel. The parallel execution of orthogonal circuits led to the simultaneous production of different fluorescent lines at different positions in the gel. The positions of the lines could be rationally manipulated by changing the mobilities of the reactants. The ability to program at the nanoscale so as to produce patterns at the macroscale is a step towards programmable, synthetic chemical systems for generating defined spatiotemporal patterns.

Direct imaging of DNA motif sequences with encoded nanoparticles

We present a method for encoded tagging and imaging of short nucleic acid motif chains (oligomotifs) using selective hybridization of heterogeneous Au nanoparticles. The resulting encoded nanoparticle string is thus representative of the underlying motif sequence. Since the nanoparticles are much more massive than the motifs; the motif chain order can be directly observed using scanning electron microscopy. Using this technique we demonstrate direct sequencing of oligomotifs in single DNA molecules consisting of four 100-bp motif chains tagged with four different types of nanoparticles. The method outlined is a precursor for a high density direct sequencing technology.

Macroporous methacrylate-based monoliths as platforms for DNA microarrays

Macroporous monoliths with different surface functionalization (reactive groups) were utilized as platforms for DNA analysis in microarray format. The slides based on a copolymer glycidyl methacrylate-co-ethylene dimethacrylate (GMA-EDMA) have been chosen as well known and thoroughly studied standard. In particular, this material has been used at optimization of DNA microanalytical procedure. The concentration and pH of spotting solution, immobilization temperature and time, blocking agent and coupling reaction duration were selected as varied parameters. The efficiency of analysis performed on 3-D monolithic platforms was compared to that established for commercially available glass slides. As a practical example, a diagnostic test for detection of CFTR gene mutation was carried out. Additionally, the part of presented work was devoted to preparation of aptamer-based test-system that allowed successful and highly sensitive detection both of DNA and protein.

Direct imaging of DNA motif sequences with encoded nanoparticles

We present a method for encoded tagging and imaging of short nucleic acid motif chains (oligomotifs) using selective hybridization of heterogeneous Au nanoparticles (Au-NP). The resulting encoded NP string is thus representative of the underlying motif sequence. As the NPs are much more massive than the motifs, the motif chain order can be directly observed using scanning electron microscopy. Using this technique we demonstrate direct sequencing of oligomotifs in single DNA molecules consisting of four 100-nt motif chains tagged with four different types of NPs. The method outlined is a precursor for a high density direct sequencing technology.

Three-dimensional hydrogel structures as optical sensor arrays, for the detection of specific DNA sequences

The fabrication and characterization of surface-attached PEG-diacrylate hydrogel structures and their application as sensing platforms for the detection of specific target sequences are reported. Hydrogel structures were formed by a photopolymerization process, using substrate-bound Eosin Y molecules for the production of free radicals. We have demonstrated that this fabrication process allows for control over hydrogel growth down to the micrometer scale. Confocal imaging revealed relatively large pore structures for 25% (v/v) PEG-diacrylate hydrogels, which appear to lie in tightly packed layers. Our data suggest that these pore structures decrease in size for hydrogels with increasing levels of PEG-diacrylate. Surface coverage values calculated for hydrogels immobilized with 21-mer DNA probe sequences were significantly higher compared to those previously reported for 2- and 3-dimensional sensing platforms, on the order of 10(16)molecules cm(-2). Used as sensing platforms in DNA hybridization assays, a detection limit of 3.9 nM was achieved for hybridization reactions between 21-mer probe and target sequences. The ability of these hydrogel sensing platforms to discriminate between wild-type and mutant allele sequences was also demonstrated, down to target concentrations of 1-2 nM. A reduction in the hybridization time down to a period of 15 min was also achieved, while still maintaining confident results, demonstrating the potential for future integration of these sensing platforms within Lab-on-Chip or diagnostic devices.

Nonvolatile copolymer compositions for fabricating gel element microarrays

By modifying polymer compositions and cross-linking reagents, we have developed a simple yet effective manufacturing strategy for copolymerized three-dimensional gel element arrays. A new gel-forming monomer, 2-(hydroxyethyl) methacrylamide (HEMAA), was used. HEMAA possesses low volatility and improves the stability of copolymerized gel element arrays to on-chip thermal cycling procedures relative to previously used monomers. Probe immobilization efficiency within the new polymer was 55%, equivalent to that obtained with acrylamide (AA) and methacrylamide (MA) monomers. Nonspecific binding of single-stranded targets was equivalent for all monomers. Increasing cross-linker chain length improved hybridization kinetics and end-point signal intensities relative to N,N-methylenebisacrylamide (Bis). The new copolymer formulation was successfully applied to a model orthopox array. Because HEMAA greatly simplifies gel element array manufacture, we expect it (in combination with new cross-linkers described here) to find widespread application in microarray science.

In situ techniques and digital image analysis methods for quantifying spatial localization patterns of nitrifiers and other microorganisms in biofilm and flocs

The spatial localization patterns of microorganisms in multispecies biofilms reflect numerous phenomena that influence sessile microbial life, such as substrate concentration gradients within the biofilm and biological interactions with other biofilm populations. Quantitative and population-specific in situ analyses of spatial patterns have a high potential to provide novel insights into the biology of biofilm organisms, including yet uncultured microbes, but such approaches have been developed and used in a few studies only. Here, we outline digital image analysis methods to quantify the coaggregation, mutual avoidance, or random distribution of microbial populations in biofilm and flocs. A protocol is provided for fluorescence in situ hybridization with rRNA-targeted probes, which preserves the three-dimensional biofilm architecture for confocal microscopy and image analysis, and the combined use of these approaches is demonstrated by spatial analyses of nitrifying bacteria in complex biofilm samples.

Simple one-step process for immobilization of biomolecules on polymer substrates based on surface-attached polymer networks

For the miniaturization of biological assays, especially for the fabrication of microarrays, immobilization of biomolecules at the surfaces of the chips is the decisive factor. Accordingly, a variety of binding techniques have been developed over the years to immobilize DNA or proteins onto such substrates. Most of them require rather complex fabrication processes and sophisticated surface chemistry. Here, a comparatively simple immobilization technique is presented, which is based on the local generation of small spots of surface attached polymer networks. Immobilization is achieved in a one-step procedure: probe molecules are mixed with a photoactive copolymer in aqueous buffer, spotted onto a solid support, and cross-linked as well as bound to the substrate during brief flood exposure to UV light. The described procedure permits spatially confined surface functionalization and allows reliable binding of biological species to conventional substrates such as glass microscope slides as well as various types of plastic substrates with comparable performance. The latter also permits immobilization on structured, thermoformed substrates resulting in an all-plastic biochip platform, which is simple and cheap and seems to be promising for a variety of microdiagnostic applications.

Fabrication of uniform DNA-conjugated hydrogel microparticles via replica molding for facile nucleic acid hybridization assays

We identify and investigate several critical parameters in the fabrication of single-stranded DNA conjugated poly(ethylene glycol) (PEG) microparticles based on replica molding (RM) for highly uniform and robust nucleic acid hybridization assays. The effects of PEG-diacrylate, probe DNA, and photoinitiator concentrations on the overall fluorescence and target DNA penetration depth upon hybridization are examined. Fluorescence and confocal microscopy results illustrate high conjugation capacity of the probe and target DNA, femtomole sensitivity, and sequence specificity. Combined, these findings demonstrate a significant step toward simple, robust, and scalable procedures to manufacture highly uniform and high-capacity hybridization assay particles in a well-controlled manner by exploiting many advantages that the batch processing-based RM technique offers. We envision that the results presented here may be readily applied to rapid and high-throughput hybridization assays for a wide variety of applications in bioprocess monitoring, food safety, and biological threat detection.

Nucleic acid therapeutic carriers with on-demand triggered release

Biohybrid platforms such as synthetic polymer networks engineered from artificial and natural materials hold immense potential as drug and gene delivery vehicles. Here, we report the synthesis and characterization of novel polymer networks that release oligonucleotide sequences via enzymatic and physical triggers. Chemical monomers and acrylated oligonucleotides were copolymerized into networks, and phosphoimaging revealed that 70% of the oligonucleotides were incorporated into the networks. We observed that the immobilized oligonucleotides were readily cleaved when the networks were incubated with the type II restriction enzyme BamHI. The diffusion of the cleaved fragments through the macromolecular chains resulted in relatively constant release profiles very close to zero-order. To our knowledge, this is the first study which harnesses the sequence-specificity of restriction endonucleases as triggering agents for the cleavage and release of oligonucleotide sequences from a synthetic polymer network. The polymer networks exhibited an oligonucleotide diffusion coefficient of 5.6 x 10(-8) cm(2)/s and a diffusional exponent of 0.92. Sigmoidal temperature responsive characteristics of the networks matched the theoretical melting temperature of the oligonucleotides and indicated a cooperative melting transition of the oligonucleotides. The networks were also triggered to release a RNA-cleaving deoxyribozyme, which degraded a HIV-1 mRNA transcript in vitro. To tailor release profiles of the oligonucleotides, we controlled the structure of the macromolecular architecture of the networks by varying their cross-linking content. When incubated with DNase I, networks of cross-linking content 0.15%, 0.22%, and 0.45% exhibited oligonucleotide diffusion coefficients of 1.67 x 10(-8), 7.65 x 10(-9), and 2.7 x 10(-9) cm(2)/s, and diffusional exponents of 0.55, 0.8, and 0.8, respectively. The modular nature of our platform promises to open new avenues for the creation and optimization of a rich toolbox of novel drug and gene delivery platforms. We anticipate further inquiry into nucleic acid based programmable on-demand switches and modulatory devices of exquisite sensitivity and control.

The detection of DNA hybridization on phosphorus dendrimer multilayer films by surface plasmon field enhanced-fluorescence spectroscopy

Dendrimer multilayers on gold substrates prepared via layer-by-layer (LbL) assembly technique were characterized and used as substrates for DNA immobilization/hybridization. The multilayers, built using alternately polycationic and polyanionic phosphorus dendrimers of generation 4, were studied by surface plasmon resonance (SPR) spectroscopy. By varying the concentration of NaCl, the optimized optical thickness of a single dendrimer layer (about 4.5 nm) was achieved. Using the multilayers as the substrate, a high loading of DNA probes was obtained through covalent coupling of probe DNA on dendrimer multilayer film. The following hybridization of Cy5-dye labeled complementary target DNA with immobilized probe DNA was detected by surface plasmon field-enhanced fluorescence spectroscopy (SPFS). The limit of detection of target DNA upon hybridization reached 50 pM and 30 pM on 1 bilayer and 4 bilayers, respectively. The phosphorus dendrimer multilayer films display high stability during repeated regeneration and hybridization cycles. The sensitive platforms based on dendrimer multilayers deposited in the presence of NaCl make them attractive candidates for application in DNA sensing.