In situ synthesis of oligonucleotide arrays by using surface tension

Automated high-throughput DNA synthesis and assembly

DNA synthesis and assembly primarily revolve around the innovation and refinement of tools that facilitate the creation of specific genes and the manipulation of entire genomes. This multifaceted process encompasses two fundamental steps: the synthesis of lengthy oligonucleotides and the seamless assembly of numerous DNA fragments. With the advent of automated pipetting workstations and integrated experimental equipment, a substantial portion of repetitive tasks in the field of synthetic biology can now be efficiently accomplished through integrated liquid handling workstations. This not only reduces the need for manual labor but also enhances overall efficiency. This review explores the ongoing advancements in the oligonucleotide synthesis platform, automated DNA assembly techniques, and biofoundries. The development of accurate and high-throughput DNA synthesis and assembly technologies presents both challenges and opportunities.

Uncertainties in synthetic DNA-based data storage

Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.

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.

Emerging applications of superhydrophilic-superhydrophobic micropatterns

Water on superhydrophilic surfaces spreads or is absorbed very quickly, and exhibits water contact angles close to zero. We encounter superhydrophilic materials in our daily life (e.g., paper, sponges, textiles) and they are also ubiquitous in nature (e.g., plant and tree leaves, Nepenthes pitcher plant). On the other hand, water on completely non-wettable, superhydrophobic surfaces forms spherical droplets and rolls off the surface easily. One of the most well-known examples of a superhydrophobic surface is the lotus leaf. Creating novel superhydrophobic surfaces has led to exciting new properties such as complete water repellency, self-cleaning, separation of oil and water, and antibiofouling. However, combining these two extreme states of superhydrophilicity and superhydrophobicity on the same surface in precise two-dimensional micropatterns opens exciting new functionalities and possibilities in a wide variety of applications from cell, droplet, and hydrogel microarrays for screening to surface tension confined microchannels for separation and diagnostic devices. In this Progress Report, we briefly describe the methods for fabricating superhydrophilic-superhydrophobic patterns and highlight some of the newer and emerging applications of these patterned substrates that are currently being explored. We also give an outlook on current and future applications that would benefit from using such superhydrophilic-superhydrophobic micropatterns.

MicroRNA profiling using µParaflo microfluidic array technology

The diverse functions of microRNA (miRNA) molecules have drawn broad and intensive interest in various biological fields, biomedical applications, and technology development. Which are endogeneous cellular short RNA molecules found in the cytoplasm as well as in various serum fluids. miRNAs are transcriptional and translational regulatory molecules active in cell division, growth, and apoptosis (1). Dysregulated expression of miRNAs has been implicated in various disease states and has been tested as biomarker candidates (2-4). miRNAs are endogeneous cellular short RNA molecules found in the cytoplasm as well as in various serum fluids. miRNAs are transcriptional and translational regulatory molecules active in cell division, growth, and apoptosis (Bartel, Cell 116:281-97, 2004). Dysregulated expression of miRNAs has been implicated in various disease states and has been tested as biomarker candidates (He et al., Nature 435:828-833, 2005; Lu et al., Nature 435:834-838, 2005; O'Donnell, et al., Nature 435:839-843, 2005). In this chapter, we describe the methods using μParaflo(®) microfluidic oligonucleotide microarray technology for applications in miRNA profiling. One unique feature of this technology is the flexibility that provides users with the freedom to select sequence content either for focused studies wherein only the most relevant sequences are included or for discovery studies wherein the most updated sequence content such as those newly derived from deep sequencing. This chapter provides detailed information from experimental design to sample preparation, as well as data analysis for a miRNA array experiment.

A nanocontact printing system for sub-100 nm aligned patterning

Though many aspects of contact printing have been explored extensively since its invention, there are still hurdles to overcome for multilayer printing in the nanometer regime. Here we report on an aligned nanocontact printing (nCP) system that has demonstrated a sub-100 nm alignment capability by means of moiré fringes and microspacers. To address issues in the stamp inking, we have devised a microfluidic apparatus based on the gradient capillary force for transport of ink solutions. The nCP system has been tested by printing nucleoside phosphoramidites on a nanopillar arrayed substrate. Although the nCP system was designed primarily for use in the fabrication of high density DNA nanoarrays, it has the potential to be applied to other fields of nanotechnology for nanoscale patterning.

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

We have achieved the ability to synthesize thousands of unique, long oligonucleotides (150mers) in fmol amounts using parallel synthesis of DNA on microarrays. The sequence accuracy of the oligonucleotides in such large-scale syntheses has been limited by the yields and side reactions of the DNA synthesis process used. While there has been significant demand for libraries of long oligos (150mer and more), the yields in conventional DNA synthesis and the associated side reactions have previously limited the availability of oligonucleotide pools to lengths <100 nt. Using novel array based depurination assays, we show that the depurination side reaction is the limiting factor for the synthesis of libraries of long oligonucleotides on Agilent Technologies’ SurePrint® DNA microarray platform. We also demonstrate how depurination can be controlled and reduced by a novel detritylation process to enable the synthesis of high quality, long (150mer) oligonucleotide libraries and we report the characterization of synthesis efficiency for such libraries. Oligonucleotide libraries prepared with this method have changed the economics and availability of several existing applications (e.g. targeted resequencing, preparation of shRNA libraries, site-directed mutagenesis), and have the potential to enable even more novel applications (e.g. high-complexity synthetic biology).

Surface patterning of (bio)molecules onto the inner wall of fused-silica capillary tubes

An efficient photochemical method for the site-specific immobilization and patterning of (bio)molecules inside glass capillary tubes is reported. The strategy involves the photodeprotection of reactive aminooxy groups on surfaces and subsequent reaction with aldehyde containing (bio)molecules.

Nanoscale patterns of oligonucleotides formed by electrohydrodynamic jet printing with applications in biosensing and nanomaterials assembly

The widespread use of DNA in microarrays for applications in biotechnology, combined with its promise in programmed nanomaterials assembly, unusual electronic devices, and other areas has created interest in methods for patterning DNA with high spatial resolution. Techniques based on thermal or piezoelectric inkjet printing are attractive due to their noncontacting nature and their compatibility with diverse materials and substrate types; their modest resolution (i.e., 10-20 microm) represents a major limitation for certain systems. Here we demonstrate the use of an operationally similar printing approach that exploits electrohydrodynamic forces, rather than thermal or acoustic energy, to eject DNA inks through fine nozzles, in a controlled fashion. This DNA printer is capable of resolution approaching 100 nm. A range of experiments on patterns of DNA formed with this printer demonstrates its key features. Example applications in DNA-directed nanoparticle assembly and DNA aptamer-based biosensing illustrate two representative uses of the patterns that can be formed.

Bio-Microarray Fabrication Techniques—A Review

Microarrays with biomolecules (e.g., DNA and proteins), cells, and tissues immobilized on solid substrates are important tools for biological research, including genomics, proteomics, and cell analysis. In this paper, the current state of microarray fabrication is reviewed. According to spot formation techniques, methods are categorized as "contact printing" and "non-contact printing." Contact printing is a widely used technology, comprising methods such as contact pin printing and microstamping. These methods have many advantages, including reproducibility of printed spots and facile maintenance, as well as drawbacks, including low-throughput fabrication of arrays. Non-contact printing techniques are newer and more varied, comprising photochemistry-based methods, laser writing, electrospray deposition, and inkjet technologies. These technologies emerged from other applications and have the potential to increase microarray fabrication throughput; however, there are several challenges in applying them to microarray fabrication, including interference from satellite drops and biomolecule denaturization.

Introduction: array technology - an overview

Microarray technology has its roots in high-throughput parallel synthesis of biomacromolecules, combined with combinatorial science. In principle, the preparation of arrays can be performed either by in situ synthesis of biomacromolecules on solid substrates or by spotting of ex situ synthesized biomacromolecules onto the substrate surface. The application of microarrays includes spatial addressing with target (macro) molecules and screening for interactions between immobilized probe and target. The screening is simplified by the microarray format, which features a known structure of every immobilized library element. The area of nucleic acid arrays is best developed, because such arrays are allowed to follow the biosynthetic pathway from genes to proteins, and because nucleic acid hybridization is a most straightforward screening tool. Applications to genomics, transcriptomics, proteomics, and glycomics are currently in the foreground of interest; in this postgenomic phase they are allowed to gain new insights into the molecular basis of cellular processes and the development of disease.

microParaflo biochip for nucleic acid and protein analysis

We describe in this chapter the use of oligonucleotide or peptide microarrays (arrays) based on microfluidic chips. Specifically, three major applications are presented: (1) microRNA/small RNA detection using a microRNA detection chip, (2) protein binding and function analysis using epitope, kinase substrate, or phosphopeptide chips, and (3) protein-binding analysis using oligonucleotide chips. These diverse categories of customizable arrays are based on the same biochip platform featuring a significant amount of flexibility in the sequence design to suit a wide range of research needs. The protocols of the array applications play a critical role in obtaining high quality and reliable results. Given the comprehensive and complex nature of the array experiments, the details presented in this chapter is intended merely as a useful information source of reference or a starting point for many researchers who are interested in genome- or proteome-scale studies of proteins and nucleic acids and their interactions.

High-throughput site-directed mutagenesis using oligonucleotides synthesized on DNA chips

Site-directed mutagenesis has greatly helped researchers both to understand the precise role of specific residues in coding sequences and to generate variants of proteins that have acquired new characteristics. Today's demands for more complete functional cartographies of proteins and advances in selection and screening technologies require that site-directed mutagenesis be adapted for high-throughput applications. We describe here the first generation of a library of single and multiple site-directed mutants using a mixture of oligonucleotides synthesized on DNA chips. We have used the human interleukin 15 (IL15) gene as a model, of which 37 codons were simultaneously targeted for substitution by any of eight possible codons. Ninety-six clones were sequenced, exhibiting a broad spectrum of targeted substitutions over the whole gene length with no unwanted mutations. Libraries produced using such pools of oligonucleotides open new perspectives to direct the evolution of proteins in vitro, by enabling the simple, rapid, and cost-effective generation of large tailor-made genetic diversities from any gene.

Hydrogels from a water-soluble zwitterionic polythiophene: dynamics under pH change and biomolecular interactions observed using quartz crystal microbalance with dissipation monitoring

The water-soluble zwitterionic polythiophene, poly(3-((S)-5-amino-5-carboxyl-3-oxapentyl)-2,5-thiophene) hydrochloride (POWT), is a conjugated polyelectrolyte (CPE) with properties well suited for biochip applications. CPEs readily form hydrogels when exposed to water-based buffer solutions or biomolecule solutions. In this work, we used in situ quartz crystal microbalance with dissipation (QCM-D) monitoring to collect information on the interaction between POWT films exposed to buffers with different pH and POWT/DNA chains. Our data show that POWT swells significantly when exposed to low-pH buffers, such as pH 4 acetate, this is seen as an increase in thickness and decrease in viscosity obtained via a Voight-based modeling of combined f and D QCM-D measurements. The magnitude of thickness and viscosity change upon changing from a pH 10 carbonate buffer to pH 4 acetate is 100% increase in thickness and 50% decrease in viscosity. The response of the hydrogel under pH change is well correlated with fluorescence data from POWT films on glass. The state of the hydrogel is important during interaction with biomolecules; illustrated by the observation that a swollen CPE hydrogel adsorbs a higher amount of DNA than a compacted one. In agreement with previous results, the QCM-D data confirmed that the POWT/DNA hydrogel sense complementary DNA specifically and with negligible binding of noncomplementary DNA. These results are important for efficient constructions of biochips in water environments using this class of materials.

2,2,5,5-tetramethylpyrrolidin-3-one-1-sulfinyl group for 5'-hydroxyl protection of deoxyribonucleoside phosphoramidites in the solid-phase preparation of DNA oligonucleotides

Several nitrogen-sulfur reagents have been investigated as potential 5'-hydroxyl protecting groups for deoxyribonucleoside phosphoramidites to improve the synthesis of oligonucleotides on glass microarrays. Out of the nitrogen-sulfur-based protecting groups so far investigated, the 2,2,5,5-tetramethylpyrrolidin-3-one-1-sulfinyl group exhibited near optimal properties for 5'-hydroxyl protection by virtue of the mildness of its deprotection conditions. Specifically, the iterative cleavage of a terminal 5'-sulfamidite group in the synthesis of 5'-d(ATCCGTAGCCAAGGTCATGT) on controlled-pore glass is efficiently accomplished by treatment with iodine in the presence of an acidic salt. Hydrolysis of the oligonucleotide to its 2'-deoxyribonucleosides upon exposure to snake venom phosphodiesterase and bacterial alkaline phosphatase did not reveal the formation of any nucleobase adducts or other modifications. These findings indicate that the 2,2,5,5-tetramethylpyrrolidin-3-one-1-sulfinyl group for 5'-hydroxyl protection of phosphoramidites, such as 10a-d, may lead to the production of oligonucleotide microarrays exhibiting enhanced specificity and sensitivity in the detection of nucleic acid targets.

Quantitative X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry characterization of the components in DNA

The great diversity of techniques to synthesize and use DNA microarrays has made them extremely flexible for a variety of applications. This flexibility also has made standardization difficult, leading to problems comparing data from these different systems. In this work, we use the surface science techniques of X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (TOF-SIMS) to analyze the components of DNA. The atomic ratios of the components of nucleobases, nucleosides, and nucleotides were characterized by XPS. The chemical shifts in the high-resolution XPS spectra allow for their relatively easy resolution. The unique positive and negative ions from the nucleobases, nucleosides, and nucleotides in their TOF-SIMS spectra were identified. This information was used to build a comprehensive table of all of the molecular ions. These standard spectra of DNA components can be used to predict the relative amounts of the bases within more complex molecules either by univariate analysis (i.e., by relating the base molecular ions to the sugar fragment ions within the nucleotides) or by multivariate analysis (e.g., principal component analysis). Our preliminary examination of four oligonucleotides shows promising results in that we can distinguish between two oligomers of similar composition using univariate and multivariate analysis, although additional studies are needed to expand this method to more complex oligomers.

Molecular printboards: monolayers of beta-cyclodextrins on silicon oxide surfaces

Monolayers of beta-cyclodextrin host molecules have been prepared on SiO2 surfaces. An ordered and stable cyano-terminated monolayer was modified in three consecutive surface reactions. First, the cyanide groups were reduced to their corresponding free amines using Red Al as a reducing agent. Second, 1,4-phenylene diisothiocyanate was used to react with the amine monolayer where it acts as a linking molecule, exposing isothiocyanates that can be derivatized further. Finally, per-6-amino beta-cyclodextrin was reacted with these isothiocyanate functions to yield a monolayer exposing beta-cyclodextrin. All monolayers were characterized by contact angle measurements, ellipsometric thickness measurements, Brewster angle Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and time-of-flight secondary ion mass spectrometry, which indicate the formation of a densely packed cyclodextrin surface. It was demonstrated that the beta-cyclodextrin monolayer could bind suitable guest molecules in a reversible manner. A fluorescent molecule (1), equipped with two adamantyl groups for complexation, was adsorbed onto the host monolayer from solution to form a monolayer of guest molecules. Subsequently, the guest molecules were desorbed from the surface by competition with increasing beta-cyclodextrin concentration in solution. The data were fitted using a model. An intrinsic binding constant of 3.3 +/- 1 x 10(5) M(-1) was obtained, which corresponds well to previously obtained results with a divalent guest molecule on beta-cyclodextrin monolayers on gold. In addition, the number of guest molecules bound to the host surface was determined, and a surface coverage of ca. 30% was found.

In situ synthesis of oligonucleotide microarrays

This contribution presents a brief overall look of the methods for the preparation of various types of DNA microarrays and a thorough examination of the methods for in situ synthesis of oligonucleotide microarrays.

Conceptual "Heat-Driven" approach to the synthesis of DNA oligonucleotides on microarrays

The discovery of deoxyribonucleoside cyclic N-acylphosphoramidites, a novel class of phosphoramidite monomers for solid-phase oligonucleotide synthesis, has led to the development of a number of phosphate protecting groups that can be cleaved from DNA oligonucleotides under thermolytic neutral conditions. These include the 2-(N-formyl-N-methyl)aminoethyl, 4-oxopentyl, 3-(N-tert-butyl)carboxamido-1-propyl, 3-(2-pyridyl)-1-propyl, 2-[N-methyl-N-(2-pyridyl)]aminoethyl, and 4-methythiobutyl groups. When used for 5'-hydroxyl protection of nucleosides, the analogous 1-phenyl-2-[N-methyl-N-(2-pyridyl)]aminoethyloxycarbonyl group exhibited excellent thermolytic properties, which may permit an iterative "heat-driven" synthesis of DNA oligonucleotides on microarrays. In this regard, progress has been made toward the use of deoxyribonucleoside cyclic N-acylphosphoramidites in solid-phase oligonucleotide syntheses without nucleobase protection. Given that deoxyribonucleoside cyclic N-acylphosphoramidites produce oligonucleotides with heat-sensitive phosphate protecting groups, blocking the 5'-hydroxyl of these monomers with, for example, the thermolabile 1-phenyl-2-[N-methyl-N-(2-pyridyl)]aminoethyloxycarbonyl group may provide a convenient thermo-controlled method for the synthesis of oligonucleotides on microarrays.

Analysis of gene expression in carbon tetrachloride-treated rat livers using a novel bioarray technology

The present study successfully utilizes a new ADME Rat Expression Bioarray, containing 1040 metabolism- and toxicology-linked genes, to monitor gene expression from the livers of rats treated with carbon tetrachloride (CCl(4)). Histopathological analysis, hierarchical clustering methods, and gene expression profiling are compared between the control and CCl(4)-treated animals. A total of 44 transcripts were found to be altered in response to the hepatotoxin, 19 of which were upregulated and 25 were downregulated. Some of these gene expression changes were expected and concurred with previously published data while others were novel findings.

Characterization of DNA Immobilization and Subsequent Hybridization on a 2D Arrangement of Streptavidin on a Biotin-Modified Lipid Bilayer Supported on SiO2

We show how the water content (and effective density) of thin adsorbed films composed of biomolecules can be determined using combined quartz crystal microbalance with dissipation monitoring (QCM-D) and surface plasmon resonance (SPR) analysis. In particular, these techniques, combined with theoretical treatment using a Voigt-based viscoelastic model, were applied to analyze the state of surface immobilized single stranded biotin-modified probe DNA (b-DNA) coupled via streptavidin to a biotin-doped supported phospholipid bilayer (b-SPB)). From a proper analysis, it is demonstrated how changes in effective thickness, delta(f), and the viscoelastic components (shear viscosity, eta(f), and shear elasticity, mu(f))) can be obtained during both DNA immobilization and hybridization with single stranded fully complementary target DNA. In particular, it is demonstrated how this type of analysis can be used to control the state of streptavidin arrangement for improved measurements of DNA hybridization kinetics. The latter is demonstrated by identifying a surface-coverage dependent viscoelastic behavior of immobilized b-DNA, which is shown to influence the hybridization efficiency.

Chemical approaches to reversible protein phosphorylation

Protein phosphorylation catalyzed by protein kinases plays a critical role in cellular signaling. Here we review several chemical approaches to understanding protein kinases and the consequences of protein phosphorylation. We discuss the design of bisubstrate analogue inhibitors based on a dissociative transition state, the development of reagents for cross-linking protein kinases with their substrates, the chemical rescue of mutant protein tyrosine kinases, and the application of expressed protein ligation to understanding protein phosphorylation.

Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays

Large-scale genetic screens in zebrafish have identified thousands of mutations in hundreds of essential genes. The genetic mapping of these mutations is necessary to link DNA sequences to the gene functions defined by mutant phenotypes. Here, we report two advances that will accelerate the mapping of zebrafish mutations: (1) The construction of a first generation single nucleotide polymorphism (SNP) map of the zebrafish genome comprising 2035 SNPs and 178 small insertions/deletions, and (2) the development of a method for mapping mutations in which hundreds of SNPs can be scored in parallel with an oligonucleotide microarray. We have demonstrated the utility of the microarray technique in crosses with haploid and diploid embryos by mapping two known mutations to their previously identified locations. We have also used this approach to localize four previously unmapped mutations. We expect that mapping with SNPs and oligonucleotide microarrays will accelerate the molecular analysis of zebrafish mutations.

Expression profiling with oligonucleotide arrays: technologies and applications for neurobiology

DNA microarrays have been used in applications ranging from the assignment of gene function to analytical uses in prognostics. However, the detection sensitivity, cross hybridization, and reproducibility of these arrays can affect experimental design and data interpretation. Moreover, several technologies are available for fabrication of oligonucleotide microarrays. We review these technologies and performance attributes and, with data sets generated from human brain RNA, present statistical tools and methods to analyze data quality and to mine and visualize the data. Our data show high reproducibility and should allow an investigator to discern biological and regional variability from differential expression. Although we have used brain RNA as a model system to illustrate some of these points, the oligonucleotide arrays and methods employed in this study can be used with cell lines, tissue sections, blood, and other fluids. To further demonstrate this point, we provide data generated from total RNA sample sizes of 200 ng.

Proton demand inversion in a mutant protein tyrosine kinase reaction

In contrast to previous studies that have shown that the neutral phenol serves as the nucleophile for WT Csk-promoted phosphorylation of a tyrosine-containing substrate, the phenolate ion acts as primary nucleophile for the D314N Csk-catalyzed reaction. Rate comparisons of D314N Csk-promoted phosphotransfer using a series of fluorotyrosine-containing peptide substrates reveal a near zero beta(nuc), consistent with a dissociative mechanism of phosphotransfer. These combined results argue against a hydroxy nucleophile-to-phosphate proton transfer occurring prior to an associative transition state of phosphoryl transfer.