Multiple primer extension by DNA polymerase on a novel plastic DNA array coated with a biocompatible polymer

PCR- and wash-free detection of serum miRNA via signaling probe hybridization

Detection of microRNAs (miRNAs) in the serum is an effective liquid biopsy technique for cancer diagnosis. However, conventional diagnostic methods are time-consuming and complex. Therefore, in this study, we established a signaling probe-based DNA microarray system for miRNA detection. PCR, fluorescence labeling, and washing are not necessary for signaling probes. Four probes were designed using different miRNAs as diagnostic cancer markers. The developed system is useful for various miRNAs, regardless of their target lengths (18-26-mer) and GC content (36%-89%). Here, all the assays were performed within 40 min. Overall, our signaling probe-based DNA hybridization system facilitates the simple and rapid detection of serum miRNAs without the need for gene amplification, fluorescence labeling and washing.

Cell-membrane-inspired polymers for constructing biointerfaces with efficient molecular recognition

Fabrication of devices that accurately recognize, detect, and separate target molecules from mixtures is a crucial aspect of biotechnology for applications in medical, pharmaceutical, and food sciences. This technology has also been recently applied in solving environmental and energy-related problems. In molecular recognition, biomolecules are typically complexed with a substrate, and specific molecules from a mixture are recognized, captured, and reacted. To increase sensitivity and efficiency, the activity of the biomolecules used for capture should be maintained, and non-specific reactions on the surface should be prevented. This review summarizes polymeric materials that are used for constructing biointerfaces. Precise molecular recognition occurring at the surface of cell membranes is fundamental to sustaining life; therefore, materials that mimic the structure and properties of this particular surface are emphasized in this article. The requirements for biointerfaces to eliminate nonspecific interactions of biomolecules are described. In particular, the major issue of protein adsorption on biointerfaces is discussed by focusing on the structure of water near the interface from a thermodynamic viewpoint; moreover, the structure of polymer molecules that control the water structure is considered. Methodologies enabling stable formation of these interfaces on material surfaces are also presented.

Emerging Phospholipid Nanobiomaterials for Biomedical Applications to Lab-on-a-Chip, Drug Delivery, and Cellular Engineering

The design of advanced nanobiomaterials to improve analytical accuracy and therapeutic efficacy has become an important prerequisite for the development of innovative nanomedicines. Recently, phospholipid nanobiomaterials including 2-methacryloyloxyethyl phosphorylcholine (MPC) have attracted great attention with remarkable characteristics such as resistance to nonspecific protein adsorption and cell adhesion for various biomedical applications. Despite many recent reports, there is a lack of comprehensive review on the phospholipid nanobiomaterials from synthesis to diagnostic and therapeutic applications. Here, we review the synthesis and characterization of phospholipid nanobiomaterials focusing on MPC polymers and highlight their attractive potentials for applications in micro/nanofabricated fluidic devices, biosensors, lab-on-a-chip, drug delivery systems (DDSs), COVID-19 potential usages for early diagnosis and even treatment, and artificial extracellular matrix scaffolds for cellular engineering.

Amplification-free detection of bacterial genes using a signaling probe-based DNA microarray

In this study, we developed a novel DNA microarray system that does not require fluorophore-labeling, amplification, or washing of the target nucleic acid fragments. Two types of DNA probes (so-called "signaling probes") labeled with a fluorescence dye (Cy3) and quencher molecule (BHQ2) were spotted on the DNA microarray such that fluorescent signals of Cy3 could be quenched by BHQ2 due to duplex formation between the probes. The addition of the target DNA or RNA fragments disrupted the duplex formed by the probes, resulting in the generation of fluorescence signals. We examined the assay conditions of the signaling probe-based DNA microarray, including the design of the probes, hybridization temperatures, and methods for fragmentation of target molecules. Since this approach does not require time-consuming processes, including labeling, amplification, and washing, the assay achieved specific detection of 16S rDNA and 16S rRNA extracted from Escherichia coli within 60 min, which was significantly rapid compared to conventional PCR-dependent DNA microarrays.

Synthesis and Characterization of PMBN as A Biocompatible Nanopolymer for Bio-Applications

Objective

Poly [2-methacryloyloxyethyl phosphoryl choline (MPC)-co-n-buthyl methacrylate (BMA)-co-p-nitrophenyl-oxycrabonyl poly ethylene glycol-methacrylate (ME- ONP)] (PMBN), a biocompatible terpolymer, is a unique polymer with applications that range from drug delivery systems (DDS) to scaffolds and biomedical devices. In this research, we have prepared a monomer of p-nitrophenyl-oxycarbonyl poly (ethylene glycol) methacrylate (MEONP) to synthesize this polymer. Next, we designed and prepared a smart, water soluble, amphiphilic PMBN polymer composed of MPC, BMA, and MEONP.

Materials and Methods

In this experimental study, we dissolved MPC (4 mmol, 40% mole fraction), BMA (5 mmol, 50% mole fraction), and MEONP (1 mmol, 10% mole fraction) in 20 ml of dry ethanol in two necked flasks equipped with inlet-outlet gas. The structural characteristics of the synthesized monomer and polymer were determined by Fourier transform infrared spectroscopy (FT-IR), proton nuclear magnetic resonance (H-NMR), dynamic light scattering (DLS), gel permeation chromatography (GPC), scanning electron microscope (SEM), and transmission electron microscope (TEM) analyses for the first time. We treated the polymer with two different cell lines to determine its biocompatibility.

Results

FT-IR and H-NMR analyses confirmed the synthesis of the polymer. The size of polymer was approximately 40 nm with a molecular weight (MW) of 52 kDa, which would be excellent for a nano carrier. Microscopic analyses showed that the polymer was rodshaped. This polymer had no toxicity for individual cells.

Conclusion

We report here, for the first time, the full properties of the PMBN polymer. The approximately 40 nm size with an acceptable zeta potential range of -8.47, PDI of 0.1, and rod-shaped structure indicated adequate parameters of a nanopolymer for nano bioapplications. We used this polymer to design a new smart nano carrier to treat leukemia stem cells based on a target DDS as a type of bio-application.

Photo-assisted generation of phospholipid polymer substrates for regiospecific protein conjugation and control of cell adhesion

Novel photo-reactive phospholipid polymers were synthesized for use in the preparation of nonfouling surfaces with protein conjugation capacity. Poly[2-methacryloyloxyethyl phosphorylcholine (MPC)-ran-N-methacryloyl-(l)-tyrosinemethylester (MAT)] (P(MPC/MAT)) was synthesized by conventional radical polymerization, with the MAT units capable of being oxidized by 254nm UV irradiation. Because of this photo-oxidation, active species such as catechol and quinone were alternately generated in the copolymer. A silicon wafer was subjected to surface modification through spin coating of P(MPC/MAT) from an aqueous solution for use as a model substrate. The surface was then irradiated several times with UV light. The thickness of the polymer layers formed on the Si wafers was influenced by various parameters such as polymer concentration, UV irradiation time, and composition of the MAT units in P(MPC/MAT). Oxidized MAT units were advantageous not only for polymer adhesion to a solid surface but also for protein conjugation with the adhered polymers. The amount of protein immobilized on UV-irradiated P(MPC/MAT) was dependent on the composition of the MAT units in the polymer. Furthermore, it was confirmed that protein immobilization on the polymer occurred through the oxidized MAT units because the protein adsorption was significantly reduced upon blocking these units through pretreatment with glycine. Conjugation of regiospecific protein could also be achieved through the use of a photomask. In addition, nonspecific protein adsorption was reduced on the non-irradiated regions whose surface was covered with physisorbed P(MPC/MAT). Therefore, P(MPC/MAT) can be used in the preparation of nonfouling substrates, which enable micrometer-sized manipulation of proteins through photo-irradiation. Function of proteins immobilized on MPC copolymers was also confirmed by cell adhesion test. As such, photo-reactive MPC copolymers are suitable for performing controlled protein conjugation and preparing polymer-protein hybrid platforms for use in biomedical and diagnostic devices.

STATEMENT OF SIGNIFICANCE

Novel photo-reactive phospholipid polymers have been synthesized for immobilization on solid surfaces and regiospecific protein conjugation. Tyrosine residues embedded in 2-methacryloyloxyethyl phosphorylcholine (MPC) copolymers could be photo-oxidized, resulting in polymers able to form layers on a solid surface and conjugate with proteins. Moreover, nonspecific biofouling on the surface significantly reduced when the oxidized tyrosine units in the polymer layers were blocked. Upon UV irradiation through a photomask, the UV-exposed tyrosine units were selectively oxidized, forming the only specific regions in which protein conjugation could occur.

Crosslinked duplex DNA nanogels that target specified proteins

Specific detection of protein biomarkers plays an important role in diagnostics and therapeutics. We have fabricated polymeric nanogels, which can specifically interact with the cancer biomarker thrombin to serve as a model. Two types of 2-methacryloyloxyethyl phosphorylcholine (MPC) copolymers bearing a thrombin-binding oligonucleotide aptamer and its complementary chain were independently synthesized by redox-initiated radical polymerization. These MPC polymers associate in a complimentary fashion due to double strand formation of the oligonucleotides in aqueous media, leading to the spontaneous formation of spherical nanogels. Nanogel formation was confirmed by dynamic light scattering (DLS) and transmittance microscopy. The average size of nanogel particles was 124 ± 2 nm and the nanogels were mono-dispersed (polydispersity index 0.21). Functional intercalators could be stably incorporated into nanogels through the physical interaction between the intercalators and the oligonucleotides. The ethidium bromide (EtBr)-incorporating nanogels were used as detectors for thrombin. The fluorescence intensity of solutions containing the EtBr-incorporating nanogels was decreased with an increase in the concentration of thrombin. The transformation of quadruplex-thrombin structure from complementary double-stranded structures resulted in the decrease in fluorescence intensity. In contrast, the intensity did not change when the nanogels were incubated with albumin. Thrombin is only one such model used to demonstrate this technique; oligonucleotide aptamers can be freely designed to interact with versatile bio-substances. Therefore, aptamer-crosslinked nanogels can be appropriate nanomaterials for disease diagnosis and therapy.

Genotyping of single nucleotide polymorphisms by melting curve analysis using thin film semi-transparent heaters integrated in a lab-on-foil system

The recent technological advances in micro/nanotechnology present new opportunities to combine microfluidics with microarray technology for the development of small, sensitive, single-use, point-of-care molecular diagnostic devices. As such, the integration of microarray and plastic microfluidic systems is an attractive low-cost alternative to glass based microarray systems. This paper presents the integration of a DNA microarray and an all-polymer microfluidic foil system with integrated thin film heaters, which demonstrate DNA analysis based on melting curve analysis (MCA). A novel micro-heater concept using semi-transparent copper heaters manufactured by roll-to-roll and lift-off on polyethylene naphthalate (PEN) foil has been developed. Using a mesh structure, heater surfaces have been realized in only one single metallization step, providing more efficient and homogenous heating characteristics than conventional meander heaters. A robust DNA microarray spotting protocol was adapted on Parylene C coated heater-foils, using co-polymer poly(DMA-NAS-MAPS) to enable covalent immobilization of DNA. The heaters were integrated in a microfluidic channel using lamination foils and MCA of the spotted DNA duplexes showed single based discrimination of mismatched over matched target DNA-probes. Finally, as a proof of principle, we perform MCA on PCR products to detect the Leu7Pro polymorphism of the neutropeptide Y related to increased risk of Type II diabetes, BMI and depression.

Improved loop-mediated isothermal amplification for HLA-DRB1 genotyping using RecA and a restriction enzyme for enhanced amplification specificity

Our aim was to test and develop the use of loop-mediated isothermal amplification (LAMP) for HLA-DRB1 genotyping. Initially, we found that the conventional LAMP protocols produced non-specific and variable amplification results depending on the sample DNA conditions. Experiments with different concentrations of DNase in the reaction mixture with and without T4 DNA ligase-treated samples suggested that the strand displacement activity of DNA polymerase in LAMP, at least in part, started from randomly existing nicks because T4 DNA ligase treatment of sample DNA resulted in no amplification. Such non-specific amplification due to the randomly existing nicks was improved specifically by the addition of RecA of Escherichia coli and a restriction enzyme, for example, PvuII, to the reaction mixture. We applied the modified LAMP (mLAMP) (1) to detect specific HLA-DRB1 alleles by using only specific primers for amplification or (2) for genotyping in multiple samples with a multi-probe typing system. In the latter case, HLA-DRB1 genotyping was developed by combining the mLAMP with amplicon capture using polymorphic region-specific probes fixed onto the bottom of the wells of a 96-well plate and the captured amplicons visualized as a black spot at the bottom of the well. The multi-probe human leukocyte antigen (HLA) typing method and the specific HLA allele detection method could be applied for point-of-care testing due to no requirement for specific and expensive instruments.

Cell membrane-inspired phospholipid polymers for developing medical devices with excellent biointerfaces

This review article describes fundamental aspects of cell membrane-inspired phospholipid polymers and their usefulness in the development of medical devices. Since the early 1990s, polymers composed of 2-methacryloyloxyethyl phosphorylcholine (MPC) units have been considered in the preparation of biomaterials. MPC polymers can provide an artificial cell membrane structure at the surface and serve as excellent biointerfaces between artificial and biological systems. They have also been applied in the surface modification of some medical devices including long-term implantable artificial organs. An MPC polymer biointerface can suppress unfavorable biological reactions such as protein adsorption and cell adhesion - in other words, specific biomolecules immobilized on an MPC polymer surface retain their original functions. MPC polymers are also being increasingly used for creating biointerfaces with artificial cell membrane structures.

Direct immobilization of DNA probes on non-modified plastics by UV irradiation and integration in microfluidic devices for rapid bioassay

DNA microarrays have become one of the most powerful tools in the field of genomics and medical diagnosis. Recently, there has been increased interest in combining microfluidics with microarrays since this approach offers advantages in terms of portability, reduced analysis time, low consumption of reagents, and increased system integration. Polymers are widely used for microfluidic systems, but fabrication of microarrays on such materials often requires complicated chemical surface modifications, which hinders the integration of microarrays into microfluidic systems. In this paper, we demonstrate that simple UV irradiation can be used to directly immobilize poly(T)poly(C)-tagged DNA oligonucleotide probes on many different types of plastics without any surface modification. On average, five- and fourfold improvement in immobilization and hybridization efficiency have been achieved compared to surface-modified slides with aminated DNA probes. Moreover, the TC tag only costs 30% of the commonly used amino group modifications. Using this microarray fabrication technique, a portable cyclic olefin copolymer biochip containing eight individually addressable microfluidic channels was developed and used for rapid and parallel identification of Avian Influenza Virus by DNA hybridization. The one-step, cost-effective DNA-linking method on non-modified polymers significantly simplifies microarray fabrication procedures and permits great flexibility to plastic material selection, thus making it convenient to integrate microarrays into plastic microfluidic systems.

Effects of lateral spacing on enzymatic on-chip DNA polymerization

Enzymatic on-chip DNA polymerization can be utilized to elongate surface-bound primers with DNA polymerase and to enhance the signal in the detection of target DNAs on the solid support. In order to investigate the steric effect of the enzymatic reaction on the solid support, we compared the efficiency of on-chip DNA polymerization on a high-density surface with that on a spacing-controlled surface. The spacing-controlled, 9-acid dendron-coated surface exhibited approximately 8-fold higher efficiency of on-chip DNA polymerization compared with the high-density surface. The increase in fluorescence intensity during the on-chip DNA polymerization could be fit to an exponential equation, and the saturation level of the 9-acid dendron slide was 7 times higher than that of the high-density slide. The on-chip DNA polymerization was employed to measure the transcription level of nine genes related to epithelial-to-mesenchymal transition in hepatocellular carcinoma cells. Compared to the high-density surface, the dendron-coated surface exhibited a lower detection limit in the on-chip DNA polymerization and higher correlation with transcription levels as determined by quantitative real-time PCR. Our results suggest that control of the lateral spacing of DNA strands on the solid support should significantly enhance the accessibility of DNA polymerase and the efficiency of the on-chip DNA polymerization.

In situ synthesis of DNA microarray on functionalized cyclic olefin copolymer substrate

Thermoplastic materials such as cyclic-olefin copolymers (COC) provide a versatile and cost-effective alternative to the traditional glass or silicon substrate for rapid prototyping and industrial scale fabrication of microdevices. To extend the utility of COC as an effective microarray substrate, we developed a new method that enabled for the first time in situ synthesis of DNA oligonucleotide microarrays on the COC substrate. To achieve high-quality DNA synthesis, a SiO(2) thin film array was prepatterned on the inert and hydrophobic COC surface using RF sputtering technique. The subsequent in situ DNA synthesis was confined to the surface of the prepatterned hydrophilic SiO(2) thin film features by precision delivery of the phosphoramidite chemistry using an inkjet DNA synthesizer. The in situ SiO(2)-COC DNA microarray demonstrated superior quality and stability in hybridization assays and thermal cycling reactions. Furthermore, we demonstrate that pools of high-quality mixed-oligos could be cleaved off the SiO(2)-COC microarrays and used directly for construction of DNA origami nanostructures. It is believed that this method will not only enable synthesis of high-quality and low-cost COC DNA microarrays but also provide a basis for further development of integrated microfluidics microarrays for a broad range of bioanalytical and biofabrication applications.

Modified multiple primer extension method

A multiple primer extension (MPEX) was originally developed for the hybridization, extension, and amplification of a DNA template on a planar substrate by Kinoshita et al. in 2006. Herein we present a modified MPEX method refined by our group for single nucleotide polymorphism (SNP) detection. In this method, hybridization and extension reactions are performed on a plastic S-BIO PrimeSurface substrate, with a biocompatible polymer. Its surface chemistry offers extraordinarily stable thermal properties, as well as chemical properties advantageous for enzymatic reactions on the surface. To visualize allele-specific PCR products on the surface, biotin-dUTP was incorporated into newly synthesized complementary strands during the extension reaction. The products were ultimately detected by carrying out a colorimetric reaction with a substrate solution containing 5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium. We have further successfully combined this method with multiplex PCR. We demonstrate the advantages of this combined method by analyzing representative SNPs on different linkage disequilibrium blocks of the micro opioid receptor gene (OPRM1), which is a marker gene for pain threshold.

Quantitation of non-amplified genomic DNA by bead-based hybridization and template mediated extension coupled to alkaline phosphatase signal amplification

Klenow I polymerase activity was combined with solid phase DNA hybridization to detect non-amplified genomic DNA (gDNA) sequences from Escherichia coli. Aminopropyl-controlled pore glass surface-bound oligonucleotides were hybridized to fragmented gDNA. The template-mediated extension at the 3'-terminus of the immobilized probe was then promoted in the presence of Klenow I polymerase and digoxigenin-labeled nucleotides. Detection of the extended probes was accomplished with an anti-digoxigenin alkaline phosphatase conjugate protocol coupled to colorimetric or fluorescent detection. Using the colorimetric protocol, the proof-of-concept was established. The fluorescence-based methodology, on the other hand, provided the basis for a quantitative interpretation of the data, affording a detection limit of 5 pM gDNA.

Bioinspired interface for nanobiodevices based on phospholipid polymer chemistry

This review paper describes novel biointerfaces for nanobiodevices. Biocompatible and non-biofouling surfaces are designed largely based on cell membrane structure, and the preparation and functioning of the bioinspired interface are evaluated and compared between living and artificial systems. A molecular assembly of polymers with a phospholipid polar group has been developed as the platform of the interface. At the surface, protein adsorption is effectively reduced and the subsequent bioreactions are suppressed. Through this platform, biomolecules with a high affinity to the specific molecules are introduced under mild conditions. The activity of the biomolecules is retained even after immobilization. This bioinspired interface is adapted to construct bionanodevices, that is, microfluidic chips and nanoparticles for capturing target molecules and cells. The interface functions well and has a very high efficiency for biorecognition. This bioinspired interface is a promising universal platform that integrates various fields of science and has useful applications.

All-in-one tube method for quantitative gene expression analysis in oligo-dT(30) immobilized PCR tube coated with MPC polymer

In this report, we have developed a novel quantitative RT-PCR protocol in which the procedure including mRNA purification can be performed in an all-in-one tube. To simplify gene expression analysis, oligo-dT(30) immobilized PCR tubes were used serially to capture mRNA, synthesize solid-phase cDNA, and amplify specific genes. The immobilized oligo-dT(30) can efficiently capture mRNA directly from crude human cell lysates. The captured mRNA is then amplified by one-step reverse transcription PCR (RT-PCR) with initial cDNA synthesis followed by PCR. In RT-PCR, this new reusable PCR tube device can be employed for multiple PCR amplifications with different primer sets from a solid-phase oligo-dT(30) primed cDNA library. This paper introduces a novel and highly reliable all-in-one tube method for rapid cell lysis, followed by quantitative preparation and expression analysis of target mRNA molecules with small amounts of sample. This procedure allows all steps to be carried out by sequential dilution in a single tube, without chemical extraction. We demonstrate the utility of this novel method by quantification of two housekeeping genes, beta-actin and GAPDH, in HeLa cells. We believe this new PCR device can be useful as a platform for various mRNA expression analyses, including basic research, drug screening, and molecular toxicology, as well as for molecular pathological diagnostics.

Immobilization chemistries

Among the parameters which influence the success of a microarray experiment, the attachment of the nucleic acid captures to the support surface plays a decisive role.This article attempts to review the main concepts and ideas of the multiple variants which exist in terms of the immobilization chemistries used in nucleic acid microarray technology. Starting from the attachment of unmodified nucleic acids to modified glass slides by adsorption, further strategies for the coupling of nucleic acid capture molecules to a variety of support materials are surveyed with a focus on the reactive groups involved in the respective process.After a brief introduction, an overview is given about microarray substrates with special emphasis on the approaches used for the activation of these - usually chemically inert - materials. In the next sections strategies for the "undefined" and "defined" immobilization of captures on the substrates are described. While the latter approach tries to accomplish the coupling via a defined reactive moiety of the molecule to be immobilized, the former mentioned techniques involve multiply occurring reactive groups in the capture.The article finishes with an example for microarray manufacture, the production of aminopropyltriethoxysilane (APTES) functionalized glass substrates to which PDITC homobifunctional linker molecules are coupled; on their part providing reactive functional groups for the covalent immobilization of pre-synthesized, amino-modified oligonucleotides.This survey does not seek to be comprehensive rather it tries to present and provide key examples for the basic techniques, and to enable orientation if more detailed studies are needed. This review should not be considered as a guide to how to use the different chemistries described, but instead as a presentation of various principles and approaches applied in the still evolving field of nucleic acid microarray technology.

Plastic polymers for efficient DNA microarray hybridization: application to microbiological diagnostics

Fabrication of microarray devices using traditional glass slides is not easily adaptable to integration into microfluidic systems. There is thus a need for the development of polymeric materials showing a high hybridization signal-to-background ratio, enabling sensitive detection of microbial pathogens. We have developed such plastic supports suitable for highly sensitive DNA microarray hybridizations. The proof of concept of this microarray technology was done through the detection of four human respiratory viruses that were amplified and labeled with a fluorescent dye via a sensitive reverse transcriptase PCR (RT-PCR) assay. The performance of the microarray hybridization with plastic supports made of PMMA [poly(methylmethacrylate)]-VSUVT or Zeonor 1060R was compared to that with high-quality glass slide microarrays by using both passive and microfluidic hybridization systems. Specific hybridization signal-to-background ratios comparable to that obtained with high-quality commercial glass slides were achieved with both polymeric substrates. Microarray hybridizations demonstrated an analytical sensitivity equivalent to approximately 100 viral genome copies per RT-PCR, which is at least 100-fold higher than the sensitivities of previously reported DNA hybridizations on plastic supports. Testing of these plastic polymers using a microfluidic microarray hybridization platform also showed results that were comparable to those with glass supports. In conclusion, PMMA-VSUVT and Zeonor 1060R are both suitable for highly sensitive microarray hybridizations.

Visible Genotype Sensor Array

A visible sensor array system for simultaneous multiple SNP genotyping has been developed using a new plastic base with specific surface chemistry. Discrimination of SNP alleles is carried out by an allele-specific extension reaction using immobilized oligonucleotide primers. The 3'-ends of oligonucleotide primers are modified with a locked nucleic acid to enhance their efficiency in allelic discrimination. Biotin-dUTPs included in the reaction mixture are selectively incorporated into extending primer sequences and are utilized as tags for alkaline phosphatase-mediated precipitation of colored chemical substrates onto the surface of the plastic base. The visible precipitates allow immediate inspection of typing results by the naked eye and easy recording by a digital camera equipped on a commercial mobile phone. Up to four individuals can be analyzed on a single sensor array and multiple sensor arrays can be handled in a single operation. All of the reactions can be performed within one hour using conventional laboratory instruments. This visible genotype sensor array is suitable for "focused genomics" that follows "comprehensive genomics".

A novel SNP detection technique utilizing a multiple primer extension (MPEX) on a phospholipid polymer-coated surface

Conventional methods for detecting single nucleotide polymorphisms (SNPs), including direct DNA sequencing, pyrosequencing, and melting curve analysis, are to a great extent limited by their requirement for particular detection instruments. To overcome this limitation, we established a novel SNP detection technique utilizing multiple primer extension (MPEX) on a phospholipid polymer-coated surface. This technique is based on the development of a new plastic S-BIO PrimeSurface with a biocompatible polymer; its surface chemistry offers extraordinarily stable thermal properties, as well as chemical properties advantageous for enzymatic reactions on the surface. To visualize allele-specific PCR products on the surface, biotin-dUTP was incorporated into newly synthesized PCR products during the extension reaction. The products were ultimately detected by carrying out a colorimetric reaction with substrate solution containing 4-nitro-blue tetrazolium chloride (NBT) and 5-bromo-4-chloro-3-indolyl phosphate (BCIP). We demonstrated the significance of this novel SNP detection technique by analyzing representative SNPs on 4 LD blocks of the micro opioid receptor gene. We immobilized 20 allele-specific oligonucleotides on this substrate, and substantially reproduced the results previously obtained by other methods.