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

PCR-CTPP: a new genotyping technique in the era of genetic epidemiology

A new PCR method, PCR-CTPP (polymerase chain reaction with confronting two-pair primers) was invented to genotype a relatively large number of samples in a cost-effective and time-saving manner. In this method, allele-specific DNA products are amplified by means of applying appropriately designed two-pair primers (four primers) into an ordinary PCR tube. Single genotyping for G2886T at L-myc, Arg72Pro of p53 and Glu487Lys of ALDH2 as well as duplex genotyping for C-31T of IL-1B with VNTR of IL-1RN and A385T of secretor gene with se5, are demonstrated as examples with the primers and PCR conditions.

MALDI-TOF Mass Spectrometric Method for Detection of Hybridized DNA Oligomers

Two new approaches for nucleic acid hybridizations by MALDI-TOF mass spectrometry are described. Hybridization using genomic DNA without polymerase chain reaction was demonstrated. Total genomic DNA of bacteriophages bound to charge-modified nylon membranes was identified by the hybridization of species-specific oligonucleotide probes. lambda-Phage DNA and M13 were used for the test with good success. Since MALDI-TOF mass spectrometry can be used to measure the molecular weights of different probes, mass spectrometry can be used for the detection of hybridizations with multiple probes. We demonstrate that multiple-probe hybridization can be resolved by mass spectrometry. Six probes with different mass tag were used for hybridization on a single spot. MALDI-TOF mass spectrometry was successfully used to measure these probes simultaneously. This provides a simple nonradioactive method for multiplex hybridization analysis. It has the potential to drastically increase the speed for microarray hybridization analysis in the future.

Characterization of photooxidized self-assembled monolayers and bilayers by spontaneous desorption mass spectrometry

We show that selected self-assembled monolayers (SAMs) and bilayers are readily characterized by the application of controlled photooxidation and spontaneous desorption mass spectrometry (SDMS) in the negative ion mode. Additionally, SDMS is used to characterize organic and inorganic anionic species adsorbed to the surface of a positively charged SAM surface, 2-aminoethanethiol (AET). Prominent peaks are observed that correspond both to the sulfonate form of each SAM and bilayer and to the anion form of each molecule adsorbed to AET. In addition, fragments of the oxidized thin films were also observed at m/z 80 (SO3-) and 97 (HSO4-). Other prominent fragment peaks more characteristic of the molecule are also seen in the mass spectra.

Automated mass spectrometry: a revolutionary technology for clinical diagnostics

For various diagnostic analyses and the studies of functional genomics, the use of an accurate and cost-effective analytic platform to analyze large numbers of samples is essential. An automated platform called MassArray (Sequenom, Inc, San Diego, CA), designed for high-throughput diagnostic analyses, has recently been validated. The platform combines miniaturized, two-dimensional chip arrays with proven high-fidelity enzymatic procedures and matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Nanoliter dispensing of samples in high-density formats of 384 or greater results in improved throughput and reduced costs. Automation prevails from the initial assay design through sample processing and data analysis, for the most part eliminating the labor component of assay development and implementation. The MassArray platform is being used in the following areas: (1) molecular diagnosis of genetic disease and infectious agents, (2) pharmacogenomics, (3) paternity and/or identity testing, and (4) agriculture (e.g., marker-assisted breeding). MALDI-TOF mass spectrometry can also be used for analyzing proteins; therefore, genotype/phenotype testing can be performed on a single platform.

Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms

Different chemical methods used to attach oligonucleotides by their 5'-end on a glass surface were tested in the framework of solid phase PCR where surface-bound instead of freely-diffusing primers are used to amplify DNA. Each method was first evaluated for its capacity to provide a high surface coverage of oligonucleotides essentially attached via a 5'-specific linkage that satisfyingly withstands PCR conditions and leaves the 3'-ends available for DNA polymerase activity. The best results were obtained with 5'-thiol-modified oligonucleotides attached to amino-silanised glass slides using a heterobifunctional cross-linker reagent. It was then demonstrated that the primers bound to the glass surface using the optimal chemistry can be involved in attaching and amplifying DNA molecules present in the reaction mix in the absence of freely-diffusing primers. Two distinct amplification processes called interfacial and surface amplification have been observed and characterised. The newly synthesised DNA can be detected and quantified by radioactive and fluorescent hybridisation assays. These new surface amplification processes are seen as an interesting approach for attachment of DNA molecules by their 5'-end on a solid support and can be used as an alternative route for producing DNA chips for genomic studies.

Improvement of resolution, mass accuracy, and reproducibility in reflected mode DE-MALDI-TOF analysis of DNA using fast evaporation--overlayer sample preparations

DNA analysis by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is hindered by two processes: alkali metal adduction and fragmentation of the intact ionized molecule. The adverse effects of both processes can be reduced by adding ammonium ion salts or compounds such as fructose to the sample preparations. Matrix additives improve sensitivity and resolution of DNA analysis by MALDI. In addition, spot-to-spot reproducibility, resolution, and mass accuracy for DNA oligonucleotides (< or = 12 mer) can be improved by the use of overlayer sample preparations with matrixes that have low aqueous solubilities, such as alpha-cyano-4-hydroxycinnamic acid, ferulic acid, and 2,4,6-trihydroxyacetophenone. For example, resolution for 5-12-mer oligonucleotides is greater than 7000 using overlayer matrix preparations and mass accuracy values are well below 20 ppm. In addition to these methods, a new method for analyzing DNA in positive ion mode is reported using acidified 3-hydroxypicolinic acid. This method does not lose sensitivity for higher mass oligonucleotides as quickly as overlayer methods, and spectra retain > 6000 resolution and mass accuracies of approximately 20 ppm between different overlayer depositions.

Immobilization of nucleic acids at solid surfaces: effect of oligonucleotide length on layer assembly

This report investigates the effect of DNA length and the presence of an anchoring group on the assembly of presynthesized oligonucleotides at a gold surface. The work seeks to advance fundamental insight into issues that impact the structure and behavior of surface-immobilized DNA layers, as in, for instance, DNA microarray and biosensor devices. The present study contrasts immobilization of single-stranded DNA (ssDNA) containing a terminal, 5' hexanethiol anchoring group with that of unfunctionalized oligonucleotides for lengths from 8 to 48 bases. Qualitatively, the results indicate that the thiol anchoring group strongly enhances oligonucleotide immobilization, but that the enhancement is reduced for longer strand lengths. Interestingly, examination of the probe coverage as a function of strand length suggests that adsorbed thiol-ssDNA oligonucleotides shorter than 24 bases tend to organize in end-tethered, highly extended configurations for which the long-term surface coverage is largely independent of oligonucleotide length. For strands longer than 24 bases, the surface coverage begins to decrease notably with probe length. The decrease is consistent with a less ordered arrangement of the DNA chains, presumably reflecting increasingly polymeric behavior.

Separation of nontarget compounds by DNA aptamers

The ability of DNA aptamers to separate nontarget compounds is demonstrated. Two G-quarter forming aptamers, a 15-mer and a 20-mer, were covalently linked to fused silica capillary columns to serve as stationary-phase reagents in capillary electrochromatography. Separations of binary mixtures of amino acids (D-trp and D-tyr), enantiomers (D-trp and L-trp), and polycyclic aromatic hydrocarbons were achieved. Aptamers offer several attractive features for stationary-phase reagents, including ease of synthesis and of attachment to surfaces and modification of their binding properties through minor changes in sequence.

Chip-based genotyping by mass spectrometry

Silicon chips with immobilized target DNAs were used for accurate genotyping by mass spectrometry. Genomic DNAs were amplified with PCR, and the amplified products were covalently attached to chip wells via N-succinimidyl (4-iodoacetyl)aminobenzoate (SIAB) chemistry. Primer annealing, extension, and termination were performed on a 1-microl scale directly in the chip wells in parallel. Diagnostic products thus generated were detected in situ by using matrix-assisted laser desorption ionization mass spectrometry. This miniaturized method has the potential for accurate, high-throughput, low-cost identification of genetic variations.

Conformational stability of adsorbed insulin studied with mass spectrometry and hydrogen exchange

A new method is described for direct monitoring of the conformational stability of proteins that are physically adsorbed from solution onto a solid substrate. The adsorption-induced conformational changes of insulin are studied using a combination of hydrogen/deuterium (H/D) exchange and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The effect of the surface hydrophobicity on the adsorption-induced conformational changes in the insulin structure is probed by adsorbing insulin on a hydrophilic silica and a hydrophobic methylated silica surface before subjecting the insulin molecules to the isotopic exchange process. The present study describes the experimental procedure of this new application of MALDI. Results show that insulin is more highly and more irreversibly adsorbed to a hydrophobic methylated silica surface than to a hydrophilic silica surface. Hydrogen-exchange experiments clearly demonstrate that the strong interaction of insulin with the hydrophobic surface is accompanied by a strong increase in the H/D-exchange rates and thus in a reduction in the insulin native structural stability. In contrast, H/D-exchange rates of insulin are somewhat reduced upon adsorption on silica from solution.

Surface mass spectrometry of molecular species

This tutorial discusses the predominant methods available for surface mass spectrometry (MS) of molecular species: thermal desorption spectroscopy, laser desorption MS, secondary ion MS, post-ionization of desorbed neutrals and surface matrix-assisted laser desorption/ionization. Each of these has the capability to analyze molecular species that are chemisorbed, physisorbed, covalently bound to or the predominant component of a solid surface. These surface MS methods are briefly described, then their capabilities demonstrated using data predominantly from the authors' work. Comparisons are made with related methods in conventional MS. A very brief discussion is provided on the importance of complementing surface MS data with data from x-ray photoelectron spectroscopy and other surface analysis tools.

Desorption-ionization mass spectrometry on porous silicon

Desorption mass spectrometry has undergone significant improvements since the original experiments were performed more than 90 years ago. The most dramatic change occurred in the early 1980s with the introduction of an organic matrix to transfer energy to the analyte. This reduces ion fragmentation but also introduces background ions from the matrix. Here we describe a matrix-free strategy for biomolecular mass spectrometry based on pulsed-laser desorption-ionization from a porous silicon surface. Our method uses porous silicon to trap analytes deposited on the surface, and laser irradiation to vaporize and ionize them. We show that the method works at femtomole and attomole levels of analyte, and induces little or no fragmentation, in contrast to what is typically observed with other such approaches. The ability to perform these measurements without a matrix also makes it more amenable to small-molecule analysis. Chemical and structural modification of the porous silicon has enabled optimization of the ionization characteristics of the surface. Our technique offers good sensitivity as well as compatibility with silicon-based microfluidics and microchip technologies.

Electrochemical quantitation of DNA immobilized on gold

We have developed an electrochemical method to quantify the surface density of DNA immobilized on gold. The surface density of DNA, more specifically the number of nucleotide phosphate residues, is calculated from the amount of cationic redox marker measured at the electrode surface. DNA was immobilized on gold by forming mixed monolayers of thiol-derivitized, single-stranded oligonucleotide and 6-mercapto-1-hexanol. The saturated amount of charge-compensation redox marker in the DNA monolayer, determined using chronocoulometry, is directly proportional to the number of phosphate residues and thereby the surface density of DNA. This method permits quantitative determination of both single- and double-stranded DNA at electrodes. Surface densities of single-stranded DNA were precisely varied in the range of (1-10) x 10(12) molecules/cm2, as determined by the electrochemical method, using mixed monolayers. We measured the hybridization efficiency of immobilized single-stranded DNA to complementary strands as a function of the immobilized DNA surface density and found that it exhibits a maximum with increasing surface density.

Analysing genetic information with DNA arrays

The large amount of DNA sequence information produced in recent years has created a need for high-throughput methods in biology and genetics. These include sequencing, comparing gene sequences and genotyping. DNA arrays promise a highly parallel means for analysis of DNA that is fast and cost-effective, and offers scope for application to complex systems and processes. Recent years have seen continued transfer of technology from the microelectronics industry. Rapid application of the technology to genotyping, antisense oligonucleotide selection and gene expression analysis has illustrated the general power of this approach.

Applications of mass spectrometry to the characterization of oligonucleotides and nucleic acids

Mass spectrometry-based techniques continue to undergo active development for applications to nucleic acids, fueled by methods based on electrospray and matrix-assisted laser desorption ionization. In the past two years, notable advances have occurred in multiple interrelated areas, including sequencing techniques for oligonucleotides, approaches to mixture analysis, microscale sample handling and targeted DNA assays, and improvements in instrumentation for greater sensitivity and mass resolution.

Application of nested PCR and mass spectrometry for DNA-based virus detection: HBV-DNA detected in the majority of isolated anti-HBc positive sera

DNA preparations from three different groups of serum samples were examined for HBV-DNA via a nested polymerase chain reaction assay (lower detection limit: 10 viral genomes in 100 microliters serum): Group I consisted of 11 uninfected control sera, group II consisted of sera obtained from 11 HBV infected patients and group III consisted of 21 isolated anti-HBc positive samples. The 21 samples from group III were HBV-DNA negative according to a conventional non-nested PCR assay and hybridization with a 32P-labelled probe. Using nested PCR and mass spectrometry, HBV-DNA was detected in none of group I and in all of group II samples. In 11 out of 21 (52%) of the isolated anti-HBc positive sera from group III, HBV-DNA was detected. No correlation was observed between HBV-DNA positivity and anti-HBc titers. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry provided a fast, sensitive and non-radioactive assay for the detection of PCR products without the need for gel electrophoresis or hybridization with labelled probes.