cDNA Labeling Strategies for Microarrays Using Fluorescent Dyes

Palladium-Catalyzed Synthesis of (E)-5-(3-Aminoallyl)-Uridine-5'-O-Triphosphates

This unit describes a simple, reliable, and efficient chemical method for the synthesis of 5-(3-aminoallyl)-2'-deoxyuridine-5'-O-triphosphate (AA-dUTP) and 5-(3-aminoallyl)-uridine-5'-O-triphosphate (AA-UTP), starting from the corresponding nucleoside triphosphate. The presented strategy involves regioselective iodination of nucleoside triphosphate using N-iodosuccinimide followed by the palladium-catalyzed Heck coupling with allylamine to provide the corresponding (E)-5-aminoallyl-uridine-5'-O-triphosphate in good yields. It is noteworthy that the protocol not only provides a high-purity product but also eliminates the use of toxic mercuric reagents. © 2017 by John Wiley & Sons, Inc.

A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina

Background

The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of de novo gene prediction programs, and annotation up-dating. We present a novel in silico procedure which addresses these issues and includes experimental screening, as an empirical approach is the best strategy to identify optimal probes in the in silico outcome.

Findings

We used four criteria for in silico probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS), we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus Podospora anserina and the selection of a single 60-mer probe for each of the 10,556 P. anserina CDS.

Conclusions

A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis.

High density labeling of polymerase chain reaction products with the fluorescent base analogue tCo

Fluorescent DNA of high molecular weight is an important tool for studying the physical properties of DNA and DNA-protein interactions, and it plays a key role in modern biotechnology for DNA sequencing and detection. While several DNA polymerases can incorporate large numbers of dye-linked nucleotides into primed DNA templates, the amplification of the resulting densely labeled DNA strands by polymerase chain reaction (PCR) is problematic. Here, we report a method for high density labeling of DNA in PCR reactions employing the 5'-triphosphate of 1,3-diaza-2-oxo-phenoxazine (tCo) and Deep Vent DNA polymerase. tCo is a fluorescent cytosine analogue that absorbs and emits light at 365 and 460 nm, respectively. We obtained PCR products that were fluorescent enough to directly visualize them in a gel by excitation with long UV light, thus eliminating the need for staining with ethidium bromide. Reactions with Taq polymerase failed to produce PCR products in the presence of only small amounts of dtCoTP. A comparative kinetic study of Taq and Deep Vent polymerase revealed that Taq polymerase, although it inserts dtCoTP with high efficiency opposite G, is prone to forming mutagenic tCo-A base pairs and does not efficiently extend base pairs containing tCo. These kinetics features explain the poor outcome of the PCR reactions with Taq polymerase. Since tCo substitutes structurally for cytosine, the presented labeling method is believed to be less invasive than labeling with dye-linked nucleotides and, therefore, produces DNA that is ideally suited for biophysical studies.

A rapid and inexpensive labeling method for microarray gene expression analysis

Background

Global gene expression profiling by DNA microarrays is an invaluable tool in biological research. However, existing labeling methods are time consuming and costly and therefore often limit the scale of microarray experiments and sample throughput. Here we introduce a new, fast, inexpensive method for direct random-primed fluorescent labeling of eukaryotic cDNA for gene expression analysis and compare the results obtained on the NimbleGen microarray platform with two other widely-used labeling methods, namely the NimbleGen-recommended double-stranded cDNA protocol and the indirect (aminoallyl) method.

Results

Two total RNA samples were labeled with each method and hybridized to NimbleGen expression arrays. Although all methods tested here provided similar global results and biological conclusions, the new direct random-primed cDNA labeling method provided slightly better correlation between replicates compared to the other methods and thus increased ability to find statistically significant differentially expressed genes.

Conclusion

The new direct random-primed cDNA labeling method introduced here is suitable for gene expression microarrays and provides a rapid, inexpensive alternative to existing methods. Using NimbleGen microarrays, the method produced excellent results comparable to those obtained with other methods. However, the simplicity and cost-effectiveness of the new method allows for increased sample throughput in microarray experiments and makes the process amenable to automation with a relatively simple liquid handling system.

Label-free biosensors based on optically responsive nanocomposite layers: sensitivity and dynamic range

Core-shell nanoparticle layers have proven to be a promising tool for the label-free detection of binding events. Upon reflection of white light, they exhibit pronounced extinction peaks in the UV/vis and NIR regime of the electromagnetic spectrum, which shift to higher wavelengths when molecules are adsorbed. Beside drastic simplification of the instrumentation and related reduction in cost, a significantly stronger response toward alkanethiol adsorption has been observed in previous experiments than in conventional surface plasmon resonance (SPR). However, as the amount of molecules deposited onto the nanoparticle films was unknown, no quantitative relationship could be established between the measured wavelength shifts and the surface mass density of the adsorbate. In order to facilitate quantitative molecule detection, self-assembled monolayers (SAMs) of simple and ethylene glycol (EG) terminated alkanethiols with various chain lengths were prepared on the nanoparticle-coated substrates. The measured red-shift of the extinction spectrum upon molecule adsorption was related to the amount of adsorbate as determined by X-ray photoelectron spectroscopy (XPS). For the whole range of film thicknesses studied, a linear relationship is found yielding a sensitivity factor of 0.027 nm/(ng/cm (2)). As proven by enzyme-linked immunosorbent assay (ELISA), such determined sensitivity factor can also be used to correctly predict the amount of surface-bound protein in immunoreactions from the measured wavelength shifts. It is concluded that the decay length of the evanescent electric field associated with the nanoparticle sensors is more than 100 nm and, thus, significantly larger than that observed for localized surface plasmons excited in small isolated metal clusters.

Quantitative evaluation of oligonucleotide surface concentrations using polymerization-based amplification

Quantitative evaluation of minimal polynucleotide concentrations has become a critical analysis among a myriad of applications found in molecular diagnostic technology. Development of high-throughput, nonenzymatic assays that are sensitive, quantitative and yet feasible for point-of-care testing are thus beneficial for routine implementation. Here, we develop a nonenzymatic method for quantifying surface concentrations of labeled DNA targets by coupling regulated amounts of polymer growth to complementary biomolecular binding on array-based biochips. Polymer film thickness measurements in the 20–220 nm range vary logarithmically with labeled DNA surface concentrations over two orders of magnitude with a lower limit of quantitation at 60 molecules/μm² (∼10⁶ target molecules). In an effort to develop this amplification method towards compatibility with fluorescence-based methods of characterization, incorporation of fluorescent nanoparticles into the polymer films is also evaluated. The resulting gains in fluorescent signal enable quantification using detection instrumentation amenable to point-of-care settings.

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