FastTag Nucleic Acid Labeling System: a versatile method for incorporating haptens, fluorochromes and affinity ligands into DNA, RNA and oligonucleotides

Fluorescent labeling of plasmid DNA for gene delivery: Implications of dye hydrophobicity on labeling efficiencies and nanoparticle size

Covalent fluorescent labels are important tools for monitoring the in vitro and in vivo localization of plasmid DNA nanoparticles, but must meet several criteria including high DNA labeling efficiencies and minimal impact on nanoparticle size. We developed a novel fluorescent labeling strategy utilizing an aryl azide photolabel conjugated to a short cationic peptide to label plasmid DNA with Cyanine 5 and sulfo-Cyanine 5. Using a simple camera flash apparatus, photolabel-peptide-dyes can be conjugated to DNA in minutes with preservation of DNA structure and minimal dye photobleaching. The addition of two anionic sulfonates to the Cyanine 5 core greatly improved labeling efficiencies from ~13 to ~53% and mitigated PEGylated polyacridine peptide-DNA nanoparticle size increases over a range of labeling densities. Comparison of our sulfo-Cyanine 5 peptide label to the Mirus Bio Label IT-Cy5 kit revealed that while both did not affect nanoparticle sizes appreciably, labeling efficiencies with our conjugate were higher, possibly due to the higher positive charge density on the peptide linker. The results from this work provide important considerations for choosing fluorophore tags to track DNA nanoparticles.

Profiling the transcriptome with RNA SPOTs

Single molecule FISH (smFISH) has been the gold standard in quantifying individual transcripts abundances. Here, we demonstrate the scaling up of smFISH to the transcriptome level by profiling of 10,212 different mRNAs from mouse fibroblast and embryonic stem cells. This methods, called RNA SPOTs (Sequential Probing of Targets), provides an accurate and low-cost alternative to sequencing in profiling transcriptomes.

FISH for mapping single copy genes

During the past two decades fluorescent in-situ hybridization (FISH) has become a standard technique to directly localize, orient, and order genes in the genomes of a wide range of species. Despite the availability of a variety of probes, probe labeling and signal-detection systems, and advanced image analysis software, the core procedures used to carry out FISH remain the same. A detailed overview of these procedures, including target preparation (metaphase/interphase chromosomes and DNA fibers), probe labeling, in-situ hybridization, signal detection, and imaging, is here provided in a stepwise manner.

Integrated cell manipulation system--CMOS/microfluidic hybrid

Manipulation of biological cells using a CMOS/microfluidic hybrid system is demonstrated. The hybrid system starts with a custom-designed CMOS (complementary metal-oxide semiconductor) chip fabricated in a semiconductor foundry. A microfluidic channel is post-fabricated on top of the CMOS chip to provide biocompatible environments. The motion of individual biological cells that are tagged with magnetic beads is directly controlled by the CMOS chip that generates microscopic magnetic field patterns using an on-chip array of micro-electromagnets. Furthermore, the CMOS chip allows high-speed and programmable reconfiguration of the magnetic fields, substantially increasing the manipulation capability of the hybrid system. Extending from previous work that verified the concept of the hybrid system, this paper reports a set of manipulation experiments with biological cells, which further confirms the advantage of the hybrid approach. To enhance the biocompatibility of the system, the microfluidic channel is redesigned and the temperature of the device is monitored by on-chip sensors. Combining microelectronics and microfluidics, the CMOS/microfluidic hybrid system presents a new model for a cell manipulation platform in biological and biomedical applications.

Enhanced sensitivity and stability in two-color in situ hybridization by means of a novel chromagenic substrate combination

Double in situ hybridization analysis is a fundamental technique for studying the expression of two genes with high temporal and spatial resolution. However, due to the lack of sensitivity in current detection methods, this approach is powerful only when at least one transcript is abundantly expressed. Here, we report a new enzyme/chromagenic substrate combination that provides sufficient sensitivity for detecting two less abundant transcripts and stability for subsequent paraffin sectioning.

Disposition and gene expression characteristics in solid tumors and skeletal muscle after direct injection of naked plasmid DNA in mice

Previous studies have suggested that direct injection of naked plasmid DNA (pDNA) into solid tumors can be a useful method for in vivo gene transfer into tumor cells. To gain more insight into this approach, we studied the disposition and gene expression characteristics of naked pDNA after intratumoral injection by direct comparison with those after intramuscular injection in mice. pDNA encoding reporter genes were directly injected into subcutaneous solid tumor models and skeletal muscles. Biodistribution studies using radiolabeled pDNA showed that the elimination of pDNA from the injection site was relatively fast and a part of the pDNA was absorbed from the lymphatic system after both local injections. Confocal microscopic studies using fluorescein-labeled pDNA demonstrated that pDNA distributed efficiently throughout the muscle tissue whereas pDNA localization in the tumor tissue was restricted. Characterization of gene expression clarified the variation in expression level between tumor preparations and some factors affecting the expression level in the tumor. Reporter gene expression was significantly inhibited by simultaneous administration of some polyanions in both cases, suggesting that a specific mechanism may be involved in the naked pDNA uptake by muscle and tumor cells. These findings provide useful information for direct naked pDNA delivery into solid tumors.

Efficient uptake and rapid degradation of plasmid DNA by murine dendritic cells via a specific mechanism

In spite of the important roles of dendritic cells in DNA-based therapies, the cellular uptake mechanism of plasmid DNA (pDNA) in dendritic cells is poorly understood. The present study was undertaken to investigate the binding and uptake of pDNA in vitro using a murine dendritic cell line, DC2.4 cells. A significant and time-dependent cellular association of [32P]pDNA with DC2.4 cells was observed at 37 degrees C and this fell markedly at 4 degrees C. The binding and uptake of [32P]pDNA were significantly inhibited by cold pDNA, polyinosinic acid (poly[I]), dextran sulfate, or heparin, but not by polycytidylic acid (poly[C]), dextran, or EDTA, suggesting that a specific mechanism mediated by a receptor like the macrophage scavenger receptor may be involved. The TCA precipitation experiments showed that DC2.4 cells rapidly endocytosed and degraded a significant amount of [32P]pDNA at 37 degrees C and released the degradation products into the medium. The pDNA degradation was also significantly inhibited by poly[I], but not poly[C]. The rate of pDNA degradation by DC2.4 cells was significantly higher than that by macrophages. A confocal microscopic study using fluorescein-labeled pDNA confirmed the rapid internalization and degradation of pDNA by the dendritic cells. Taken together, these results indicate that pDNA is efficiently taken up and rapidly digested by the dendritic cells via a specific mechanism. These findings may suggest the important role of the dendritic cells in the innate immune system for host defense.