Covalent attachment of synthetic DNA to self-assembled monolayer films

Low-Temperature and High-Efficiency Solid-Phase Amplification Based on Formamide

The thermal stability of DNA immobilized on a solid surface is one of the factors that affects the efficiency of solid-phase amplification (SP-PCR). Although variable temperature amplification ensures high specificity of the reaction by precisely controlling temperature changes, excessively high temperatures during denaturation can negatively affect DNA stability. Formamide (FA) enables DNA denaturation at lower temperatures, showing potential for SP-PCR. Research on FA's impacts on DNA microarrays is still limited, necessitating further optimization in exploring the characteristics of FA in SP-PCR according to particular application needs. We immobilized DNA on a chip using a crosslinker and generated DNA microarrays through bridge amplification based on FA denaturation on our automated reaction device. We optimized the denaturation and hybridization parameters of FA, achieving a maximum cluster density of 2.83 × 104 colonies/mm2. Compared to high-temperature denaturation, FA denaturation required a lower template concentration and milder reaction conditions and produced higher cluster density, demonstrating that FA effectively improves hybridization rates on surfaces. Regarding the immobilized DNA stability, the FA group exhibited a 45% loss of DNA, resulting in a 15% higher DNA retention rate compared to the high-temperature group, indicating that FA can better maintain DNA stability. Our study suggests that using FA improves the immobilized DNA stability and amplification efficiency in SP-PCR.

Magnetic capture device for large volume sample analysis

Immunomagnetic separation (IMS) techniques employing superparamagnetic particles can successfully isolate various components from mixtures. However, their utility can be limited for large-volume samples, viscous samples, or those containing a high density of particulate matter because of the need to generate high field gradients for particle recovery. Therefore, a new class of immunomagnetic particles was devised utilizing a single, macroscopic Pyrex spinbar conjugated with biorecognition elements to address these limitations. Advantages include an inherent capacity for effective mixing, an almost instantaneous recovery of the spinbar that can be performed without expensive equipment and with no loss of magnetic particles during processing, and reduced transfer of sample matrix. As a result, spinbars can provide an effective means for IMS with large-volume assays composed of complex matrices.

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.

Comparative analysis of novel MGISEQ-2000 sequencing platform vs Illumina HiSeq 2500 for whole-genome sequencing

The MGISEQ-2000 developed by MGI Tech Co. Ltd. (a subsidiary of the BGI Group) is a new competitor of such next-generation sequencing platforms as NovaSeq and HiSeq (Illumina). Its sequencing principle is based on the DNB and the cPAS technologies, which were also used in the previous version of the BGISEQ-500 device. However, the reagents for MGISEQ-2000 have been refined and the platform utilizes updated software. The cPAS method is an advanced technology based on the cPAL previously created by Complete Genomics. In this paper, the authors compare the results of the whole-genome sequencing of a DNA sample from a Russian female donor performed on MGISEQ-2000 and Illumina HiSeq 2500 (both PE150). Two platforms were compared in terms of sequencing quality, number of errors and performance. Additionally, we performed variant calling using four different software packages: Samtools mpileaup, Strelka2, Sentieon, and GATK. The accuracy of SNP detection was similar in the data generated by MGISEQ-2000 and HiSeq 2500, which was used as a reference. At the same time, a separate indel analysis of the overall error rate revealed similar FPR values and lower sensitivity. It may be concluded with confidence that the data generated by the analyzed sequencing systems is characterized by comparable magnitudes of error and that MGISEQ-2000 and HiSeq 2500 can be used interchangeably for similar tasks like whole genome sequencing.

N-Hydroxysuccinimide-Modified Ethynylphosphonamidates Enable the Synthesis of Configurationally Defined Protein Conjugates

Herein, the application of N-hydroxysuccinimide-modified phosphonamidate building blocks for the incorporation of cysteine-selective ethynylphosphonamidates into lysine residues of proteins, followed by thiol addition with small molecules and proteins, is reported. It is demonstrated that the building blocks significantly lower undesired homo-crosslinking side products that can occur with commonly applied succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) under physiological pH. The previously demonstrated stability of the phosphonamidate moiety additionally solves the problem of premature maleimide hydrolysis, which can hamper the efficiency of subsequent thiol addition. Furthermore, a method to separate the phosphonamidate enantiomers to be able to synthesize protein conjugates in a defined configuration has been developed. Finally, the building blocks are applied to the construction of functional antibody-drug conjugates, analogously to FDA-approved, SMCC-linked Kadcyla, and to the synthesis of a functional antibody-protein conjugate.

Surface Functionalization toward Biosensing via Free-Standing Si-OH Bonds on Nonoxidized Silicon Surfaces

Usually hydroxyl groups present on top of oxidized silicon served as binding centers for a silanization reaction toward surface functionalization. In this study, we developed a novel surface functionalization strategy where hydroxyl functionalization on nonoxidized silicon surfaces are obtained. These surfaces were stable for several weeks even in ambient air at room temperature. This high stability indicates a strong spatial isolation of the hydroxyl groups because they keenly tend to undergo a condensation reaction, forming silicon oxide. To prove the applicability of the obtained hydroxylated silicon surface, we further modified the hydroxyl groups with a commonly used silane molecule, (3-aminopropyl)triethoxysilane (APTES). The functional amino groups of the APTES layer bonded to the surface were subsequently altered by N-maleoyl-β-alanin to generate a surface highly specific for the immobilization of thiol-containing biomolecules (like thiolated single-stranded DNA or cysteine-tagged proteins). All modification steps have been investigated by IR spectroscopic ellipsometry measurements.

Mechanical Contact Spectroscopy: Characterizing Nanoscale Adhesive Contacts via Thermal Forces

The adhesion of micro- and nanoparticles to solid substrates immersed in liquids is a problem of great scientific and technological importance. However, the quantitative characterization of such nanoscale adhesive contacts without rupturing them still presents a major experimental challenge. In this article, we introduce mechanical contact spectroscopy (MCS), an experimental technique for the nondestructive probing of particle adhesion in liquid environments. With MCS, the strength of adhesive contacts is inferred from residual position fluctuations of adherent particles excited by thermal forces. In particular, the strength of adhesion is correlated with the standard deviation of the particle lateral position x, with smaller position standard deviations [Formula: see text] indicating higher adhesive strength. For a given combination of particles, substrate, and immersion medium, the adhesion is characterized by the mechanical contact spectrum, which is a histogram of ξ values obtained from tracking an ensemble of adherent particles. Because the energy of thermal excitation at room temperature is very small in comparison to the typical total energy of adhesive contacts, the studied contacts remain in equilibrium during the measurement. Using MCS, we study the adhesion of micrometer-sized particles to planar solid substrates under a wide range of environmental conditions, including liquid immersion media of varying ionic strength and adhesion substrates with different chemical functionality of their surfaces. These experiments provide evidence that MCS is capable of reproducibly detecting minute changes in the particle-substrate work of adhesion while at the same time covering the range of adhesive contact strength relevant in the context of surface chemistry, biology, and microfabrication.

Langmuir Analysis of the Binding Affinity and Kinetics for Surface Tethered Duplex DNA and a Ligand-Apoprotein Complex

In this work, the hybridization and dehybridization of ssDNA with 20 bases at gold coated sensor surfaces modified with complementary 20 bases capture probe ssDNA was investigated at 18 °C by quartz crystal microbalance measurements with dissipation monitoring (QCM-D). A sequence of 20 base pairs with a melting temperature of about 64 °C was chosen, since in many biosensor studies the target molecules are DNA or RNA oligomers of similar length. It turned out that at the applied experimental conditions the DNA hybridization was irreversible, and therefore the hybridization and dehybridization process could not be described by the Langmuir model of adsorption. Nevertheless, quantitative dehybridization could be achieved by rinsing the sensor surface thoroughly with pure water. When in contrast the hybridization of a target with only 10 bases complementary to the outermost 10 bases of the 20 bases capture probe was studied, binding and unbinding were reversible, and the hybridization/dehybridization process could be satisfactorily described by the Langmuir model. For the 10 base pair sequence, the melting temperature was about 36 °C. Apparently, for Langmuir behavior, it is important that the experiments are applied at a temperature sufficiently close to the melting temperature of the sequence under investigation to ensure that at least traces of the target molecules are unhybridized (i.e., there needs to be an equilibrium between hybridized and dehybridized target molecules). To validate the reliability of our experimental approach we also studied the reconstitution and disassembly of the flavoprotein dodecin at flavin-terminated DNA monolayers, as according to previous studies it is assumed that the apododecin-flavin system can be well described by the Langmuir model. As a result, this assumption could be verified. Using three different approaches, K_D values were obtained that differ not more than by a factor of 4.

Remarkable Differences in Spin Couplings for Various Self-Paired Dimers of Ring-Expansion-Radicalized Uracil: A Basis for the Design of Magnetically Anisotropic Assemblies

The spin-coupling properties of a series of radicalized uracil (rU) dimer diradicals with different H-bonding modes is examined. Each rU has four double H-bonding sites [the amide units: two at the Watson-Crick face (upper site WC₁ and lower site WC₂ ), a Hoogsteen site (HO), and a minor-groove site (MI)], and ten homogeneous dimers (rU-rU) can self-pair with well-defined diradical characters and comparable stability to the native U dimers. More interestingly, all these dimers exhibit distinctly different spin-coupling characters (ferromagnetic (FM) versus antiferromagnetic (AFM) and large- versus small-magnitude spin couplings), indicative of remarkable magnetic-coupling anisotropy of rU. This observation originates from the fusion of a cyclopentadienyl radical to U, which leads to uneven spin-density distribution. In rU, the fused five-membered radical ring can spin-polarize to the edge in the minor groove, and thus dimerization of rU leads to different H-bonded structures with remarkably different magnetic couplings. The calculated larger magnetic coupling constants J are 1003.7 and 540.2 cm^-1 for the WC₂ -HO and MI-HO H-bonding modes between rU, which exhibit considerably large FM couplings, the MI-MI, WC₁ -WC₂ and WC₂ -WC₂ modes show moderate FM couplings (J=0.4-77 cm^-1 ), and the other modes exhibit moderate or weak AFM couplings. These observations indicate that the HO and MI sites are favorable spin-coupling sites. In addition, the H-bond lengths and electronic structures of the H-bonding sites, proton transfer, and extra H-bonding interaction with the surroundings can also affect the magnetic couplings of the base pairs. Clearly, the unique magnetic coupling anisotropy of rU provides a promising application basis for the design and assembly of bio-inspired anisotropically magnetic membranes and even magnetism-tunable building blocks for novel magnetic nanoscale devices.

Manipulating the adhesion of electroless nickel-phosphorus film on silicon wafers by silane compound modification and rapid thermal annealing

In this study, the effect of 3-2-(2-aminoethylamino) ethylamino propyl trimethoxysilane (ETAS) modification and post rapid thermal annealing (RTA) treatment on the adhesion of electroless plated nickel-phosphorus (ELP Ni-P) film on polyvinyl alcohol-capped palladium nanoclusters (PVA-Pd) catalyzed silicon wafers is systematically investigated. Characterized by pull-off adhesion, atomic force microscopy, X-ray spectroscopy and water contact angle, a time-dependent, three-staged ETAS grafting mechanism including islandish grafting, a self-assembly monolayer (SAM) and multi-layer grafting is proposed and this mechanism is well correlated to the pull-off adhesion of ELP Ni-P film. In the absence of RTA, the highest ELP Ni-P film adhesion occurs when ETAS modification approaches SAM, where insufficient or multi-layer ETAS grafting fails to provide satisfactory results. On the other hand, if RTA is applied, the best ELP Ni-P film adhesion happens when ETAS modification is islandish owing to the formation of nickel silicide, where SAM or multi-layer ETAS modification cannot provide satisfactory adhesion because the interaction between ETAS and PVA-Pd has been sabotaged during RTA. Evidenced by microstructural images, we also confirmed that ETAS can act as an efficient barrier layer for nickel diffusion to bulk silicon.

Inhibition of Tetrahydrofuran Hydrate Formation in the Presence of Polyol-Modified Glass Surfaces

Glycerol was conjugated to glass test tube surfaces in four configurations by employing two different silane spacers, covalent attachment to glycerol at either the 1- or the 2-position, and with a succinic acid spacer. The resulting surfaces were tested for their ability to inhibit the nucleation of tetrahydrofuran hydrate (THF hydrate) in comparison with polyvinylpyrrolidone (PVP), a known polymeric inhibitor of THF hydrate formation. Contact angle measurements were used as an indication of surface modification throughout the glass derivatization steps. Of the four final surfaces modified with glycerol, only the coating with (3-aminopropyl)triethoxysilane (APTES) and glycerol coupled at the 1-position (leaving a free 1,2-diol) showed significant inhibition of the formation of THF hydrate. The corresponding N-[3-(trimethoxysilyl)propyl]-ethylenediamine (AEAPTMS) coating with glycerol coupled at the 1-position did not show a significant difference over the untreated test tubes. Attachment of glycerol at the 2-position yielded a coating with no benefit over the untreated test tubes regardless of the silane used, and a surface modified with APTES and succinic acid alone enhanced the formation of THF hydrate. The ability to inhibit THF hydrate formation using a polyol-modified surface is a first step in the development of a coating that, alone or in combination with known gas hydrate inhibitors, could be used to prevent gas hydrates from plugging pipelines in field applications.

A Quasi-direct LC-MS/MS-based Targeted Proteomics Approach for miRNA Quantification via a Covalently Immobilized DNA-peptide Probe

MicroRNAs (miRNAs) play a vital role in regulating gene expression and are associated with a variety of cancers, including breast cancer. Their distorted and unique expression is a potential marker in clinical diagnoses and prognoses. Thus, accurate determination of miRNA expression levels is a prerequisite for their applications. However, the assays currently available for miRNA detection typically require pre-enrichment, amplification and labeling steps, and most of the assays are only semi-quantitative. Therefore, we developed a quasi-direct liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics approach to quantify target miRNA by innovatively converting the miRNA signal into the mass response of a reporter peptide via a covalently immobilized DNA-peptide probe. Specifically, the probe containing the targeted proteomics-selected substrate/reporter peptide, GDRAVQLGVDPFR/AVQLGVDPFR, and the DNA sequence complementary to the target miRNA (i.e., miR-21) was first immobilized on APMTS modified silica nanoparticles using PDITC. After the immobilized probe was recognized and hybridized with the target miRNA, the excess probe was degraded using MBN and followed by a trypsin digestion of the hybrids. The reporter peptide was released and quantified using LC-MS/MS. The obtained LOQ was 5 pM. Finally, the developed assay was used for the quantitative analysis of miR-21 in breast cells and tissue samples.

Base Layer Influence on Protonated Aminosilane Gradient Wettability

Protonated amine gradients have been prepared on silicon wafers via programmed controlled rate infusion (CRI) with varying degrees of hydrophobicity and characterized by X-ray photoelectron spectroscopy (XPS) and static and Wilhelmy plate dynamic contact angle measurements. Initially, base layers were spin coated from sols containing tetramethoxysilane (TMOS) and either phenyltrimethoxysilane (PTMOS), dimethyldimethoxysilane (DMDMOS), or octyltrimethoxysilane (OTMOS, C8). Amine gradients were then prepared from 3-aminopropyltriethoxysilane (APTEOS) via CRI. Gradients were exposed to concentrated HCl vapor for amine protonation. XPS showed that NH₂ functional groups were distributed in a gradient fashion as a result of CRI controlling the time of exposure to APTEOS. Interestingly, the overall extent of N modification depended on the type of base layer used for gradient formation. The C8-derived base layer had about half the amount of nitrogen on the surface as compared to those prepared from TMOS, which was attributed to a reduction in the number and accessibility of surface silanol groups. The wettability and contact angle (CA) hysteresis were also dependent on the base layer and varied along the length of the gradient. The greatest CA change across the length of the gradient was observed on the gradient formed on the C8-derived base layer. Likewise, the CA hysteresis was approximately 2 times larger on the C8-modified surfaces, indicative of greater chemical inhomogeneity. In contrast to uniformly modified substrates, Wilhelmy plate CA analysis that involves the immersion of samples gave a unique S-shaped CA distance curve for the gradients. The three curve segments correspond to hydrophilic, hydrophobic, and a middle connecting region. Importantly, these curves give precise CAs along the gradient that reflect the surface chemistry and coverage defined by programmed CRI processing.

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.

High-Performance Three-Dimensional Tubular Nanomembrane Sensor for DNA Detection

We report an ultrasensitive label-free DNA biosensor with fully on-chip integrated rolled-up nanomembrane electrodes. The hybridization of complementary DNA strands (avian influenza virus subtype H1N1) is selectively detected down to attomolar concentrations, an unprecedented level for miniaturized sensors without amplification. Impedimetric DNA detection with such a rolled-up biosensor shows 4 orders of magnitude sensitivity improvement over its planar counterpart. Furthermore, it is observed that the impedance response of the proposed device is contrary to the expected behavior due to its particular geometry. To further investigate this difference, a thorough model analysis of the measured signal and the electric field calculation is performed, revealing enhanced electron hopping/tunneling along the DNA chains due to an enriched electric field inside the tube. Likewise, conformational changes of DNA might also contribute to this effect. Accordingly, these highly integrated three-dimensional sensors provide a tool to study electrical properties of DNA under versatile experimental conditions and open a new avenue for novel biosensing applications (i.e., for protein, enzyme detection, or monitoring of cell behavior under in vivo like conditions).

Use of a DNA film on a self-assembled monolayer for investigating the physical process of DNA damage induced by core electron ionization

PURPOSE

A novel two-layer sample composed of a deoxyribonucleic acid (DNA) film and self-assembled monolayer (SAM) was prepared on an inorganic surface to mimic the processes in which DNA is damaged by soft X-ray irradiation.

MATERIALS AND METHODS

A mercaptopropyltrimethoxysilane (MPTS) SAM was formed on a sapphire surface, then oligonucleotide (OGN) molecules were adsorbed on the MPTS-SAM. The thicknesses and chemical states of the layers were determined by X-ray photoelectron spectroscopy (XPS) and near-edge X-ray fine structure (NEXAFS) around the phosphorus (P) and sulfur (S) K-edges. To induce the damage to the OGN molecules, the sample was irradiated with synchrotron soft X-rays. The chemical state of the OGN molecules before and after irradiation was examined by NEXAFS around the nitrogen (N) K-edge region.

RESULTS

The thickness of the MPTS-OGN layer was approximately 7.7 nm. The S atom of the OGN molecules was located at the bottom of the OGN layer. The peak shape of the N K-edge NEXAFS spectra of the MPTS-OGN layers clearly changed following irradiation.

CONCLUSIONS

The MPTS-OGN layer formed on the sapphire surface. The chemical states and the structure of the interface were elucidated using synchrotron soft X-rays. The OGN molecules adsorbed on the MPTS films decomposed upon exposure to soft X-ray irradiation.

Polymerase Chain Reaction on a Viral Nanoparticle

The field of synthetic biology includes studies that aim to develop new materials and devices from biomolecules. In recent years, much work has been carried out using a range of biomolecular chassis including α-helical coiled coils, β-sheet amyloids and even viral particles. In this work, we show how hybrid bionanoparticles can be produced from a viral M13 bacteriophage scaffold through conjugation with DNA primers that can template a polymerase chain reaction (PCR). This unprecedented example of a PCR on a virus particle has been studied by flow aligned linear dichroism spectroscopy, which gives information on the structure of the product as well as a new protototype methodology for DNA detection. We propose that this demonstration of PCR on the surface of a bionanoparticle is a useful addition to ways in which hybrid assemblies may be constructed using synthetic biology.

Amphiphilic Macromolecule Self-Assembled Monolayers Suppress Smooth Muscle Cell Proliferation

A significant limitation of cardiovascular stents is restenosis, where excessive smooth muscle cell (SMC) proliferation following stent implantation causes blood vessel reocclusion. While drug-eluting stents minimize SMC proliferation through releasing cytotoxic or immunosuppressive drugs from polymer carriers, significant issues remain with delayed healing, inflammation, and hypersensitivity reactions associated with drug and polymer coatings. Amphiphilic macromolecules (AMs) comprising a sugar-based hydrophobic domain and a hydrophilic poly(ethylene glycol) tail are noncytotoxic and recently demonstrated a concentration-dependent ability to suppress SMC proliferation. In this study, we designed a series of AMs and studied their coating properties (chemical composition, thickness, grafting density, and coating uniformity) to determine the effect of headgroup chemistry on bioactive AM grafting and release properties from stainless steel substrates. One carboxyl-terminated AM (1cM) and two phosphonate- (Me-1pM and Pr-1pM) terminated AMs, with varying linker lengths preceding the hydrophobic domain, were grafted to stainless steel substrates using the tethering by aggregation and growth (T-BAG) approach. The AMs formed headgroup-dependent, yet uniform, biocompatible adlayers. Pr-1pM and 1cM demonstrated higher grafting density and an extended release from the substrate over 21 days compared to Me-1pM, which exhibited lower grafting density and complete release within 7 days. Coinciding with their release profiles, Me-1pM and 1cM coatings initially suppressed SMC proliferation in vitro, but their efficacy decreased within 7 and 14 days, respectively, while Pr-1pM coatings suppressed SMC proliferation over 21 days. Thus, AMs with phosphonate headgroups and propyl linkers are capable of sustained release from the substrate and have the ability to suppress SMC proliferation during the restenosis that occurs in the 3-4 weeks after stent implantation, demonstrating the potential for AM coatings to provide sustained delivery via desorption from coated coronary stents and other metal-based implants.

Immobilization techniques for microarray: challenges and applications

The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials) on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.

Silicon nanowire field-effect-transistor based biosensors: from sensitive to ultra-sensitive

Silicon nanowire field effect transistors (SiNW-FETs) have shown great promise as biosensors in highly sensitive, selective, real-time and label-free measurements. While applications of SiNW-FETs for detection of biological species have been described in several publications, less attention has been devoted to summarize the conjugating methods involved in linking organic bio-receptors with the inorganic transducer and the strategies of improving the sensitivity of devices. This article attempts to focus on summarizing the various organic immobilization approaches and discussing various sensitivity improving strategies, that include (I) reducing non-specific binding, (II) alignment of the probes, (III) enhancing signals by charge reporter, (IV) novel architecture structures, and (V) sensing in the sub-threshold regime.

Self-assembly of 50 bp poly(dA)·poly(dT) DNA on highly oriented pyrolytic graphite via atomic force microscopy observation and molecular dynamics simulation

This study has investigated the formation patterns resulting from the self-assembly of deoxyribonucleic acid (DNA) on highly oriented pyrolytic graphite (HOPG), using both experimental and molecular dynamics approaches. Under optimized conditions based on pretreatment of HOPG surface and specific solution concentrations, DNA is found to self-assemble to form various patterned networks. The associated self-assembly mechanism is elucidated using coarse-grained molecular dynamics simulations and fractal dimension analysis. The results of this work demonstrate an effective technique allowing the formation of arrays of negatively charged biomacromolecules on negatively charged HOPG surfaces.

DNA-modified electrodes fabricated using copper-free click chemistry for enhanced protein detection

A method of DNA monolayer formation has been developed using copper-free click chemistry that yields enhanced surface homogeneity and enables variation in the amount of DNA assembled; extremely low-density DNA monolayers, with as little as 5% of the monolayer being DNA, have been formed. These DNA-modified electrodes (DMEs) were characterized visually, with AFM, and electrochemically, and were found to facilitate DNA-mediated reduction of a distally bound redox probe. These low-density monolayers were found to be more homogeneous than traditional thiol-modified DNA monolayers, with greater helix accessibility through an increased surface area-to-volume ratio. Protein binding efficiency of the transcriptional activator TATA-binding protein (TBP) was also investigated on these surfaces and compared to that on DNA monolayers formed with standard thiol-modified DNA. Our low-density monolayers were found to be extremely sensitive to TBP binding, with a signal decrease in excess of 75% for 150 nM protein. This protein was detectable at 4 nM, on the order of its dissociation constant, with our low-density monolayers. The improved DNA helix accessibility and sensitivity of our low-density DNA monolayers to TBP binding reflects the general utility of this method of DNA monolayer formation for DNA-based electrochemical sensor development.

A glimpse into past, present, and future DNA sequencing

Current advances in DNA sequencing technologies are dropping down sequencing cost while increasing throughput at a pace never shown before. Past-decade great milestones, as the establishment of a reference human genome (amongst others) and large-scale human genetic variation study in the 1000 Genome project are, in conjunction with the use of these techniques, triggering advances in many areas of basic and applied science. These tools, stored in and combined with the vast amount of information present in biological online databases are, with the use of automated interpretation and analysis tools, allowing the fulfillment of increasingly ambitious studies in many areas and also are democratizing the access to information, interpretation and technologies, being the first opportunity for researchers to assess the influence of genetics in complex events as multifactorial diseases, evolutionary studies, metagenomics, transcriptomics, etc. In this review, we present the current state of the art of these technologies, focusing on second generation sequencing, from sample and library preparation to sequencing chemistries and bioinformatic software available for final data analysis and visualisation, with its possible applications. We also make an overview of first and third generation, due to its historical importance and for being the upcoming future tools for genetic analysis, respectively.

Peptide nucleic acid (PNA)-DNA duplexes: comparison of hybridization affinity between vertically and horizontally tethered PNA probes

We compare the PNA-DNA duplex hybridization characteristics of vertically tethered and new horizontally tethered PNA probes on solid surfaces. The horizontal 15-mer PNA probe has been synthesized with linker molecules attached at three locations (γ-points) positioned along the PNA backbone that provides covalent attachment of the probe with the backbone aligned parallel to the surface, which is important for DNA hybridization assays that use electric field effect sensors for detection. A radioactive labeled assay and real-time surface plasmon resonance (SPR) biosensor are used to assess the probe surface density, nonspecific binding, and DNA hybridization affinity, respectively, of the new PNA probe configuration. The estimated equilibrium dissociation constants of the horizontally tethered duplex and the vertically tethered duplex are of the same order of magnitude (KD ≈ 5 nM), which indicates a sufficient hybridization affinity for many electronic biosensors that benefit from the horizontal alignment, which minimizes the effects of counterion screening.

Drop drying on surfaces determines chemical reactivity - the specific case of immobilization of oligonucleotides on microarrays

BACKGROUND

Drop drying is a key factor in a wide range of technical applications, including spotted microarrays. The applied nL liquid volume provides specific reaction conditions for the immobilization of probe molecules to a chemically modified surface.

RESULTS

We investigated the influence of nL and μL liquid drop volumes on the process of probe immobilization and compare the results obtained to the situation in liquid solution. In our data, we observe a strong relationship between drop drying effects on immobilization and surface chemistry. In this work, we present results on the immobilization of dye labeled 20mer oligonucleotides with and without an activating 5'-aminoheptyl linker onto a 2D epoxysilane and a 3D NHS activated hydrogel surface.

CONCLUSIONS

Our experiments identified two basic processes determining immobilization. First, the rate of drop drying that depends on the drop volume and the ambient relative humidity. Oligonucleotides in a dried spot react unspecifically with the surface and long reaction times are needed. 3D hydrogel surfaces allow for immobilization in a liquid environment under diffusive conditions. Here, oligonucleotide immobilization is much faster and a specific reaction with the reactive linker group is observed. Second, the effect of increasing probe concentration as a result of drop drying. On a 3D hydrogel, the increasing concentration of probe molecules in nL spotting volumes accelerates immobilization dramatically. In case of μL volumes, immobilization depends on whether the drop is allowed to dry completely. At non-drying conditions, very limited immobilization is observed due to the low oligonucleotide concentration used in microarray spotting solutions. The results of our study provide a general guideline for microarray assay development. They allow for the initial definition and further optimization of reaction conditions for the immobilization of oligonucleotides and other probe molecule classes to different surfaces in dependence of the applied spotting and reaction volume.

Overview of DNA microarrays: types, applications, and their future

This unit provides an overview of DNA microarrays. Microarrays are a technology in which thousands of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. This overview first discusses the history of microarrays and the antecedent technologies that led to their development. This is followed by discussion of the methods of manufacture of microarrays and the most common biological applications. The unit ends with a brief description of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies.

A pivot-hinge-style DNA immobilization method with adaptable surface concentration based on oligodeoxynucleotide-phosphorothioate chemisorption on gold surfaces

The chemisorption of oligodeoxynucleotide phosphorothioate (s-oligo) is reported. A series of s-oligo DNAs was designed for use as capture probe DNA molecules. The s-oligo DNAs consist of the K-ras gene (5'-GGA GCT GGT GGC-3') and a dodecamer deoxyriboadenosine, both of which lie on either side of an s-oligo DNA sequence. By primarily focusing on the capture probe DNA having five-successive s-oligo sequences, e37, the immobilization chemistry of e37 was examined; atomic force microscopy achieved the direct visualization of individual molecules on Au(111) substrates, while a series of surface analyses, including IR, ellipsometry, and microgravimetry, showed that the s-oligo functional groups played a pivotal role in the surface-adlayer through the gold-thiol interaction. Interestingly, the amount of immobilization showed a definite relationship with the number of s-oligo linkages introduced, which should be important to regulate the concentration of the capture probe DNA molecules on the surface. Some preliminary studies using ferrocene-modified complementary sequences indicated that electrochemical labeling and readouts were possible.

Angle-resolved XPS analysis and characterization of monolayer and multilayer silane films for DNA coupling to silica

We measure silane density and Sulfo-EMCS cross-linker coupling efficiency on aminosilane films by high-resolution X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) measurements. We then characterize DNA immobilization and hybridization on these films by (32)P-radiometry. We find that the silane film structure controls the efficiency of the subsequent steps toward DNA hybridization. A self-limited silane monolayer produced from 3-aminopropyldimethylethoxysilane (APDMES) provides a silane surface density of ~3 nm(-2). Thin (1 h deposition) and thick (19 h deposition) multilayer films are generated from 3-aminopropyltriethoxysilane (APTES), resulting in surfaces with increased roughness compared to the APDMES monolayer. Increased silane surface density is estimated for the 19 h APTES film, due to a ∼32% increase in surface area compared to the APDMES monolayer. High cross-linker coupling efficiencies are measured for all three silane films. DNA immobilization densities are similar for the APDMES monolayer and 1 h APTES. However, the DNA immobilization density is double for the 19 h APTES, suggesting that increased surface area allows for a higher probe attachment. The APDMES monolayer has the lowest DNA target density and hybridization efficiency. This is attributed to the steric hindrance as the random packing limit is approached for DNA double helices (dsDNA, diameter ≥ 2 nm) on a plane. The heterogeneity and roughness of the APTES films reduce this steric hindrance and allow for tighter packing of DNA double helices, resulting in higher hybridization densities and efficiencies. The low steric hindrance of the thin, one to two layer APTES film provides the highest hybridization efficiency of nearly 88%, with 0.21 dsDNA/nm(2). The XPS data also reveal water on the cross-linker-treated surface that is implicated in device aging.

Fabrication of oligonucleotide and protein arrays on rigid and flexible substrates coated with reactive polymer multilayers

We report a top-down approach to the fabrication of oligonucleotide and protein arrays on surfaces coated with ultrathin, amine-reactive polymer multilayers fabricated by the covalent "layer-by-layer" (LbL) assembly of polyethyleneimine (PEI) and the amine-reactive, azlactone-functionalized polymer poly(2-vinyl-4,4-dimethylazlactone) (PVDMA). Manual spotting of amine-terminated oligonucleotide probe sequences on planar glass slides coated with PEI/PVDMA multilayers (~35 nm thick) yielded arrays of immobilized probes that hybridized fluorescently labeled complementary sequences with high signal intensities, high signal-to-noise ratios, and high sequence specificity. Treatment of residual azlactone functionality with the nonfouling small-molecule amine d-glucamine resulted in regions between the features of these arrays that resisted adsorption of protein and permitted hybridization in complex media containing up to 10 mg/mL protein. The residual azlactone groups in these films were also exploited to immobilize proteins on film-coated surfaces and fabricate functional arrays of proteins and enzymes. The ability to deposit PEI/PVDMA multilayers on substrates of arbitrary size, shape, and composition permitted the fabrication of arrays of oligonucleotides on the surfaces of multilayer-coated sheets of poly(ethylene terephthalate) and heat-shrinkable polymer film. Arrays fabricated on these flexible plastic substrates can be bent, cut, resized, and manipulated physically in ways that are difficult using more conventional rigid substrates. This approach could thus contribute to the development of new assay formats and new applications of biomolecule arrays. The methods described here are straightforward to implement, do not require access to specialized equipment, and should also be compatible with automated liquid-handling methods used to fabricate higher-density arrays of oligonucleotides and proteins on more traditional surfaces.

Synthesis and chromatography-free purification of PNA-PEO conjugates for the functionalisation of gold sensors

Peptide Nucleic Acids (PNAs) linked to high molecular weight (MW) poly(ethylene oxide) (PEO) derivatives could be useful conjugates for the direct functionalisation of gold surfaces dedicated to Surface Plasmon Resonance (SPR)-based DNA sensing. However their use is hampered by the difficulty to obtain them through a convenient and economical route. In this work we compared three synthetic strategies to obtain PNA-high MW PEO conjugates composed of (a) a 15-mer PNA sequence as the probe complementary to genomic DNA of Mycobacterium tuberculosis, (b) a PEO moiety (2 or 5 KDa MW) and (c) a terminal trityl-protected thiol necessary (after acidic deprotection) for grafting to gold surfaces. The 15-mer PNA was obtained by solid-phase synthesis. Its amino terminal group was later condensed to bi-functional PEO derivatives (2 and 5 KDa MW) carrying a Trt-cysteine at one end and a carboxyl group at the other end. The reaction was carried out either in solution, using HATU or PyOxim as coupling agents, or through the solid-phase approach, with 49.6%, 100% and 5.2% yield, respectively. A differential solvent extraction strategy for product purification without the need for chromatography is described. The ability of the 5 KDa PEO conjugate to function as a probe for complementary DNA detection was demonstrated using a Grating-Coupling Surface Plasmon Resonance (GC-SPR) system. The optimized PEO conjugation and purification protocols are economical and simple enough to be reproduced also within laboratories that are not highly equipped for chemical synthesis.

Chemical silicon surface modification and bioreceptor attachment to develop competitive integrated photonic biosensors

Methodology for the functionalization of silicon-based materials employed for the development of photonic label-free nanobiosensors is reported. The studied functionalization based on organosilane chemistry allowed the direct attachment of biomolecules in a single step, maintaining their bioavailability. Using this immobilization approach in probe microarrays, successful specific detection of bacterial DNA is achieved, reaching hybridization sensitivities of 10 pM. The utility of the immobilization approach for the functionalization of label-free nanobiosensors based on photonic crystals and ring resonators was demonstrated using bovine serum albumin (BSA)/anti-BSA as a model system.

Porous silicon-based nanostructured microparticles as degradable supports for solid-phase synthesis and release of oligonucleotides

We describe the preparation of several types of porous silicon (pSi) microparticles as supports for the solid-phase synthesis of oligonucleotides. The first of these supports facilitates oligonucleotide release from the nanostructured support during the oligonucleotide deprotection step, while the second type of support is able to withstand the cleavage and deprotection of the oligonucleotides post synthesis and subsequently dissolve at physiological conditions (pH = 7.4, 37°C), slowly releasing the oligonucleotides. Our approach involves the fabrication of pSi microparticles and their functionalisation via hydrosilylation reactions to generate a dimethoxytrityl-protected alcohol on the pSi surface as an initiation point for the synthesis of short oligonucleotides.

Organic transistors with ordered nanoparticle arrays as a tailorable platform for selective, in situ detection

The use of organic transistors as sensing platforms provides a number of distinct advantages over conventional detection technologies, including their tunability, portability, and ability to directly transduce binding events without tedious and expensive labeling procedures. However, detection efforts using organic transistors lack a general method to uniquely specify and detect a target of interest. While highly sensitive liquid- and vapor-phase sensors have been previously reported, detection has been restricted either to the serendipitous interaction of the analyte molecules with the organic semiconductor or to the covalent functionalization of the semiconductor with receptor groups to enhance specificity. However, the former technique cannot be regularly relied upon for tailorable sensing while the latter may result in unpredictable decreases in electronic performance. Thus, a method to provide modular receptor sites on the surface of an organic transistor without damaging the device will significantly advance the field, especially regarding biological species detection. In this work, we utilized a block copolymer to template ordered, large-area arrays of gold nanoparticles, with sub-100 nm center-to-center spacing onto the surface of an organic transistor. This highly modular platform is designed for orthogonal modification with a number of available chemical and biological functional groups by taking advantage of the well-studied gold-thiol linkage. Herein, we demonstrate the functionalization of gold nanoparticles with a mercury-binding oligonucleotide sequence. Finally, we demonstrate the highly selective and robust detection of mercury(II) using this platform in an underwater environment.

In situ Synthesis of Oligonucleotide Arrays on Surfaces Coated with Crosslinked Polymer Multilayers

We report an approach to the in situ synthesis of oligonucleotide arrays on surfaces coated with crosslinked polymer multilayers. Our approach makes use of methods for the 'reactive' layer-by-layer assembly of thin, amine-reactive multilayers using branched polyethyleneimine (PEI) and the azlactone-functionalized polymer poly(2-vinyl-4,4'-dimethylazlactone) (PVDMA). Post-fabrication treatment of film-coated glass substrates with d-glucamine or 4-amino-1-butanol yielded hydroxyl-functionalized films suitable for the Maskless Array Synthesis (MAS) of oligonucleotide arrays. Glucamine-functionalized films yielded arrays of oligonucleotides with fluorescence intensities and signal-to-noise ratios (after hybridization with fluorescently labeled complementary strands) comparable to those of arrays fabricated on conventional silanized glass substrates. These arrays could be exposed to multiple hybridization-dehybridization cycles with only moderate loss of hybridization density. The versatility of the layer-by-layer approach also permitted synthesis directly on thin sheets of film-coated poly(ethylene terephthalate) (PET) to yield flexible oligonucleotide arrays that could be readily manipulated (e.g., bent) and cut into smaller arrays. To our knowledge, this work presents the first use of polymer multilayers as a substrate for the multi-step synthesis of complex molecules. Our results demonstrate that these films are robust and able to withstand the ~450 individual chemical processing steps associated with MAS (as well as manipulations required to hybridize, image, and dehybridize the arrays) without large-scale cracking, peeling, or delamination of the thin films. The combination of layer-by-layer assembly and MAS provides a means of fabricating functional oligonucleotide arrays on a range of different materials and substrates. This approach may also prove useful for the fabrication of supports for the solid-phase synthesis and screening of other macromolecular or small-molecule agents.

Cell patterning using a template of microstructured organosilane layer fabricated by vacuum ultraviolet light lithography

Micropatterning techniques have become increasingly important in cellular biology. Cell patterning is achieved by various methods. Photolithography is one of the most popular methods, and several light sources (e.g., excimer lasers and mercury lamps) are used for that purpose. Vacuum ultraviolet (VUV) light that can be produced by an excimer lamp is advantageous for fabricating material patterns, since it can decompose organic materials directly and efficiently without photoresist or photosensitive materials. Despite the advantages, applications of VUV light to pattern biological materials are few. We have investigated cell patterning by using a template of a microstructured organosilane layer fabricated by VUV lithography. We first made a template of a microstructured organosilane layer by VUV lithography. Cell adhesive materials (poly(d-lysine) and polyethyleneimine) were chemically immobilized on the organosilane template, producing a cell adhesive material pattern. Primary rat cardiac and neuronal cells were successfully patterned by culturing them on the pattern substrate. Long-term culturing was attained for up to two weeks for cardiac cells and two months for cortex cells. We have discussed the reproducibility of cell patterning and made suggestions to improve it.

Resonance energy-transfer studies of the conformational change on the adsorption of oligonucleotides to a silica interface

Time-resolved evanescent wave-induced fluorescence studies have been carried out on a series of fluorescently labeled oligonucleotide sequences adsorbed to a silica surface from solution. The fluorescence decay profiles of a fluorescent energy donor group undergoing resonance energy transfer to a nonemissive energy-acceptor molecule have been analyzed in terms of a distribution of donor-acceptor distances to reveal the conformational changes that occur in these oligonucleotides upon adsorption. Evanescent wave-induced time-resolved Förster resonance energy-transfer (EW-TRFRET) measurements indicate that at a high electrolyte concentration, there is localized separation of the oligonucleotide strands, and the helical structure adopts an "unraveled" conformation as a result of adsorption. This is attributed to the flexibility within the oligonucleotide at high electrolyte concentration allowing multiple segments of the oligonucleotide to have direct surface interaction. In contrast, the EW-TRFRET measurements at a lower electrolyte concentration reveal that the oligonucleotide retains its helical conformation in a localized extended state. This behavior implies that the rigidity of the oligonucleotide at this electrolyte concentration restricts direct interaction with the silica to a few segments, which correspondingly introduces kinks in the double helix conformation and results in significant oligonucleotide segmental extension into solution.