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A simple scheme using a hairpin DNA aptasensor was established to detect Salmonella Typhimurium (S. Typhimurium). The hairpin DNA aptasensor was a single-stranded oligonucleotide including both a target-binding sequence and a reporting DNAzyme called horseradish peroxidase-mimicking G-quadruplex. Four hairpin DNA aptasensors were investigated to optimize the sequence with two enzymatic substrates for different signaling modes. Covalent conjugation of hemin on an aptasensor strand was preliminarily executed in colorimetric assays and then conducted with p-coumaric acid in chemiluminescence assays, to lower the background signal arisen from free hemin. A limit of detection (LOD) of this detection scheme was 100 CFU mL(-1) in colorimetric assays and was even further improved to 2 CFU mL(-1) in chemiluminescent assays. The present detection scheme is expected to have application as a simple, rapid method for detection of various types of hazardous targets.

Validation of long-term DNA stability and integrity are essential for the use of DNA in data storage applications. Because of this, we evaluated the plasmid-based DNA data storage in a manner that preserves DNA stability and integrity. A document consisting of 2046 words was encoded with DNA sequences using Perl script, and the encoded DNA sequences were synthesized for information storage. The DNA comprised a total of 22 chemically synthesized DNA fragments with 400 nucleotides each, which were incorporated into a plasmid vector. A long-term DNA stability study demonstrated that 3-year stored plasmid containing text information showed DNA stability at controlled conditions of −20 °C. The plasmid DNA under accelerated aging conditions (AAC) up to 65 °C for 20 days, which corresponds to approximately 20 years of storage at −20 °C, also exhibited no significant differences in DNA stability compared to newly produced plasmid. Also, the 3-year old plasmid stored at −20 °C and the AAC-tested plasmid stored up to 65 °C for 20 days had functional integrity and nucleotide integrity comparable to control sample, thereby allowing for retrieval of the original error-free text data. Finally, the nucleotides were sequenced, and then decoded to retrieve the original data, thereby allowing us to read the text with 100% accuracy, and amplify the DNA with a simple and quick bacterial transformation. To the best of our knowledge, this is the first report on examining the long-term stability and integrity of plasmid-based DNA data storage. Taken together, our results indicate that plasmid DNA data storage can be useful for long-term archival storage to recover the source text in a reproducible and accountable manner.

We report the development of on-chip fluorescence switching system based on DNA strand displacement and DNA hybridization for the construction of a rewritable and randomly accessible data storage device. In this study, the feasibility and potential effectiveness of our proposed system was evaluated with a series of wet experiments involving 40 bits (5 bytes) of data encoding a 5-charactered text (KRIBB). Also, a flexible data rewriting function was achieved by converting fluorescence signals between “ON” and “OFF” through DNA strand displacement and hybridization events. In addition, the proposed system was successfully validated on a microfluidic chip which could further facilitate the encoding and decoding process of data. To the best of our knowledge, this is the first report on the use of DNA hybridization and DNA strand displacement in the field of data storage devices. Taken together, our results demonstrated that DNA-based fluorescence switching could be applicable to construct a rewritable and randomly accessible data storage device through controllable DNA manipulations.

We identify and investigate several critical parameters in the fabrication of single-stranded DNA conjugated poly(ethylene glycol) (PEG) microparticles based on replica molding (RM) for highly uniform and robust nucleic acid hybridization assays. The effects of PEG-diacrylate, probe DNA, and photoinitiator concentrations on the overall fluorescence and target DNA penetration depth upon hybridization are examined. Fluorescence and confocal microscopy results illustrate high conjugation capacity of the probe and target DNA, femtomole sensitivity, and sequence specificity. Combined, these findings demonstrate a significant step toward simple, robust, and scalable procedures to manufacture highly uniform and high-capacity hybridization assay particles in a well-controlled manner by exploiting many advantages that the batch processing-based RM technique offers. We envision that the results presented here may be readily applied to rapid and high-throughput hybridization assays for a wide variety of applications in bioprocess monitoring, food safety, and biological threat detection.

Important properties for a biosensor are the sensitive detection of target DNA at low concentration, the specific and accurate distinction of the target and other DNA having a similar sequence, and measurement capability over a wide range of target concentrations. To these ends, generation 3 polyamidoamine (PAMAM) dendrimer was used to improve DNA chip properties. PAMAM dendrimer surface amine moieties were modified to biotin and immobilized on glass slides using biotin-avidin conjugation. The surface morphologies of the avidin-biotin-dendrimer complexes were observed using atomic force microscopy and scanning electron microscopy. Detection sensitivity for fluorescence-labeled target DNA increased approximately 4-fold by the dendrimer coating. Dendrimer coating also markedly improved the dynamic range and detection of single nucleotide polymorphisms. Dendrimer complex morphology had little effect on the sensitivity.

STATs (signal transducers and activators of transcription) are proteins with dual functions: signal transducers in the cytoplasm and transcriptional activators in the nucleus. STAT proteins act as transcription factors activated by phosphorylation on its tyrosine residues upon stimulation by various cytokines. The phosphorylated STAT molecules then form homo- or heterodimers through SH2-mediated interaction and translocate into the nucleus to activate the transcription of various target genes. STAT5 recognizes the interferon-gamma activated site TTCNNNGAA (GAS sequence) in the promoter region of the beta-casein gene. Except for prolactin-dependent beta-casein production in mammary gland cells, the biological consequences of STAT5a activation in various systems are not clear. Here we showed that STAT5a was phosphorylated 10 min after desferrioxamine (DFO) treatment, and reached a maximum induction at 4 h in mammary epithelial cells (HC11) and transfected COS-7 cells. Under hypoxic conditions (2% O2), a maximal phosphorylation of STAT5a was observed within 6 h. EMSA (electrophoretic mobility shift assay) showed that DFO or hypoxia enhanced the binding activities of STAT5a DNA to beta-casein gene promoter in mammary epithelial cells (HC11) and transfected COS-7 cells. These results showed that DFO or hypoxia induces tyrosine phosphorylation of STAT5a and also increases the binding activity of STAT5a DNA in mammary epithelial cells. Our data suggest that the STAT5 may act as a mediator in hypoxia-mediated gene expression.