Diagnosis of HNF-1alpha mutations on a PNA zip-code microarray by single base extension

Separation-free single-base extension assay with fluorescence resonance energy transfer for rapid and convenient determination of DNA methylation status at specific cytosine and guanine dinucleotide sites

A separation-free single-base extension (SBE) assay utilizing fluorescence resonance energy transfer (FRET) was developed for rapid and convenient interrogation of DNA methylation status at specific cytosine and guanine dinucleotide sites. In this assay, the SBE was performed in a tube using an allele-specific oligonucleotide primer (i.e., extension primer) labeled with Cy3 as a FRET donor fluorophore at the 5'-end, a nucleotide terminator (dideoxynucleotide triphosphate) labeled with Cy5 as a FRET acceptor, a PCR amplicon derived from bisulfite-converted genomic DNA, and a DNA polymerase. A single base-extended primer (i.e., SBE product) that was 5'-Cy3- and 3'-Cy5-tagged was formed by incorporation of the Cy5-labeled terminator into the 3'-end of the extension primer, but only if the terminator added was complementary to the target nucleotide. The resulting SBE product brought the Cy3 donor and the Cy5 acceptor into close proximity. Illumination of the Cy3 donor resulted in successful FRET and excitation of the Cy5 acceptor, generating fluorescence emission from the acceptor. The capacity of the developed assay to discriminate as low as 10% methylation from a mixture of methylated and unmethylated DNA was demonstrated at multiple cytosine and guanine dinucleotide sites.

Ultrasensitive DNA detection based on target-triggered rolling circle amplification and fluorescent poly(thymine)-templated copper nanoparticles

An ultrasensitive DNA detection method is developed based on target-triggered rolling circle amplification coupled with fluorescent poly(thymine)-templated copper nanoparticles.

Light-Directed Synthesis of High-Density Peptide Nucleic Acid Microarrays

Peptide nucleic acids (PNAs) are a class of nucleic acid mimics that can bind to the complementary DNA or RNA with high specificity and sensitivity. PNA-based microarrays have distinct characteristics and have improved performance in many aspects compared to DNA microarrays. A new set of PNA monomers has been synthesized and used as the building blocks for the preparation of high density PNA microarrays. These monomers have their backbones protected by the photolabile group 2-(2-nitrophenyl)propyloxy carbonyl (NPPOC), and their exocyclic amino groups protected by amide carbonyl groups. A light-directed synthesis system was designed and applied to the in situ synthesis of a PNA microarray with a density of over 10,000 probes per square centimeter. This PNA microarray was able to detect single and multiple base-mismatches correctly with a high discrimination ratio.

Universal probe amplification: multiplex screening technologies for genetic variations

In order to achieve multiplex screening of genetic variations, multiplex amplification of target genomic DNA is necessary. Universal amplification technology meets this requirement by simultaneously amplifying a number of different regions within the target genomic DNA using a single pair of universal primers and thus eliminating the limitations associated with the use of multiple pairs of primers. We comprehensively review universal probe amplification and its use with multiplex technologies for the identification of the most representative genetic variation, i. e. single nucleotide polymorphisms. The progress and key issues relating to universal probe amplification are discussed and the representative technologies are summarized with an emphasis on their application for the identification of susceptibility to human diseases.

Application of the ASLP technology to a novel platform for rapid and noise-free multiplexed SNP genotyping

A novel multiplexing method, which relies on universal amplification of separated ligation-dependent probes (ASLP), has been developed to genotype single-nucleotide polymorphisms (SNPs). The ASLP technique employs two allele-specific oligonucleotides (ASO), modified with universal forward primer sequences at the 5'-end and a common locus-specific oligonucleotide (LSO) extended with a universal separation (US) sequence at the 3'-end. In the process, allele-specific ligation first takes place when target genomic DNA is hybridized by perfectly matching the ASO together with the LSO. A separation probe, which consists of a universal reverse primer sequence labeled with biotin at the 5'-end and complementary sequence of US at the 3'-end, is then applied to the resulting ligation product. During the extension reaction of the separation probe, the ligated probes dissociate from target genomic DNA in the form of a double-stranded DNA and are separated from the reaction mixture, which includes genomic DNA and unligated probes, by simply using streptavidin-coated magnetic beads. PCR amplification of the separated ligation products is then carried out by using universal primers and the PCR products are hybridized on a DNA microarray using the RecA protein. The advantageous features of the new method were demonstrated by using it to genotype 15 SNP markers for cultivar identification of pepper in a convenient and correct manner.

Charge-neutral morpholino microarrays for nucleic acid analysis

A principal challenge in microarray experiments is to facilitate hybridization between probe strands on the array with complementary target strands from solution while suppressing any competing interactions that the probes and targets may experience. Synthetic DNA analogs, whose hybridization to targets can exhibit qualitatively different dependence on experimental conditions than for nucleic acid probes, open up an attractive alternative for improving selectivity of array hybridization. Morpholinos (MOs), a class of uncharged DNA analogs, are investigated as microarray probes instead of DNA. MO microarrays were fabricated by contact printing of amino-modified probes onto aldehyde slides. In addition to covalent immobilization, MOs were found to efficiently immobilize through physical adsorption; such physically adsorbed probes could be removed by post-printing washes with surfactant solutions. Hybridization of double-stranded DNA targets to MO microarrays revealed a hybridization maximum at intermediate ionic strengths. The decline in hybridization at lower ionic strengths was attributed to an electrostatic barrier accumulated from hybridized DNA targets, whereas at higher ionic strengths it was attributed to stabilization of target secondary structure in solution. These trends, which illustrate ionic strength tuning of forming on-array relative to solution secondary structure, were supported by a stability analysis of MO/DNA and DNA/DNA duplexes in solution.

Membrane-based hybridization capture of intracellular peptide nucleic acid

Peptide nucleic acid (PNA) is a chimeric oligonucleotide with nucleotide-derived bases and a peptide backbone. Compared with natural nucleotides, PNA has several advantages, including improved stability and high sequence discrimination during duplex formation. Despite its potential for therapeutic application, analysis technologies have not been generalized, mainly due to ambiguous physiochemical properties resembling those of nucleic acids as well as protein. Here we present a PNA detection method: sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by electrotransfer to a Western blotting membrane and then hybridization with a radiolabeled oligonucleotide probe. This method is useful for evaluating the quality of synthetic PNA and determining its intracellular localization.

An electrochemical molecular switch for one-step, reusable detection of a single-base mutation of DNA

A new strategy for one-step, reusable and sensitive detection of a single-base mutation based on an electrochemical molecular switch is developed in the present work. When the hybridization reaction takes place in the presence of target DNA, the Fc-labeled terminal of the open switch molecule can be captured by the probe through the predesigned complementary bases of both sequences. By this method, a signal-on sensor featuring both generalizability and simplicity towards reagentless detection of DNA with sensitivity and selectivity electrochemical system is built on. The approach had been demonstrated with the identification of a single-base mutation of alpha-thalassemia point mutation in Hb Constant Spring codon 142 (TAA --> CAA). The wild-type and mutant-type of the synthetic 16 mer DNA sequences as the model targets were successfully discriminated. The results showed that the response signal was linear to the logarithm of the target concentration in the range from 0.01 to 100 pM with a detection limit of 0.01 pM. The regeneration experiment demonstrated that the sensor interface can be easily and successfully regenerated. All these revealed that the present system is a promising candidate for single-base mutation discrimination.

Peptide nucleic acid-based array for detecting and genotyping human papillomaviruses

We describe a novel array for accurate and reliable genotyping of human papillomavirus (HPV) using peptide nucleic acid (PNA) probes. In order to exploit the superior hybridization properties of PNA with target HPV DNAs, we developed a novel PNA array (PANArray HPV). PANArray HPV enables the detection and genotyping of HPVs using 32 type-specific PNA capture probes for medically important HPVs. All tested HPV types showed highly unique hybridization patterns with type-specific PNA probes. PNA array results showed stable specificities and sensitivities after up to 13 months of storage at room temperature. Also, we demonstrated the superior specificity, sensitivity, and stability of PNA arrays for HPV genotyping. We compared the genotyping results of the PNA array to sequencing with MY09/11 PCR products derived from 72 clinical samples. The results showed excellent agreement between the PNA array and sequencing, except for samples reflecting multiple infections. The results from the PNA array were compared with those of type-specific PCR when discrepant results occurred owing to multiple infections. The results for the PNA array matched those of type-specific PCR in all cases. Newly developed PNA arrays show excellent specificity and sensitivity and long shelf life. Our results suggest that the PNA array represents a reliable alternative to conventional DNA arrays for HPV genotyping, as well as for diagnostics.

A simple gold nanoparticle-mediated immobilization method to fabricate highly homogeneous DNA microarrays having higher capacities than those prepared by using conventional techniques

A simple, highly efficient immobilization method to fabricate DNA microarrays, that utilizes gold nanoparticles as the mediator, has been developed. The fabrication method begins with electrostatic attachment of amine-modified DNA to gold nanoparticles. The resulting gold-DNA complexes are immobilized on conventional amine or aldehyde functionalized glass slides. By employing gold nanoparticles as the immobilization mediator, implementation of this procedure yields highly homogeneous microarrays that have higher binding capacities than those produced by conventional methods. This outcome is due to the increased three-dimensional immobilization surface provided by the gold nanoparticles as well as the intrinsic effects of gold on emission properties. This novel immobilization strategy gives microarrays that produce more intense hybridization signals for the complementary DNA. Furthermore, the silver enhancement technique, made possible only in the case of immobilized gold nanoparticles on the microarrays, enables simple monitoring of the integrity of the immobilized DNA probe.

A polydiacetylene microchip based on a biotin-streptavidin interaction for the diagnosis of pathogen infections

A micropatterned polydiacetylene (PDA) chip, utilizing the unique fluorogenic property of PDA and a specific biotin-streptavidin (STA) interaction, is constructed to detect pathogen infections. To construct the PDA chip, biotin-modified diacetylene liposomes are immobilized on aldehyde glass and conjugated with STA, followed by UV irradiation to polymerize the STA-functionalized diacetylene liposomes. Genomic DNA of a model pathogen, Chlamydia trachomatis, is isolated from human samples and biotin-labeled target DNA is obtained through PCR amplification using biotin-11-dUTP. Owing to the stimulus caused by the biotin-STA interaction, the biotinylated DNA induces an intense fluorescence signal on the immobilized PDA. By using this strategy, it is possible to diagnose Chlamydia infections by applying DNA samples from several nonhealthy humans to a single PDA chip. The results of this study serve as the basis for a new strategy for fluorogenic PDA microarray-based diagnosis of pathogen infections.

SNPs detection by a single-strand specific nuclease on a PNA zip-code microarray

In this report, a reliable peptide nucleic acid (PNA) microarray-based method for accurately detecting single nucleotide polymorphism (SNP) in human genes is described. The technique relies on the mismatched cleavage activity of a single-strand specific (SSS) nuclease. PCR amplification was performed to prepare gene fragments containing the mutation sites. The amplified fragments were then employed as templates for the SSS nuclease reaction using chimeric probes, modified with biotin at the 5' end and extended with a unique anchoring zip-code complement sequence at the 3' end. The SSS nuclease promotes cleavage of heteroduplex DNAs at base mismatched positions to produce crumbled chimeric probes in the presence of imperfectly matching template strands. In contrast, the probes remain intact when they interact with perfectly matched template strands. Only the non-fragmented probes generate fluorescence signals after treatment with streptavidin-Cy3 on the PNA zip-code array. This methodology was used to successfully genotype selected Korean-specific BRCA mutation sites with wild type and mutant samples. The investigation has led to the development of a reliable SSS nuclease-based system for the diagnosis of human genetic mutations or SNPs.

Direct and nondestructive verification of PNA immobilization using click chemistry

The fluorogenic 1,3-Huisgen dipolar cycloaddition reaction was used as part of a novel immobilization strategy of PNA capture probes on a microarray. By using this click chemistry, azidocoumarin-anchored PNA probes were immobilized on phenyl acetylene-modified glass slides with the simultaneous generation of the fluorescent triazolylcoumarin moiety. Since the emitting moieties are generated in the immobilization reaction itself, fluorescent signals can be used to directly monitor the integrity of immobilization in a nondestructive manner. By using this strategy, PNA microarrays were prepared and successfully employed to perform microarray-based diagnosis of selected mutations in the breast cancer susceptibility gene BRCA1.

Towards an automatic classification of protein structural domains based on structural similarity

Background

Formal classification of a large collection of protein structures aids the understanding of evolutionary relationships among them. Classifications involving manual steps, such as SCOP and CATH, face the challenge of increasing volume of available structures. Automatic methods such as FSSP or Dali Domain Dictionary, yield divergent classifications, for reasons not yet fully investigated. One possible reason is that the pairwise similarity scores used in automatic classification do not adequately reflect the judgments made in manual classification. Another possibility is the difference between manual and automatic classification procedures. We explore the degree to which these two factors might affect the final classification.

Results

We use DALI, SHEBA and VAST pairwise scores on the SCOP C class domains, to investigate a variety of hierarchical clustering procedures. The constructed dendrogram is cut in a variety of ways to produce a partition, which is compared to the SCOP fold classification.

Ward's method dendrograms led to partitions closest to the SCOP fold classification. Dendrogram- or tree-cutting strategies fell into four categories according to the similarity of resulting partitions to the SCOP fold partition. Two strategies which optimize similarity to SCOP, gave an average of 72% true positives rate (TPR), at a 1% false positive rate. Cutting the largest size cluster at each step gave an average of 61% TPR which was one of the best strategies not making use of prior knowledge of SCOP. Cutting the longest branch at each step produced one of the worst strategies.

We also developed a method to detect irreducible differences between the best possible automatic partitions and SCOP, regardless of the cutting strategy. These differences are substantial. Visual examination of hard-to-classify proteins confirms our previous finding, that global structural similarity of domains is not the only criterion used in the SCOP classification.

Conclusion

Different clustering procedures give rise to different levels of agreement between automatic and manual protein classifications. None of the tested procedures completely eliminates the divergence between automatic and manual protein classifications. Achieving full agreement between these two approaches would apparently require additional information.

Enzyme-catalyzed signal amplification for electrochemical DNA detection with a PNA-modified electrode

The signal amplification technique of peptide nucleic acid (PNA)-based electrochemical DNA sensor was developed in a label-free and one-step method utilizing enzymatic catalysis. Electrochemical detection of DNA hybridization on a PNA-modified electrode is based on the change of surface charge caused by the hybridization of negatively charged DNA molecules. The negatively charged mediator, ferrocenedicarboxylic acid, cannot diffuse to the DNA hybridized electrode surface due to the charge repulsion with the hybridized DNA molecule while it can easily approach the neutral PNA-modified electrode surface without the hybridization. By employing glucose oxidase catalysis on this PNA-based electrochemical system, the oxidized mediator could be immediately reduced leading to greatly increased electrochemical signals. Using the enzymatic strategy, we successfully demonstrated its clinical utility by detecting one of the mutation sequences of the breast cancer susceptibility gene BRCA1 at a sample concentration lower than 10(-9) M. Furthermore, a single base-mismatched sample could be also discriminated from a perfectly matched sample.

Technology insight: microarrays--research and clinical applications

For microarrays, the transition from research to clinical and diagnostic applications is well underway. Microarrays use a range of specific probes that are immobilized in known locations on a support matrix; this technique can measure levels of specific DNA, RNA and proteins, as well as carbohydrates and lipids. It is anticipated that analysis of these levels will lead to identification of biomarkers for the diagnosis, treatment and prognosis of a wide range of diseases. So far, this type of analysis has been particularly useful in clinical oncology, but the technology is being actively and successfully explored for diseases such as diabetes, endocrine tumors and endocrine modulators of tumors. There are now many commercial sources of microarrays, which have robust quality-control procedures in place. Progress will be enhanced when biomarkers can be established, statistical approaches can be refined and when we better understand the interactions of genes and of particular gene loci in disease progression.

Oligonucleotide microarrays: immobilization of phosphorylated oligonucleotides on epoxylated surface

A facile and efficient method for direct immobilization of phosphorylated oligonucleotides on an epoxy-activated glass surface is described. The new immobilization strategy has been analyzed for its performance in DNA microarray under both microwave and thermal conditions. It reflects high immobilization efficiency ( approximately 23%), and signal-to-noise ratio ( approximately 98) and resulted in high hybridization efficiency ( approximately 36%) in comparison to those obtained with standard methods, viz., NTMTA ( approximately 9.76%) and epoxide-amine ( approximately 9.82%). The probes immobilized through the new strategy were found to be heat-stable, since the performance of microarray decreased by only approximately 7% after subjecting it to 20 PCR-like heat cycles, suggesting that the chemistry could be used in integrated PCR/microarray devices. The immobilization of probes following the proposed chemistry resulted in spots of superior quality in terms of spot morphology, spot homogeneity, and signal reproducibility. The constructed microarrays have been successfully used for the discrimination of nucleotide mismatches. In conclusion, these features make the new immobilization strategy ideal for facile, efficient, and cost-effective manufacturing of DNA microarrays.

Light-directed synthesis of peptide nucleic acids (PNAs) chips

We report herein the light-directed synthesis of peptide nucleic acids (PNAs) microarray using PNA monomers protected by photolabile protecting groups and a maskless technique that uses a digital micromirror array system to form virtual masks. An ultraviolet image from the virtual mask was cast onto the active surface of a glass substrate, which was mounted in a flow cell reaction chamber connected to a peptide synthesizer. Light exposure was followed by automatic chemical coupling cycles and these steps were repeated with different virtual masks to grow the desired PNA probes in a selected pattern. In a preliminary experiment, an array of PNA probes with dimensions of 4.11 mm x 4.11 mm was generated on each slide. Each synthesis region in the final array measured 210 microm x 210 microm for a total of 256 sites. The center-to-center space was 260 microm. It was observed from the hybridization pattern of the fluorescently labeled oligonucleotide targets that the fluorescence intensities of the matched, and mismatched sequences showed substantial difference, demonstrating specificity in the identification of complementary sequences. This opens the way to exploit processes from the microelectronics industry for the fabrication of PNA microarrays with high densities.

Surface plasmon resonance imaging on a microchip for detection of DNA-modified gold nanoparticles deposited onto the surface in a non-cross-linking configuration

Recently we reported that gold nanoparticles (GNPs) with fully matched duplexes on their surfaces are selectively deposited onto walls of poly(dimethylsiloxane) (PDMS) microchannels at high salt concentrations. In this study, the surface plasmon resonance (SPR) imaging technique was applied to monitor this phenomenon for improvement of detection sensitivity and elucidation of the phenomenon. The microchip was fabricated by bonding a surface-patterned PDMS plate and a gold thin film-deposited glass substrate. Probe oligonucleotide-modified GNPs were hybridized with target oligonucleotides to make fully matched or single-base-mismatched duplexes. The hybridized GNP solution was mixed with an NaCl solution in a Y-shaped microchannel. The deposition of the GNPs onto the gold sensor surface was detected by SPR imaging. Discrimination of the targets was possible with limit of detection of 32 nM (19 fmol) without temperature control in 5 min. Detailed analysis indicated that a seed layer of GNPs was initially adsorbed onto the sensor surface regardless of the target sequence. Therefore, in combination with a portable SPR device, the proposed method is promising for point-of-care testing of single-nucleotide polymorphsims.

ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification

Background

Current classification of protein folds are based, ultimately, on visual inspection of similarities. Previous attempts to use computerized structure comparison methods show only partial agreement with curated databases, but have failed to provide detailed statistical and structural analysis of the causes of these divergences.

Results

We construct a map of similarities/dissimilarities among manually defined protein folds, using a score cutoff value determined by means of the Receiver Operating Characteristics curve. It identifies folds which appear to overlap or to be "confused" with each other by two distinct similarity measures. It also identifies folds which appear inhomogeneous in that they contain apparently dissimilar domains, as measured by both similarity measures. At a low (1%) false positive rate, 25 to 38% of domain pairs in the same SCOP folds do not appear similar. Our results suggest either that some of these folds are defined using criteria other than purely structural consideration or that the similarity measures used do not recognize some relevant aspects of structural similarity in certain cases. Specifically, variations of the "common core" of some folds are severe enough to defeat attempts to automatically detect structural similarity and/or to lead to false detection of similarity between domains in distinct folds. Structures in some folds vary greatly in size because they contain varying numbers of a repeating unit, while similarity scores are quite sensitive to size differences. Structures in different folds may contain similar substructures, which produce false positives. Finally, the common core within a structure may be too small relative to the entire structure, to be recognized as the basis of similarity to another.

Conclusion

A detailed analysis of the entire available protein fold space by two automated similarity methods reveals the extent and the nature of the divergence between the automatically determined similarity/dissimilarity and the manual fold type classifications. Some of the observed divergences can probably be addressed with better structure comparison methods and better automatic, intelligent classification procedures. Others may be intrinsic to the problem, suggesting a continuous rather than discrete protein fold space.

Optical technologies for the read out and quality control of DNA and protein microarrays

Microarray formats have become an important tool for parallel (or multiplexed) monitoring of biomolecular interactions. Surface-immobilized probes like oligonucleotides, cDNA, proteins, or antibodies can be used for the screening of their complementary targets, covering different applications like gene or protein expression profiling, analysis of point mutations, or immunodiagnostics. Numerous reviews have appeared on this topic in recent years, documenting the intriguing progress of these miniaturized assay formats. Most of them highlight all aspects of microarray preparation, surface chemistry, and patterning, and try to give a systematic survey of the different kinds of applications of this new technique. This review places the emphasis on optical technologies for microarray analysis. As the fluorescent read out of microarrays is dominating the field, this topic will be the focus of the review. Basic principles of labeling and signal amplification techniques will be introduced. Recent developments in total internal reflection fluorescence, resonance energy transfer assays, and time-resolved imaging are addressed, as well as non-fluorescent imaging methods. Finally, some label-free detection modes are discussed, such as surface plasmon microscopy or ellipsometry, since these are particularly interesting for microarray development and quality control purposes.

Development of a peptide nucleic acid array platform for the detection of genetically modified organisms in food

Two previously developed platforms, a multiplex polymerase chain reaction (PCR) and a peptide nucleic acid (PNA) array, the former allowing for the simultaneous detection of five transgenes and two endogenous controls in food and feed matrices and the latter for the assessment of the identity of amplified PCR products, were combined in order to develop a PNA array device for the screening of genetically modified organisms (GMOs) in food. PNA probes were opportunely designed, synthesized, and deposited on commercial slides. The length of the probes as well as the distance of the probes from the surface were evaluated and found to be critical points. The most suitable probes were found to be 15-mer PNAs linked to the slide surface by means of two 2-(2-aminoethoxy)ethoxyacetic acids as spacers. The device was tested on a model system constituted by flour samples containing a mixture of standards at known concentrations of transgenic material, in particular Roundup Ready soybean and Bt11, Bt176, Mon810, and GA21 maize: The DNA was amplified using the specific multiplex PCR method and tested on the PNA array. The method proposed was found to be able to correctly identify every GMO present in the tested samples.