High-density, covalent attachment of DNA to silicon wafers for analysis by maldi-tof mass spectrometry

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.

Responsive surface bioaffinity binding to construct flexible and sensitive electrochemical aptasensors

A responsive surface bioaffinity binding strategy was developed for the fabrication of simple, flexible and amplified electrochemical aptasensors.

Binary Colloidal Crystal Layers as Platforms for Surface Patterning of Puroindoline-Based Antimicrobial Peptides

The ability of bacteria to form biofilms and the emergence of antibiotic-resistant strains have prompted the need to develop the next generation of antibacterial coatings. Antimicrobial peptides (AMPs) are showing promise as molecules that can address these issues, especially if used when immobilized as a surface coating. We present a method that explores how surface patterns together with the selective immobilization of an AMP called PuroA (FPVTWRWWKWWKG-NH₂) can be used to both kill bacteria and also as a tool to study bacterial attachment mechanisms. Surface patterning is achieved using stabilized self-assembled binary colloidal crystal (BCC) layers, allowing selective PuroA immobilization to carboxylated particles using N-(3-dimethylaminopropyl)-N'-ethyl carbodiimide (EDC) hydrochloride/N-hydroxysuccinimide (NHS) coupling chemistry. Covalent immobilization of PuroA was compared with physical adsorption (i.e., without the addition of EDC/NHS). The AMP-functionalized colloids and BCC layers were characterized by X-ray photoelectron spectroscopy, ζ potentials, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Surface antimicrobial activity was assessed by viability assays using Escherichia coli. MALDI-TOF MS analysis revealed that although not all of PuroA was successfully covalently immobilized, a relatively low density of PuroA (1.93 × 10¹³ molecules/cm² and 7.14 × 10¹² molecules/cm² for covalent and physical immobilization, respectively) was found to be sufficient at significantly decreasing the viability of E. coli by 70% when compared to that of control samples. The findings provide a proof of concept that BCC layers are a suitable platform for the patterned immobilization of AMPs and the importance of ascertaining the success of small-molecule grafting reactions using surface-MALDI, something that is often assumed to be successful in the field.

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.

DNA-Based Nanobiosensors as an Emerging Platform for Detection of Disease

Detection of disease at an early stage is one of the biggest challenges in medicine. Different disciplines of science are working together in this regard. The goal of nanodiagnostics is to provide more accurate tools for earlier diagnosis, to reduce cost and to simplify healthcare delivery of effective and personalized medicine, especially with regard to chronic diseases (e.g., diabetes and cardiovascular diseases) that have high healthcare costs. Up-to-date results suggest that DNA-based nanobiosensors could be used effectively to provide simple, fast, cost-effective, sensitive and specific detection of some genetic, cancer, and infectious diseases. In addition, they could potentially be used as a platform to detect immunodeficiency, and neurological and other diseases. This review examines different types of DNA-based nanobiosensors, the basic principles upon which they are based and their advantages and potential in diagnosis of acute and chronic diseases. We discuss recent trends and applications of new strategies for DNA-based nanobiosensors, and emphasize the challenges in translating basic research to the clinical laboratory.

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.

Polymer-binding peptides for the noncovalent modification of polymer surfaces: effects of peptide density on the subsequent immobilization of functional proteins

Peptides that specifically bind to polyetherimide (PEI) were selected, characterized, and used for the noncovalent modification of the PEI surface. The peptides were successfully identified from a phage-displayed peptide library. A chemically-synthesized peptide composed of the Thr-Gly-Ala-Asp-Leu-Asn-Thr sequence showed an extremely high binding constant for the PEI films (5.6 × 10(8) M(-1)), which was more than three orders of magnitude greater than that for the reference polystyrene films. The peptide was biotinylated and immobilized onto the PEI films to further immobilize streptavidin (SAv). The amount of SAv bound depended on the density of immobilized peptide. It gradually increased with an increasing density of immobilized peptide and achieved a maximum (2.1 pmol cm(-2)) at a peptide density of 19.8 pmol cm(-2). The ratio of peptide used for immobilizing SAv at the maximum value was only 11%, and was partially due to the low accessibility of SAv to the biotin moieties on the PEI films. Moreover, the amount of SAv bound gradually decreased at higher peptide densities, suggesting that the clustering of the peptides also inhibited the binding of SAv. Furthermore, peptides on the PEI films promoted the uniform immobilization of SAv with less structural denaturing. The immobilized SAv was able to further immobilize probe DNA to hybridize with its complementary DNA. These present results suggest that the density of immobilized peptide has a great impact on the surface modifications using polymer-binding peptides.

Holographically Fabricated Dye-Doped Nanoporous Polymers as Matrix for Laser Desorption/Ionization Mass Spectrometry

We report laser desorption/ionization mass spectrometry using a dye-doped nanoporous polymer matrix. The nanoporous polymer matrix was fabricated through a holographic interference patterning technique. The periodically aligned nanopores in the resulting polymer matrix produced a high surface-to-volume ratio that facilitates the homogeneous cocrystallization of the matrix and an analyte (i.e., peptide in this demonstration). To generate nanostructures with further enhanced functionalities, dyes were also incorporated into the photopolymer. We demonstrate that by using the dye-doped nanoporous polymer matrix, we can identify peptides with an enhanced signal from the peptides and decreased noise from the ion fragmentation. These results indicate that the dye-doped nanoporous polymer matrix we use here can be a promising platform for laser desorption/ionization mass spectrometry.

Liposome-based chemical barcodes for single molecule DNA detection using imaging mass spectrometry

We report on a mass-spectrometry (time-of-flight secondary ion mass spectrometry, TOF-SIMS) based method for multiplexed DNA detection utilizing a random array, where the lipid composition of small unilamellar liposomes act as chemical barcodes to identify unique DNA target sequences down to the single molecule level. In a sandwich format, suspended target-DNA to be detected mediates the binding of capture-DNA modified liposomes to surface-immobilized probe-DNA. With the lipid composition of each liposome encoding a unique target-DNA sequence, TOF-SIMS analysis was used to determine the chemical fingerprint of the bound liposomes. Using high-resolution TOF-SIMS imaging, providing sub-200 nm spatial resolution, single DNA targets could be detected and identified via the chemical fingerprint of individual liposomes. The results also demonstrate the capability of TOF-SIMS to provide multiplexed detection of DNA targets on substrate areas in the micrometer range. Together with a high multiplexing capacity, this makes the concept an interesting alternative to existing barcode concepts based on fluorescence, Raman, or graphical codes for small-scale bioanalysis.

Surface Analysis of Photolithographic Patterns using ToF-SIMS and PCA

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a surface analysis technique well-suited to detect and identify trace surface species. With the latest analyzers, ion sources and data analysis methods, imaging ToF-SIMS provides detailed 2-D and 3-D surface reactivity maps. Coupling multivariate analysis methods such as principal component analysis (PCA) with ToF-SIMS provides a powerful method for differentiating spatial regions with different chemistries. ToF-SIMS and PCA are used in this study to image and analyze a two-component photolithograph-patterned surface chemistry currently published and commercialized for bioassays, bio-chips and cell-based biosensors. A widely used reactive surface coupling chemistry, N-hydroxysuccinimide (NHS), and 2-methoxyethylamine (MeO) were co-patterned into adjacent regions on a commercial microarray polymer coating using standard photolithography methods involving deposition, patterning and removal of a routinely used photoresist material. After routine processing, ToF-SIMS and PCA of the patterned surface revealed significant residual photoresist material remaining at the interface of the NHS/MeO patterns, as well as lower concentrations of residual photoresist material remaining within the MeO-containing regions, providing spatial mapping and residue analysis not evident from other characterization techniques. As detection of surface photoresist residue remains an inherent challenge in photolithographic processing of a wide array of materials, the use of ToF-SIMS coupled with PCA is shown to be a high-resolution characterization tool with the high sensitivity and specificity required for surface quality control measurements following photolithography and pattern development relevant to many current processes.

A minimally invasive microdevice for molecular sampling and analysis

In this paper, we present a new minimally invasive biopsy microdevice adapted to proteomic mass spectrometry analysis. The concept is born from a multidisciplinary collaboration in fields of proteomics, cancer research, and microtechnology. In mixing different skills, we have developed and manufactured a miniaturized biopsy device using microtechnology techniques in order to minimize tissue damage during surgical gesture. Dedicated chemically functionalized areas were added to the device in order to increase capture yield and specificity during tissue contact. Fields of application range from cancer research to the study of neurodegenerative diseases.

Biochemical assays of immobilized oligonucleotides with mass spectrometry

This paper reports the use of mass spectrometry to characterize oligonucleotides immobilized to the surfaces of biochips. Biotinylated oligonucleotides were immobilized to self-assembled monolayers that present a streptavidin layer and then treated with a complementary strand to present short duplexes. Treatment of the surface with 5-methoxysalicylic acid and ammonium citrate matrix allows the individual oligonucleotides to be observed by matrix-assisted laser desorption/iozation and time-of-flight mass spectrometry (MALDI-TOF MS). Examples are shown wherein this method is applied to assays of hybridization, of cleavage by a deoxyribozyme, of a dephosphorylation reaction, and of the adducts formed on treatment of DNA with cis-platin. This work provides an early example of the application of mass spectrometry to DNA biochips and may substantially expand the applications of the now common oligonucleotide arrays.

X-ray photoelectron spectroscopy, time-of-flight secondary ion mass spectrometry, and principal component analysis of the hydrolysis, regeneration, and reactivity of N-hydroxysuccinimide-containing organic thin films

N-Hydroxysuccinimide (NHS) esters are widely used as leaving groups to activate covalent coupling of amine-containing biomolecules onto surfaces in academic and commercial surface immobilizations. Their intrinsic hydrolytic instability is well-known and remains a concern for maintaining stable, reactive surface chemistry, especially for reliable longer term storage. In this work, we use X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry (TOF-SIMS) to investigate surface hydrolysis in NHS-bearing organic thin films. Principal component analysis (PCA) of both positive and negative ion TOF-SIMS data was used to correlate changes in the well-defined NHS ester oligo(ethylene glycol) (NHS-OEG) self-assembled monolayers to their surface treatment. From PCA results, multivariate peak intensity ratios were developed for monitoring NHS reactivity, thin-film thickness, and oxidation of the monolayers during surface hydrolysis. Aging in ambient air for up to 7 days resulted in hydrolysis of some fraction of bound NHS groups, oxidation of some resident thiol groups, and deposition of adventitious hydrocarbon contaminants onto the monolayers. Overnight film immersion under water produced complete hydrolysis and removal of the NHS chemistry, as well as removal of some of the thiolated OEG chains. NHS regeneration of the hydrolyzed surfaces was assessed using the same multivariable peak intensity ratio as well as surface coupling with amine-terminated molecules. Both aqueous and organic NHS regeneration methods produced surfaces with bound NHS concentrations approximately 50% of the bound NHS concentration on freshly prepared NHS-OEG monolayers. Precise methods for quantifying NHS chemistry on surfaces are useful for quality control processes required in surface technologies that rely on reliable and reproducible reactive ester coupling. These applications include microarray, microfluidic, immunoassay, bioreactor, tissue engineer-ing, and biomedical device fabrication.

Label-Free Single-Nucleotide Polymorphism Detection Using a Cationic Tetrahedralfluorene and Silica Nanoparticles

We developed a simple method that is able to provide label-free sequence-specific DNA detection with single-nucleotide polymorphism (SNP) detection selectivity. This method makes use of both DNA probe immobilized silica nanoparticles and optically amplifying light harvesting molecules. The recognition is accomplished by sequence-specific hybridization between the DNA probes on the silica nanoparticles and the targets of interest. After subsequent treatment with ethidium bromide (EB), a cationic tetrahedralfluorene was added to electrostatically associate with the DNA molecules on the nanoparticle surface, leading to sensitized EB emission via fluorescence resonance energy transfer (FRET). Because of the selective response of the tetrahedralfluorene to intercalated EB, the perfectly matched DNA targets were distinctively differentiated from those with mutations. The presence of tetrahedralfluorene provides improved detection sensitivity and selectivity, as compared to the use of EB alone as a signal reporter. The demonstrated highly selective label-free detection method laid the ground work for the future development of disposable and real-time testing kits in SNP screenings.

Probing proteins on functionalized silicon surfaces using matrix-assisted laser desorption/ionization mass spectrometry

Flat H-terminated Si(111) substrates modified with alkyl monolayers terminated with hydrophobic and hydrophilic functional groups were prepared using known surface functionalization methods and characterized by FTIR, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). The surfaces were then used for the study of non-specific binding of proteins from complex mixtures (using standard mixture of proteins with average molecular weight approximately 6-66 kDa) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Protein adsorption on these surfaces (following on-probe fractionation of the mixture) was found to be dependent on the nature of surface functional groups, and nature and pH of rinsing solutions used. The results obtained in this work demonstrate that simple silicon-based surface modifications can be effective for direct analysis of complex mixtures by MALDI-MS. Preliminary results obtained using similarly functionalized porous silicon substrates proved that such substrates are (due to their increased surface areas) better performing than flat silicon.

Surface Modification for DNA and Protein Microarrays

Microarrays of biomolecules are emerging as powerful tools for genomics, proteomics, and clinical assays, since they make it possible to screen biologically important binding events in a parallel and high throughput fashion. Because the microarrays are fabricated on a solid support, coating of the surface and immobilization strategy of the biomolecules are major issues for successful microarray fabrication. This review deals with both DNA microarrays and protein microarrays, and focuses on the various modification approaches for the two-dimensional surface materials and three-dimensional ones. In addition, the immobilization strategies including adsorption, covalent attachment, physical entrapment, and affinity attachment of the biomolecules are summarized, and advantage and limitation of representative efforts are discussed.

Controlled loading of oligodeoxyribonucleotide monolayers onto unoxidized crystalline silicon; fluorescence-based determination of the surface coverage and of the hybridization efficiency; parallel imaging of the process by Atomic Force Microscopy

Unoxidized crystalline silicon, characterized by high purity, high homogeneity, sturdiness and an atomically flat surface, offers many advantages for the construction of electronic miniaturized biosensor arrays upon attachment of biomolecules (DNA, proteins or small organic compounds). This allows to study the incidence of molecular interactions through the simultaneous analysis, within a single experiment, of a number of samples containing small quantities of potential targets, in the presence of thousands of variables. A simple, accurate and robust methodology was established and is here presented, for the assembling of DNA sensors on the unoxidized, crystalline Si(100) surface, by loading controlled amounts of a monolayer DNA-probe through a two-step procedure. At first a monolayer of a spacer molecule, such as 10-undecynoic acid, was deposited, under optimized conditions, via controlled cathodic electrografting, then a synthetic DNA-probe was anchored to it, through amidation in aqueous solution. The surface coverage of several DNA-probes and the control of their efficiency in recognizing a complementary target-DNA upon hybridization were evaluated by fluorescence measurements. The whole process was also monitored in parallel by Atomic Force Microscopy (AFM).

Engineering Silicon Oxide Surfaces Using Self-Assembled Monolayers

Although a molecular monolayer is only a few nanometers thick it can completely change the properties of a surface. Molecular monolayers can be readily prepared using the Langmuir-Blodgett methodology or by chemisorption on metal and oxide surfaces. This Review focuses on the use of chemisorbed self-assembled monolayers (SAMs) as a platform for the functionalization of silicon oxide surfaces. The controlled organization of molecules and molecular assemblies on silicon oxide will have a prominent place in "bottom-up" nanofabrication, which could revolutionize fields such as nanoelectronics and biotechnology in the near future. In recent years, self-assembled monolayers on silicon oxide have reached a high level of sophistication and have been combined with various lithographic patterning methods to develop new nanofabrication protocols and biological arrays. Nanoscale control over surface properties is of paramount importance to advance from 2D patterning to 3D fabrication.

Electrochemical Interrogation of DNA Monolayers on Gold Surfaces

In this report, we systematically investigated DNA immobilization at gold surfaces with electrochemical techniques. Comparative cyclic voltammetric and chronocoulometric studies suggested that DNA monolayers immobilized at gold surfaces were not homogeneous. Nonspecific Au-DNA interactions existed even with the treatment of mercaptohexanol, which was known to competitively remove loosely bound DNA at gold surfaces. While both thiolated and nonthiolated DNA formed monolayers on gold surfaces, their hybridization abilities were distinctly different. In contrast to thiolated DNA probes, nonthiolated DNA probes immobilized at gold surfaces were essentially nonhybridizable. The experimental results presented here might be useful for the design of high-performance electrochemical DNA sensors.

Aptamer stationary phase for protein capture in affinity capillary chromatography

The thrombin-binding DNA aptamer was used with thrombin as a model system to investigate protein capture using aptamer stationary phases in affinity capillary chromatography. The aptamer was covalently attached to the inner surface of a bare fused-silica glass capillary to serve as the stationary phase. Proteins were loaded onto the capillary via an applied pressure. The capillary was then washed to remove unbound and non-specifically associated proteins. Finally, the bound protein was released and eluted using 20 mM Tris buffer containing 8 M urea, pH 7.3, at 50 degrees C. Eluate was collected after each step (load, wash and elute) and relative amounts of protein each were compared using fluorescence spectroscopy. The identity of the protein in the collections was confirmed using matrix assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry. The experiment was repeated for thrombin on a bare (unmodified) capillary and a capillary coated with a scrambled-sequence, non-G-quartet forming oligonucleotide that does not bind with thrombin. The results show that the aptamer stationary phase captures approximately three times as much thrombin as the control columns. The experiment was also repeated using human serum albumin (HSA) alone and in an equimolar mixture with thrombin. HSA was not retained on the aptamer capillary, nor did it affect the capture of thrombin from the mixture.

Point mutation detection with the sandwich method employing hydrogel nanospheres by the surface plasmon resonance imaging technique

We propose a surface modification procedure to construct DNA arrays for use in surface plasmon resonance (SPR) imaging studies for the highly sensitive detection of a K-ras point mutation, enhanced with hydrogel nanospheres. A homobifunctional alkane dithiol was adsorbed on Au film to obtain the thiol surface, and ethyleneglycol diglycidylether (EGDE) was reacted to insert the ethyleneglycol moiety, which can suppress nonspecific adsorption during SPR analysis. Then streptavidin (SA) was immobilized on EGDE using tosyl chloride activation. Biotinylated DNA ligands were bound to the SA surface via biotin-SA interaction to fabricate DNA arrays. In SPR analysis, the DNA analyte was exposed on the DNA array and hybridized with the immobilized DNA probes. Subsequently, the hydrogel nanospheres conjugated with DNA probes were bound to the DNA analytes in a sandwich configuration. The DNA-carrying nanospheres led to SPR signal enhancement and enabled us to discriminate a K-ras point mutation in the SPR difference image. The application of DNA-carrying hydrogel nanospheres for SPR imaging assays was a promising technique for high throughput and precise detection of point mutations.

Aptamer-enhanced laser desorption/ionization for affinity mass spectrometry

The thrombin-binding DNA aptamer was used for affinity capture of thrombin in MALDI-TOF-MS. The aptamer was covalently attached to the surface of a glass slide that served as the MALDI surface. Results show that thrombin is retained at the aptamer-modified surface while nonspecific proteins, such as albumin, are removed by rinsing with buffer. Upon application of the low-pH MALDI matrix, the G-quartet structure of the aptamer unfolds, releasing the captured thrombin. Following TOF-MS analysis, residual matrix and protein can be washed from the surface, and buffer can be applied to refold the aptamers, allowing the surface to be reused. Selective capture of thrombin from mixtures of thrombin and albumin and of thrombin and prothrombin from human plasma was demonstrated. This simple approach to affinity capture, isolation, and detection holds potential for analysis, sensing, purification, and preconcentration of proteins in biological fluids.

Direct determination of the peptide content in microspheres by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A quantitative determination of peptides incorporated into poly(d,l-lactide-co-glycolide) microspheres by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was accomplished in a single step without pretreatment for extracting the peptide from the microsphere. The conventional extraction methods often underestimate the actual amount of peptide because of incomplete extraction from the microspheres or loss during the procedures. In this study, the microspheres dissolved in acetonitrile containing 0.1% trifluoroacetic acid were mixed with matrix solution containing the internal standard, and the peptide content was directly determined by MALDI-TOF MS. The drug content values determined by MALDI-TOF MS in both the leuprolide- and salmon calcitonin-incorporated microspheres were closer to the theoretical contents than those determined by the conventional extraction method. This method using MALDI-TOF MS could be a good alternative to time-consuming and less-accurate conventional methods.

X-ray photoelectron spectroscopy and infrared spectroscopy study of maleimide-activated supports for immobilization of oligodeoxyribonucleotides

Surface-tethered nucleic acids are widely applied in solid-phase assays in which complementary strands must be detected against a complex mixture of other sequences. In response to such needs, numerous methods have been developed for immobilizing nucleic acids on solid supports. Often, detailed analysis of associated chemical transformations and of potential side reactions is difficult to obtain. Combined use of planar and high surface area powder supports allows characterization using surface as well as bulk diagnostic techniques. This approach is followed in the present study in which X-ray photoelectron spectroscopy (XPS), transmission infrared spectroscopy (FTIR) and reactivity titrations are used to investigate siliceous supports modified with an aminosilane precursor followed by a maleimide-bearing crosslinker for attachment of nucleic acids. The supports retain maleimide activity for approximately a day when stored under buffer, but deactivation is accelerated under basic conditions or by incomplete conversion of the precursor aminosilane monolayer. Reactions involving the olefinic bond of the imide as well as its carbonyl groups are observed and analyzed. Attachment of sulfhydryl-terminated oligodeoxyribonucleotides is highly site specific, and immobilized strands exhibit excellent hybridization activity. Quantitative use of XPS for label-free determination of DNA coverage based on calibration against reference materials is also described.

Enzymatic reaction of the immobilized enzyme on porous silicon studied by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry

Desorption/ionization on silicon mass spectrometry (DIOS-MS) is a matrix-free technique that allows for the direct desorption/ionization of low-molecular-weight compounds with little or no fragmentation of analytes. This technique has a relatively high tolerance for contaminants commonly found in biological samples. DIOS-MS has been applied to determine the activity of immobilized enzymes on the porous silicon surface. Enzyme activities were also monitored with the addition of a competitive inhibitor in the substrate solution. It is demonstrated that this method can be applied to the screening of enzyme inhibitors. Furthermore, a method for peptide mapping analysis by in situ digestion of proteins on the porous silicon surface modified by trypsin, combined with matrix-assisted laser desorption/ionization-time of flight-MS has been developed.

Surface-MALDI mass spectrometry in biomaterials research

Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) has been used for over a decade for the determination of purity and accurate molecular masses of macromolecular analytes, such as proteins, in solution. In the last few years the technique has been adapted to become a new surface analysis method with unique capabilities that complement established biomaterial surface analysis methods such as XPS and ToF-SSIMS. These new MALDI variant methods, which we shall collectively summarize as Surface-MALDI-MS, are capable of desorbing adsorbed macromolecules from biomaterial surfaces and detecting their molecular ions with high mass resolution and at levels much below monolayer coverage. Thus, Surface-MALDI-MS offers unique means of addressing biomaterial surface analysis needs, such as identification of the proteins and lipids that adsorb from multicomponent biological solutions in vitro and in vivo, the study of interactions between biomaterial surfaces and biomolecules, and identification of surface-enriched additives and contaminants. Surface-MALDI-MS is rapid, experimentally convenient, overcomes limitations in mass resolution and sensitivity of established biochemical techniques such as SDS-PAGE, and can in some circumstances be used for the quantitative analysis of adsorbed protein amounts. At this early stage of development, however, limitations exist: in some cases proteins are not detectable, which appears to be related to tight surface binding. This review summarizes ways in which Surface-MALDI-MS methods have been applied to the study of a range of issues in biomaterials surfaces research.

Strategies for covalent attachment of DNA to beads

Several covalent attachment chemistries were tested for the immobilization of DNA onto glass beads. The comparison was based on the ability of these chemistries to produce derivatized beads that give good hybridization signals. Cyanuric chloride, isothiocyanate, nitrophenyl chloroformate, and hydrazone chemistries gave us the best (yet comparable) hybridization signals. We further characterized the cyanuric chloride method for the number of attachment sites, number of hybridizable sites, hybridization kinetics, effect of linker length on hybridization intensity and stability of the derivatized beads.

Reaction of N-phenyl maleimide with aminosilane monolayers

Reaction of N-phenyl maleimide (NPM) with silica surfaces modified with a self-assembled monolayer of (aminopropyl)triethoxysilane (APTES) was investigated using infrared spectroscopy (FTIR), elemental analysis, and titration assays. This reaction is of interest as a test case for using amine-maleimide coupling for immobilization of biomolecules. Addition of NPM to surface APTES residues was consistently sub-stoichiometric, with typical yields of about 75% on monolayers with a coverage of 1.15 APTES residues/nm2. Titration analysis found negligible presence of imide alkene C=C bonds in modified supports, indicating that addition of NPM to APTES proceeded via amine attack at the imide olefinic bond. FTIR measurements also revealed presence of amide bands which intensified over periods of 10 h. These observations were attributed to a slower secondary process in which APTES amines attack imide carbonyls to produce amide linkages. Stability of NPM-modified surfaces was examined under room temperature storage in pH 7 buffer up to 72 h and for 2 h exposure to buffer at temperatures up to 90 degrees C. It was found that stability was determined by robustness of APTES-silica attachment, with about 30% loss under the harshest conditions investigated.

Capillary electrochromatographic separation of bovine milk proteins using a G-quartet DNA stationary phase

DNA oligonucleotides that form G-quartet structures were used as stationary phase reagents for separation of bovine milk proteins, including alpha-casein, beta-casein, kappa-casein, alpha-lactalbumin and beta-lactoglobulin. Both artificial protein mixtures and a skim milk sample were analyzed. The separations were performed using open-tubular capillary electrochromatography, in which the oligonucleotides were covalently attached to the inner surface of a fused-silica capillary. Better resolution was achieved using the G-quartet-coated capillaries than was achieved using either a bare capillary or a capillary coated with an oligonucleotide that does not form a G-quartet structure. A 4-plane G-quartet-forming stationary phase was able to resolve three peaks for alpha-casein and to detect thermal denaturation of the proteins in the milk sample. The results suggest that G-quartet stationary phases could be used to separate very similar protein structures, such as those arising from genetic variations or post-translational modifications.

Aptamers as analytical reagents

Many important analytical methods are based on molecular recognition. Aptamers are oligonucleotides that exhibit molecular recognition; they are capable of specifically binding a target molecule, and have exhibited affinity for several classes of molecules. The use of aptamers as tools in analytical chemistry is on the rise due to the development of the "systematic evolution of ligands by exponential enrichment" (SELEX) procedure. This technique allows high-affinity aptamers to be isolated and amplified when starting from a large pool of oligonucleotide sequences. These molecules have been used in flow cytometry, biosensors, affinity probe electrophoresis, capillary electrochromatography, and affinity chromatography. In this paper, we will discuss applications of aptamers which have led to the development of aptamers as chromatographic stationary phases and applications of these stationary phases; and look towards future work which may benefit from the use of aptamers as stationary phases.

Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) time-of-flight mass spectrometry (TOFMS) play an essential role in the analysis of biological molecules, not only peptides and proteins, but also DNA and RNA. Tandem mass spectrometry used for sequence analysis has been a major focus of technological developments in mass spectrometry, but accurate mass measurements by high-resolution TOFMS are equally important. This paper describes the role that high mass measurement accuracy can play in DNA composition assignment and discusses the influence of several parameters on mass measurement accuracy in both MALDI and ESI mass spectra. Five oligonucleotides (5-13mers) were used to test the resolving power and mass measurement accuracy obtained with MALDI and ESI instruments with reflectron TOF mass analyzers. The results from the experimental studies and additional theoretical calculations provide a basis to predict the practical utility of high-resolution TOFMS for the analysis of larger oligonucleotides.

Open-tubular capillary electrochromatography of bovine beta-lactoglobulin variants A and B using an aptamer stationary phase

DNA aptamers that form a G-quartet conformation were covalently attached to a capillary surface for open-tubular capillary electrochromatographic separation of bovine beta-lactoglobulin variants A and B, which vary by 2 of their 162 amino acid residues. Separation was achieved using a 4-plane, G-quartet aptamer stationary phase with tris(hydroxymethyl)aminomethane (Tris) or phosphate buffer as the mobile phase. In control experiments, separation did not occur using either an oligonucleotide of similar base composition but which does not form a G-quartet structure, or using capillary zone electrophoresis on a bare capillary under similar experimental conditions. Separation was achieved using a capillary coated only with the covalent linker molecule. In phosphate buffer, the separations were similar for aptamer-coated and linker-only stationary phases, while in Tris buffer, retention times were almost doubled for the linker-only capillary. When Tris buffer is the mobile phase, there appears to be weaker interactions between the proteins and the stationary phase that may result in a gentler, less denaturing separation than is commonly achieved using hydrocarbon-based stationary phases.

MALDI TOF mass spectrometry: an emerging platform for genomics and diagnostics

Matrix-assisted laser desorption/ionization-time of flight (MALDI TOF) mass spectrometry has become, in recent years, a tool of choice for large molecule analyses. The platform is ideal for analysis of protein and nucleic acid sequence, structure and purity. MALDI TOF is the method of choice for quality assurance in oligo and peptide synthesis. Exact mass measurements along with signal intensity detection provide a high level of quality assurance as to the accuracy of the measurement. This accuracy has the potential to significantly lower the level of indeterminate assays that require retest.