Solid-phase Polymerase Chain Reaction Research Articles

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.

Widespread yet persistent low abundance of TIM5-like cyanophages in the oceans.

Ocean ecosystems are inhabited by a diverse set of viruses that impact microbial mortality and evolution. However, the distribution and abundances of specific viral lineages, particularly those from the large bank of rare viruses, remains largely unknown. Here, we assessed the diversity and abundance of the TIM5-like cyanophages. The sequencing of three new TIM5-like cyanophage genomes and environmental amplicons of a signature gene from the Red Sea revealed highly conserved gene content and sequence similarity. We adapted the polony method, a solid-phase polymerase chain reaction assay, to quantify TIM5-like cyanophages during three 2000 km expeditions in the Pacific Ocean and four annual cycles in the Red Sea. TIM5-like cyanophages were widespread, detected at all latitudes and seasons surveyed throughout the photic zone. Yet they were generally rare, ranging between <100 and 4000 viruses·ml-1 . Occasional peaks in abundance of 10- to 100-fold were observed, reaching 71,000 viruses·ml-1 . These peaks were ephemeral and seasonally variable in the Red Sea. Infection levels, quantified during one such peak, were very low. These characteristics of low diversity and abundance, as well as variable outbreaks, distinguishes the TIM5-like lineage from other major cyanophage lineages and illuminates that rare virus lineages can be persistent and widespread in the oceans.

Fluorescent Semiconductor Nanorods for the Solid-Phase Polymerase Chain Reaction-Based, Multiplexed Gene Detection of Mycobacterium tuberculosis.

The spread of infectious diseases with significantly high mortality rates can wreak devastating damage on global health systems and economies, underscoring the need for better disease diagnostic platforms. Solid-phase polymerase chain reaction (SP-PCR) potentially combines the advantages of conventional PCR-based diagnostics with the capability of multiplexed detection, given that the spatial separation between primers circumvents unwanted primer-primer interactions. However, the generally low efficiency of solid-phase amplification results in poor sensitivity and limits its use in detection schemes. We present an SP-PCR-based, multiplexed pulldown fluorescence assay for the detection of Mycobacterium tuberculosis (MTB), utilizing highly fluorescent oligonucleotide-functionalized CdSe/CdS and CdSe1-xSx/CdS nanorods (NRs) as multicolor hybridization probes. The large surface area of the NRs allows for their easy capture and pulldown, but without contributing significantly to the interparticle photon reabsorption when clustered at the pulldown sites. The NR nanoprobes were specifically designed to target the hotspot regions of the rpoB gene of MTB, which have been implicated in resistance to standard rifampicin treatment. The implementation of the semiconductor NRs as photostable multicolor fluorophores in a multiplexed SP-PCR-based detection scheme allowed for the identification of multiple hotspot regions with sub-picomolar levels of sensitivity and high specificity in artificial sputum. While this work demonstrates the utility of semiconductor NRs as highly fluorescent chromophores that can enable SP-PCR as a sensitive and accurate technique for multipathogen diagnostics, the flexible surface chemistry of the NRs should allow them to be applicable to a wide variety of detection motifs.

Specificities of multi-primer polymerase chain reaction optimization for the detection of infectious pneumonia agents in human

Objectives. The objectives of this work are the development of a multi-primer system based on the polymerase chain reaction (PCR) aimed at the simultaneous detection of six bacterial pathogens that cause human pneumonia and the determination of the parameters important for the optimization of this multi-primer system, including solid-phase PCR systems (biological microarrays).Methods. To determine the optimal parameters of the system, PCR methods were used in monoplex and multiplex formats.Results. Primers for Staphylococcus aureus, Pseudomonas aeruginosa, Haemophilus influenza, Legionella pneumophila, Klebsiella pneumoniae, and Streptococcus pneumoniae detection were designed, and the PCR cycling conditions were optimized. The patterns of primer design for solidphase PCR were revealed.Conclusions. The developed prototype of a system specifically identifies six clinically significant bacterial pathogens. It could be expanded for the analysis of viral and fungal pathogens and used in clinical diagnostics. A prototype of a system for pathogenic agent detection in the immobilized phase (biological microarray) was created.

A Complete Protocol for Rapid and Low-Cost Fabrication of Polymer Microfluidic Chips Containing Three-Dimensional Microstructures Used in Point-of-Care Devices.

This protocol provides insights into the rapid, low-cost, and largescale fabrication of polymer microfluidic chips containing three-dimensional microstructures used in point-of-care devices for applications such as detection of pathogens via molecular diagnostic methods. The details of the fabrication methods are described in this paper. This study offers suggestions for researchers and experimentalists, both at university laboratories and in industrial companies, to prevent doom fabrication issues. For a demonstration of bio-application in point-of-care testing, the 3D microarrays fabricated are then employed in multiplexed detection of Salmonella (Salmonella Typhimurium and Salmonella Enteritidis), based on a molecular detection technique called solid-phase polymerase chain reaction (SP-PCR).

Solid Phase PCR on 3D Microstructure ArrayChip for Pathogen Detection Application.

Advanced free angle photolithography (FAPL) is presented for making 3D supercritical angle fluorescence (SAF) microstructures and transfer them on to polymeric chips using injection molding technique for low-cost microfluidic devices embedded with optical sensing structures. A solid phase polymerase chain reaction (SP-PCR) is used as model technique, which allows rapid and sensitive detection of pathogen DNA on-chip. This article presents the detailed fabrication of SAF structure and SP-PCR application on SAF structure for pathogen detection. This protocol of developing SAF structures using the FAPL process, increases the number of SAF per mm2. FAPL was performed via a motorized stage to control the angle of incidence and to achieve the desired bucket-shapes (dimensions of 50 μm to 150 μm with a slope) required for the 3D optical sensing. Due to the unique properties of SAF structures, it enhances the fluorescent signal by 46 times. Increasing the number of SAF structures and reducing the size resulted in reduction of sample volume required per test along with improvement in the limit of detection (LOD) due to a smaller size. This article also presents the experimental details of SP-PCR using DNA oligos bound to the SAF structures for on-chip pathogen detection and a comparison between different sizes of SAF structures. The direct on-chip SP-PCR paves the path for the application of this technique in point-of-care devices.

Fabrication of 3D microstructure array on chip for rapid pathogen detection

An advanced process of free angle photolithography (FAPL) is used for making 3D supercritical angle fluorescence (SAF) structures and transfer them to the polymeric chip by injection molding for low-cost microfluidic devices with the embedded optical sensing. The FAPL was performed via a motorized stage to control the angle of incidence of light and achieve the desired shape with dimension from 50 μm to 150 μm and slope required for the 3D optical structure. These 3D structures are used for enhancement of fluorescent signal through the unique properties of SAF. The presented SAF structure has a reduced active area (50 μm) that allows enrichment of the fluorescence efficiency and reduces the amount of sample required for detection on the polymeric microfluidic chip. Herein, we are presenting reduced dimension of SAF structures, fabricated by FAPL process and increases the number of SAF per mm2 area. This also reduced the volume of sample required per test. Improvement in the limit of detections (LOD) is observed when using the small dimensions of SAF. Solid phase polymerase chain reaction (SP-PCR) on these SAF structures permits for on-chip pathogen detection. These 3D structures have the potential to be widely used in microfluidic chips as a tool for signal enrichment and low-cost point of care systems for optical detection.

Microdevice-based solid-phase polymerase chain reaction for rapid detection of pathogenic microorganisms.

We demonstrate the integration of DNA amplification and detection functionalities developed on a lab‐on‐a‐chip microdevice utilizing solid‐phase polymerase chain reaction (SP‐PCR) for point‐of‐need (PON) DNA analyses. First, the polycarbonate microdevice was fabricated by thermal bonding to contain microchambers as reservoirs for performing SP‐PCR. Next, the microchambers were subsequently modified with polyethyleneimine and glutaraldehyde for immobilizing amine‐modified forward primers. During SP‐PCR, the immobilized forward primers and freely diffusing fluorescence‐labeled reverse primers cooperated to generate target amplicons, which remained covalently attached to the microchambers for the fluorescence detection. The SP‐PCR microdevice was used for the direct identifications of two widely detected foodborne pathogens, namely Salmonella spp. and Staphylococcus aureus, and an alga causing harmful algal blooms annually in South Korea, Cochlodinium polykrikoides. The SP‐PCR microdevice would be versatilely applied in PON testing as a universal platform for the fast identification of foodborne pathogens and environmentally threatening biogenic targets.

DNA microarray-based solid-phase PCR on copoly (DMA–NAS–MAPS) silicon coated slides: An example of relevant clinical application

In a previous study we developed a highly sensitive DNA microarray for the detection of common KRAS oncogenic mutations, which has been proven to be highly specific in assigning the correct genotype without any enrichment strategy even in the presence of minority mutated alleles. However, in this approach, the need of a spotter for the deposition of the purified PCR products on the substrates and the purification step of the conventional PCR are serious drawbacks. To overcome these limitations we have introduced the solid-phase polymerase chain reaction (SP-PCR) to form the array of PCR products starting from the oligonucleotide primers. This work was possible thanks to the great thermal stability of the copoly (DMA–NAS–MAPS) coating which withstands PCR thermal cycling temperatures. As an example of the application of this platform we performed the analysis of six common mutations in the codon 12 of KRAS gene (G12A, G12C, G12D, G12R, G12S, and G12V). In conclusion solid-phase PCR, combined with dual-color hybridization, allows mutation analysis in a shorter time span and is more suitable for automation.

Real‐Time Monitoring of Solid‐Phase PCR Using Fiber‐Optic SPR

Real-time monitoring of solid-phase DNA amplification using a surface plasmon resonance sensor (SPR) with gold nanobead signal enhancement is presented. The sensor is applied in the quantification of a DNA aptamer and subsequent melting curve analysis. The system is suited for application in medical and food-safety diagnostics, and for the study and optimization of solid-phase polymerase chain reaction.

DNA microarray-based solid-phase RT-PCR for rapid detection and identification of influenza virus type A and subtypes H5 and H7

Endemic of avian influenza virus (AIV) in Asia and epizootics in some European regions have caused considerable public concern on a possible pandemic of AIV. A rapid method for virus detection and effective surveillance in wild avian, poultry production as well as in humans is required. In this article, a DNA microarray-based solid-phase polymerase chain reaction (PCR) approach has been developed for rapid detection of influenza virus type A and for simultaneous identification of pathogenic virus subtypes H5 and H7. This solid-phase RT-PCR method combined reverse-transcription amplification of RNA extract in the liquid phase with sequence-specific nested PCR on the solid phase. A simple ultraviolet cross-linking method was used to immobilize the DNA probes over an unmodified glass surface, which makes solid-phase PCR a convenient possibility for AIV screening. The testing of 33 avian fecal and tracheal swab specimens was completed in less than 2 h with 94% accuracy.

High-Performance Single Cell Genetic Analysis Using Microfluidic Emulsion Generator Arrays

High-throughput genetic and phenotypic analysis at the single cell level is critical to advance our understanding of the molecular mechanisms underlying cellular function and dysfunction. Here we describe a high-performance single cell genetic analysis (SCGA) technique that combines high-throughput microfluidic emulsion generation with single cell multiplex polymerase chain reaction (PCR). Microfabricated emulsion generator array (MEGA) devices containing 4, 32, and 96 channels are developed to confer a flexible capability of generating up to 3.4 x 10(6) nanoliter-volume droplets per hour. Hybrid glass-polydimethylsiloxane diaphragm micropumps integrated into the MEGA chips afford uniform droplet formation, controlled generation frequency, and effective transportation and encapsulation of primer functionalized microbeads and cells. A multiplex single cell PCR method is developed to detect and quantify both wild type and mutant/pathogenic cells. In this method, microbeads functionalized with multiple forward primers targeting specific genes from different cell types are used for solid-phase PCR in droplets. Following PCR, the droplets are lysed and the beads are pooled and rapidly analyzed by multicolor flow cytometry. Using Escherichia coli bacterial cells as a model, we show that this technique enables digital detection of pathogenic E. coli O157 cells in a high background of normal K12 cells, with a detection limit on the order of 1/10(5). This result demonstrates that multiplex SCGA is a promising tool for high-throughput quantitative digital analysis of genetic variation in complex populations.

The role of DNA diffusion in solid phase polymerase chain reaction with gel-immobilized primers in planar and capillary microarray format.

The solid phase polymerase chain reaction (PCR) on a gel-based microarray system was studied under various durations of individual stages of the PCR cycle and spatial restriction of the reaction volume. Combining the experimental study with numerical modeling, we demonstrated that the diffusion of the PCR product in and out of a microarray element during the annealing and melting stages, respectively, is the main factor responsible for distinctive features of the studied type of PCR. The restriction of reaction volume leads to faster PCR signal growth. Particularly, the capillary array, whereby gel-based microarray elements are located on a glass bar inserted into capillary chamber, was found to be a suitable format for the development of the platform.

High-throughput SNP genotyping based on solid-phase PCR on magnetic nanoparticles with dual-color hybridization

Single-nucleotide polymorphisms (SNPs) are one-base variations in DNA sequence that can often be helpful when trying to find genes responsible for inherited diseases. In this paper, a microarray-based method for typing single nucleotide polymorphisms (SNPs) using solid-phase polymerase chain reaction (PCR) on magnetic nanoparticles (MNPs) was developed. One primer with biotin-label was captured by streptavidin coated magnetic nanoparticles (SA-MNPs), and PCR products were directly amplified on the surface of SA-MNPs in a 96-well plate. The samples were interrogated by hybridization with a pair of dual-color probes to determine SNP, and then genotype of each sample can be simultaneously identified by scanning the microarray printed with the denatured fluorescent probes. The C677T polymorphisms of methylenetetrahydrofolate reductase (MTHFR) gene from 126 samples were interrogated using this method. The results showed that three different genotypes were discriminated by three fluorescence patterns on the microarray. Without any purification and reduction procedure, and all reactions can be performed in the same vessel, this approach will be a simple and labor-saving method for SNP genotyping and can be applicable towards the automation system to achieve high-throughput SNP detection.

Ten Polymorphisms of Estrogen-Metabolizing Genes and a Family History of Colon Cancer—An Association Study of Multiple Gene-Gene Interactions

Estrogen replacement therapy is associated with a reduced risk of colon cancer. Therefore, we evaluated the following ten estrogen metabolism-associated single-nucleotide polymorphisms (SNPs) by sequencing-on-chip technology using solid-phase polymerase chain reaction (PCR) on oligonucleotide microarrays: catechol-O-methyltransferase (COMT) Val158Met G-->A, 17-beta-hydroxysteroid dehydrogenase type 1 (HSD17) vlV A-->C, cytochrome P-450 (CYP) 17 A2 allele T-->C, CYP1A1 MspI RFLP T-->C, CYP1A1 Ile462Val A-->G, CYP19 Arg264Cys C-->T, CYP19 C1558T C-->T, CYP 1B1 Leu432Val, CYP1B1 Asn453Ser, and estrogen receptor (ER) alpha IVS1 -401-->C in 76 patients with a family history of colon cancer and 722 healthy controls. Using stepwise logistic regression models, we found that none of the investigated SNPs is associated with a family history of colon cancer in a univariate and multivariate logistic regression model. In addition, when all two-way interactions of the investigated SNPs were ascertained, no significant interactions between SNPs were observed. In conclusion, we found no association between the carriage of one or multiple SNPs of the estrogen metabolism and a family history of colon cancer.

Polymorphisms associated with thrombophilia and vascular homeostasis and the timing of menarche and menopause in 728 white women

Genetic factors have been proposed as modulators of the timing of natural menopause. Single nucleotide polymorphisms (SNPs) of genes associated with thrombophilia and vascular homeostasis may interfere with ovarian function and thus are candidate genes for early menopause. We attempted to assess the association of SNPs and the timing of menarche and natural and surgical menopause in an ethnically homogenous cohort of Middle European white women. In the present cross-sectional study, eight SNPs of six genes involved in vascular function and homeostasis were analyzed by sequencing-on-chip using solid-phase polymerase chain reaction on oligonucleotide microarrays in 728 white women: factor V (F5) Leiden G1691A, factor II (F2) prothrombin G20210A, plasminogen activator inhibitor1 (PAI-1) 4G/5G, angiotensinogen (AGT) Met235Thr, endothelial nitric oxide synthase (NOS3) T768C and NOS3 Glu298Asp, apolipoprotein E-1 (APOE-1) Cys112Arg, and APOE-2 Arg158Cys. The women's reproductive and medical histories were correlated to genotypes. In a univariate analysis, current smoking (P = 0.01) and the presence of at least one mutant allele of F5 Leiden (P = 0.03) and APOE-2 (P = 0.03) were significantly associated with a reduced age at natural menopause. The presence of at least one mutant allele of F5 Leiden (P = 0.02) and a body mass index above 25 kg/m (P = 0.009) were significantly associated with an increased risk for surgical menopause by premenopausal hysterectomy (odds ratio = 2.6, 95% CI, 1.2-5.6; odds ratio = 1.9, 95% CI, 1.2-3.0, respectively). Age at menarche was not affected by the carriage of any of the investigated SNPs. Applying stepwise linear regression models considering all two-way interactions, no interactions were found among different SNPs or between SNPs and environmental and lifestyle parameters. We identified various genetic and personal history parameters influencing age at natural menopause and the risk of undergoing premenopausal hysterectomy. To the best of our knowledge, we present the largest study to date determining SNPs as contributors to the genetic control of the timing of natural and surgical menopause.

Estrogen-metabolizing gene polymorphisms in the assessment of breast carcinoma risk and fibroadenoma risk in Caucasian women.

Genes encoding enzymes involved in estrogen metabolism are held to be candidate genes for associations with breast disease. In these candidate genes, no critical combination of single-nucleotide polymorphisms (SNPs) for assessing breast carcinoma risk has been reported to date. In a large case-control study, the authors investigated 10 estrogen-metabolizing SNPs in 396 patients with breast carcinoma, 154 patients with fibroadenoma, and 1936 healthy control patients without breast carcinoma in their personal history. The following 10 SNPs were analyzed using sequencing-on-chip technology via a solid-phase polymerase chain reaction assay performed on oligonucleotide microarrays: catechol-O-methyltransferase Val158Met G-->A, 17-beta-hydroxysteroid dehydrogenase type 1 vIV A-->C, cytochrome P-450 (CYP) family 17 A2 allele T-->C, CYP1A1-1 MspI restriction fragment length polymorphism (RFLP) T-->C, CYP1A1-2 Ile462Val A-->G, CYP19-1 Trp39Arg T-->C, CYP19-2 Arg264Cys C-->T, CYP19-3 Cys1558Thr C-->T, steroid-5-alpha reductase type 2 Val89Leu G-->C, and vitamin D receptor BsmI RFLP. A total of 21,350 genotypes were evaluated. Associations and two-way interaction models were calculated using stepwise logistic regression. In a multiple model, CYP1A1-1 (P = 0.004) and CYP1A1-2 (P = 0.03) were found to be associated with significantly decreased and increased risks of breast carcinoma, respectively. When two-way interactions involving investigated SNPs were ascertained, no significant interactions among polymorphisms were noted. Comparison of patients with fibroadenoma with control patients revealed significantly increased and decreased risks of fibroadenoma when the mutant alleles of CYP17 (P = 0.02) and CYP1A1-1 (P = 0.04), respectively, were present. The authors obtained the first SNP data indicating that CYP17 and CYP1A1-1 play a role in the pathogenesis of fibroadenoma. Although the authors were not able to develop interaction models involving SNPs, they did provide evidence that CYP1A1 is a low-penetrance susceptibility gene with respect to breast carcinoma in a large series of Caucasian women.

Polymorphisms of thrombophilic and vasoactive genes and severe preeclampsia: a pilot study.

Carriage of thrombophilic and vasoactive polymorphic alleles has been associated with various pregnancy complications. The effect of carrying multiple polymorphisms is not known. We conducted a case-control study to determine the association between eight polymorphisms of thrombophilic and vasoactive genes and the risk of severe preeclampsia. The following polymorphisms were analyzed by sequencing-on-chip-technology using solid-phase polymerase chain reaction on oligonucleotide microarrays: factor 5 (F5) Leiden, factor 2 (F2)-prothrombin G20210A, plasminogen activator inhibitor (PAI)-1 4G/5G, nitric oxide synthase (NOS) 3 T768C, NOS 3 Glu298Asp, angiotensinogen (AGT) Met235Thr, estrogen receptor (ER) alpha Pvu II, and mineralcorticoid receptor (MLR) Ser810Leu. The study comprised 24 patients with severe preeclampsia and 24 controls from a cohort of consecutive white women treated at the Obstetrics Department of the University of Vienna Medical School. Genotypes were correlated with clinical data. The investigated polymorphisms did not influence the risk of severe preeclampsia independently. When separately considering the simultaneous carriage of multiple thrombophilic or vasoactive polymorphisms, neither the combined carriage of thrombophilic polymorphisms (F5 Leiden, F2 G20210A, PAI-1 4G/5G), nor the combined carriage of vasoactive polymorphisms (NOS 3 T768C, NOS 3 Glu298Asp, AGT Met235Thr) conferred an increased risk of severe preeclampsia. Cumulative genotype frequencies for at least two homozygous mutant genotypes, however, were nine of 24 (38%) and two of 24 (8%) for the study and control groups, respectively (P <.05). All of these nine women with severe preeclampsia had at least two homozygous mutant genotypes of four polymorphisms, ie, F5 Leiden, NOS 3 T768C, NOS 3 Glu298Asp, or ER alpha Pvu II. Our data fail to document an independent significant influence of the investigated polymorphisms on the risk of severe preeclampsia. In an attempt to build a multigenetic model of severe preeclampsia, the combination of F5 Leiden, NOS 3 T768C, NOS 3 Glu298Asp, and ER alpha Pvu II was the most effective combination to predict the presence of severe preeclampsia in this small series of white women.

Polymerase chain reaction (PCR) for the detection of celery ( Apium graveolens ) in food

A method based upon polymerase chain reaction (PCR) for the detection of celery (Apium graveolens) in food was developed. The method involves DNA isolation by chaotropic or non-chaotropic solid-phase extraction and PCR with primers oriented to the sequence of the nuclear gene encoding mannitol dehydrogenase. The PCR method was shown to be specific for celery, producing a 279 bp fragment with four celery varieties and negative results with other species commonly present together with celery in food products (16 samples). The detection limit of PCR was 490–1530 pg DNA, which corresponds to 102 genome copies. When evaluated with model samples of celery in meat pâtes, a detection limit of 0.1% (w/w) was determined. When used to analyse food products from the market (dried vegetable seasonings, dehydrated bouillons), all four products declared to contain celery were correctly identified as positive and all three products in which celery was not declared were identified as negative.

Detection of Single Base Alterations in Genomic DNA by Solid Phase Polymerase Chain Reaction on Oligonucleotide Microarrays

DNA microarray technology holds significant promise for human DNA diagnostics. A number of technical approaches directed at the parallel identification of mutations or single nucleotide polymorphisms make use of polymerase-based specificity, like minisequencing or allele-specific primer elongation. These techniques, however, require separate laborious sample amplification, preparation, and purification steps, making large-scale analyses time and cost consuming. Here, we address this challenge by applying an experimental setup using simultaneous solid and liquid phase PCR on polyethyleneimine-coated glass slides, a novel microarray support allowing on-chip amplification reactions with exquisite specificity. A gene-specific oligonucleotide tiling array contains covalently attached allele-specific primers which interrogate single nucleotide positions within a genomic region of interest. During a thermal cycling reaction amplification products remain covalently bound to the solid support and can be visualized and analyzed by the incorporation of fluorescent dyes. Using the described procedure we unequivocally defined the presence of point mutations in the human tumor suppressor gene p53 directly from a natural DNA source. This semi-multiplex solid phase amplification format allowed the rapid and correct identification of 20 nucleotide positions from minute amounts of human genomic DNA. Our results suggest that this approach might constitute a vital component of future integrated DNA chip devices used in gene analysis.