Size and topology of exogenous DNA as determinant factors of transgene transcription in mammalian cells

A Novel Terminator Primer and Enhancer Reagents for Direct Expression of PCR-Amplified Genes in Mammalian Cells

Escherichia coli plasmids are commonly used for gene expression experiments in mammalian cells, while PCR-amplified DNAs are rarely used even though PCR is a much faster and easier method to construct recombinant DNAs. One difficulty may be the limited amount of DNA produced by PCR. For direct utilization of PCR-amplified DNA in transfection experiments, efficient transfection with a smaller amount of DNA should be attained. For this purpose, we investigated two enhancer reagents, polyethylene glycol and tRNA, for a chemical transfection method. The addition of the enhancers to a commercial transfection reagent individually and synergistically exhibited higher transfection efficiency applicable for several mammalian cell culture lines in a 96-well plate. By taking advantage of a simple transfection procedure using PCR-amplified DNA, SV40 and rabbit β-globin terminator lengths were minimized. The terminator length is short enough to design in oligonucleotides; thus, terminator primers can be used for the construction and analysis of numerous mutations, deletions, insertions, and tag-fusions at the 3'-terminus of any gene. The PCR-mediated gene manipulation with the terminator primers will transform gene expression by allowing for extremely simple and high-throughput experiments with small-scale, multi-well, and mammalian cell cultures.

Physical Characterization of Gemini Surfactant-Based Synthetic Vectors for the Delivery of Linear Covalently Closed (LCC) DNA Ministrings

In combination with novel linear covalently closed (LCC) DNA minivectors, referred to as DNA ministrings, a gemini surfactant-based synthetic vector for gene delivery has been shown to exhibit enhanced delivery and bioavailability while offering a heightened safety profile. Due to topological differences from conventional circular covalently closed (CCC) plasmid DNA vectors, the linear topology of LCC DNA ministrings may present differences with regards to DNA interaction and the physicochemical properties influencing DNA-surfactant interactions in the formulation of lipoplexed particles. In this study, N,N-bis(dimethylhexadecyl)-α,ω-propanediammonium(16-3-16)gemini-based synthetic vectors, incorporating either CCC plasmid or LCC DNA ministrings, were characterized and compared with respect to particle size, zeta potential, DNA encapsulation, DNase sensitivity, and in vitro transgene delivery efficacy. Through comparative analysis, differences between CCC plasmid DNA and LCC DNA ministrings led to variations in the physical properties of the resulting lipoplexes after complexation with 16-3-16 gemini surfactants. Despite the size disparities between the plasmid DNA vectors (CCC) and DNA ministrings (LCC), differences in DNA topology resulted in the generation of lipoplexes of comparable particle sizes. The capacity for ministring (LCC) derived lipoplexes to undergo complete counterion release during lipoplex formation contributed to improved DNA encapsulation, protection from DNase degradation, and in vitro transgene delivery.

Effects of size and topology of DNA molecules on intracellular delivery with non-viral gene carriers

Background

Efforts to improve the efficiency of non-viral gene delivery require a better understanding of delivery kinetics of DNA molecules into clinically relevant cells. Towards this goal, three DNA molecules were employed to investigate the effects of DNA properties on cellular delivery: a circular plasmid DNA (c-DNA), a linearized plasmid DNA (l-DNA) formulated by single-site digestion of c-DNA, and smaller linear gene cassette generated by PCR (pcr-DNA). Four non-viral gene carriers were investigated for DNA delivery: polyethyleneimine (PEI), poly-L-Lysine (PLL), palmitic acid-grafted PLL (PLL-PA), and Lipofectamine-2000™. Particle formation, binding and dissociation characteristics, and DNA uptake by rat bone marrow stromal cells were investigated.

Results

For individual carriers, there was no discernible difference in the morphology of particles formed as a result of carrier complexation with different DNA molecules. With PEI and PLL carriers, no difference was observed in the binding interaction, dissociation characteristics, and DNA uptake among the three DNA molecules. The presence of serum in cell culture media did not significantly affect the DNA delivery by the polymeric carriers, unlike other lipophilic carriers. Using PEI as the carrier, c-DNA was more effective for transgene expression as compared to its linear equivalent (l-DNA) by using the reporter gene for Enhanced Green Fluorescent Protein. pcr-DNA was the least effective despite being delivered into the cells to the same extent.

Conclusion

We conclude that the nature of gene carriers was the primary determinant of cellular delivery of DNA molecules, and circular form of the DNA was more effectively processed for transgene expression.

Emerging vectors and targeting methods for nonviral gene therapy

Until recently, nonviral vectors were outside the mainstream of gene transfer technology. Recent problems in clinical trials using viral vectors renewed interest in these methods. The clinical usefulness of nonviral methods is still hindered by their relatively low gene delivery/transgene expression efficiencies. Vectors must navigate a series of obstacles before the therapeutic gene can be expressed. This review considers these barriers and the properties of components of nonviral vectors that are essential for nucleic acid transfer. Although developments of new physical methods (hydrodynamic delivery, ultrasound, electroporation) have made a significant impact on gene transfer efficiency, various chemical carriers (lipids and polymers) have been shown to achieve high-level gene delivery and functional expression. Success of nonviral gene targeting will depend not only on the efficacy, but also safety of this methodology, and this aspect is also discussed. Understanding problems associated with nonviral targeting can also help in designing better viral vectors. In fact, interplay between viral and nonviral technologies should lead to a continued refinement of both methodologies.

Role of the spacer of cationic gemini amphiphiles in the condensation of DNA

The condensation of calf thymus DNA into the cholesteric-like psi-phase was observed by circular dichroism in liposome suspensions formulated with specific cationic gemini surfactants. The stereochemistry of the gemini spacer, the presence of specific functional groups, and the covalent link between the headgroups are fundamental issues in the condensation of DNA. Transmission electron microscopy images showed a multilamellar morphology, which corresponds with condensation.

Linear double-stranded DNA that mimics an infective tail of virus genome to enhance transfection

Our previous work showed that a natural beta-(1-->3)-d-glucan schizophyllan (SPG) can form a stable complex with single-stranded oligonucleotides (ssODNs). When protein transduction peptides were attached to SPG and this modified SPG was complexed with ssODNs, the resultant complex could induce cellular transfection of the bound ODNs, without producing serious cytotoxicity. However, no technique was available to transfect double-stranded DNAs (dsDNA) or plasmid DNA using SPG. This paper presents a new approach to transfect dsDNA, showing preparation and transfection efficiency for a minimal-size gene having a loop-shaped poly(dA)(80) on both ends. This poly(dA) loops of dsDNA can form a complex with SPG. An siRNA-coding dsDNA with the poly(dA) loop was complexed with Tat-attached SPG to silence luciferase expression. When LTR-Luc-HeLa cells that can express luciferase under the control of the LTR promoter were exposed to this complex, the expression of luciferase was suppressed (i.e., RNAi effect was enhanced). Cytotoxicity studies showed that the Tat-SPG complex induced much less cell death compared to polyethylenimine, indicating that the proposed method caused less harm than the conventional method. The Tat-SPG/poly(dA) looped dsDNA complex had a structure similar to the viral genome in that the dsDNA ends were able to induce transfection and protection. The present work identifies the SPG and poly(dA) looped minimum-sized gene combination as a candidate for a non-toxic gene delivery system.

Long-term RNA interference from optimized siRNA expression constructs in adult mice

DNA constructs for small interfering RNA (siRNA) expression in mammalian cells have the potential for longer-term target gene knockdown than synthetic siRNAs. We compared in adult mice the efficacy and longevity of target gene knockdown from siRNA expression cassettes contained in plasmids, PCR-generated linear constructs or PCR constructs containing "dumbbell" ends using the hydrodynamic delivery method. Plasmid siRNA expression constructs were more effective than PCR constructs for target gene knockdown. The efficacy of the PCR constructs was improved by addition of short extensions beyond the transcription termination signal and greatly improved by addition of dumbbell ends. Constructs containing the H1 promoter were significantly less effective in mice than those containing the U6 promoter, whereas both promoters functioned equally well in cultured cells. Target gene knockdown perdured for at least 20 weeks in mice after delivery of either PCR or plasmid siRNA expression cassettes. These results will help guide RNAi vector design.

Efficient Transfection of DNA by Liposomes Formulated with Cationic Gemini Amphiphiles

Cationic liposomes formulated with neutral 1,2-dimyristoyl-sn-glycero-3-phosphocholine and cationic gemini surfactants were used for transfecting different cell lines with a reporter gene. The efficiency in the transfection has been correlated to the high extent of DNA condensation observed by circular dichroism, condensation shown to depend heavily on the gemini spacer structure. Transfection efficiency was better than that obtained with a commercial lipofection kit.

An NLS peptide covalently linked to linear DNA does not enhance transfection efficiency of cationic polymer based gene delivery systems

BACKGROUND

Transfection with non-viral gene delivery vectors, such as cationic polymers, generally results in low transgene expression in vivo. This is likely due to poor cytoplasmic transport and intra-nuclear DNA delivery.

METHODS

In this study two strategies to improve nuclear import were investigated. Linear DNA constructs with or without an NLS peptide were prepared by PCR. Alternatively, linear DNA obtained by enzymatic cleavage followed by capping of both ends with DNA-hairpins was used. An NLS peptide was attached to one of the capped ends of the linear DNA. Both biodegradable (pDMAEAppz) and non-degradable polymers (PEI or pDMAEMA) were used to complex the DNA. Several cell types, dividing and non-dividing, were transfected with the linear DNA constructs containing a SV40-derived NLS peptide. Nuclear import of the DNA constructs was studied using digitonin-permeabilized cells.

RESULTS

Linear DNA prepared by PCR proved not useful as it was degraded from the 3'end. Linear DNA capped with hairpins was more successful with regard to stability. However, Cells transfected with linear DNA constructs by electroporation or by using cationic polymers with linear DNA containing a NLS peptide, failed to show significantly higher luciferase expression levels when compared to cells transfected with plasmid DNA or linear DNA without an NLS peptide attached. No nuclear localization was observed in digitonin-permeabilized cells.

CONCLUSION

Taken together, these data demonstrate that this nuclear localisation signal when attached to DNA is neither able to improve transfection efficiency of cationic polymers nor the nuclear import of the DNA constructs.

Proposal of new modification technique for linear double-stranded DNAs using the polysaccharide schizopyllan

A natural polysaccharide schizophyllan (SPG) has been known to form a stable complex with poly(dA). We attached a poly(dA)(80) tail to the both ends of a linear double-stranded DNA, which had been prepared from a plasmid DNA vector. The poly(dA) tailed DNA verified to form complex with SPG by gel electrophoresis and atomic force microscopy (AFM). AFM images indicated that the complexes exhibit a dumbbell-like architecture, that is, quite similar to that of adenovirus genome. The complex demonstrated excellent exonuclease resistance, probably because of the protection effect by SPG complexation.

Intraarterial delivery of naked plasmid DNA expressing full-length mouse dystrophin in the mdx mouse model of duchenne muscular dystrophy

Our previous studies have demonstrated that the intraarterial delivery of naked plasmid DNA leads to high levels of foreign gene expression throughout the muscles of the targeted limb. Although the procedure was first developed in rats and then extended to nonhuman primates, the present study has successfully implemented the procedure in normal mice and the mdx mouse model for Duchenne muscular dystrophy. After intraarterial delivery of plasmid DNA expressing the normal, full-length mouse dystrophin from either the cytomegalovirus promoter or a muscle-specific human desmin gene control region, mdx mouse muscle stably expressed dystrophin in 1-5% of the myofibers of the injected hind limb for at least 6 months. This expression generated an antibody response but no apparent cellular response.

Approaches to enhance the efficacy of DNA vaccines

DNA vaccines consist of antigen-encoding bacterial plasmids that are capable of inducing antigen-specific immune responses upon inoculation into a host. This method of immunization is advantageous in terms of simplicity, adaptability, and cost of vaccine production. However, the entry of DNA vaccines and expression of antigen are subjected to physical and biochemical barriers imposed by the host. In small animals such as mice, the host-imposed impediments have not prevented DNA vaccines from inducing long-lasting, protective humoral, and cellular immune responses. In contrast, these barriers appear to be more difficult to overcome in large animals and humans. The focus of this article is to summarize the limitations of DNA vaccines and to provide a comprehensive review on the different strategies developed to enhance the efficacy of DNA vaccines. Several of these strategies, such as altering codon bias of the encoded gene, changing the cellular localization of the expressed antigen, and optimizing delivery and formulation of the plasmid, have led to improvements in DNA vaccine efficacy in large animals. However, solutions for increasing the amount of plasmid that eventually enters the nucleus and is available for transcription of the transgene still need to be found. The overall conclusions from these studies suggest that, provided these critical improvements are made, DNA vaccines may find important clinical and practical applications in the field of vaccination.

Cell type-specific gene expression, mediated by TFL-3, a cationic liposomal vector, is controlled by a post-transcription process of delivered plasmid DNA

The issue of whether the TFL-3, a recently developed cationic liposome, achieves efficient gene expression in different mammalian cell lines (NIH/3T3, LLC, A431 and HeLa cells) was examined. The issue of whether gene expression is related to the amount of plasmid DNA (pDNA) delivered in cells or nuclei following transfection was also examined. The cells were transfected for 1h with pDNA/TFL-3 lipoplexes, and the transfection efficiency was determined by means of a luciferase activity assay. The amount of intracellular and intranuclear pDNA following the transfection was also quantitatively determined. Successful transgene expressions in all cell lines we tested were observed under our experimental conditions, suggesting that the TFL-3 represents a suitable nonviral vector system for the successful gene expression in mammalian cells in vitro. The degree and rate of gene expression were dependent on the type of cells used as well as the incubation time after transfection, but these parameters were independent of the amount of gene delivered to cells and nuclei. These results suggest that TFL-3 mediated gene expression is largely controlled by the process of post-transcription of the delivered pDNA, and not by the process of cellular entry of pDNA and cytoplasmic trafficking of pDNA into nuclei, which is dependent on the cell type. Therefore, the results obtained here clearly suggest that the cell type-specific improvement in transcription efficiency of pDNA and translation of the derived mRNA, together with an improved delivery system to enhance the nuclear delivery of pDNA, is necessary to achieve efficient transgene expression in mammalian cells.

Pharmacokinetic and pharmacodynamic considerations in gene therapy

During gene therapy the concentration of plasmid DNA or oligonucleotides in the plasma can be quite different from their concentrations in the nucleus or cytosol where they exert their actions. For a better understanding of the apparent discrepancies between pharmacokinetics (PK) and pharmacodynamics (PD), a new concept for intracellular PK with an emphasis on the final efficacy of gene transcription is needed. Here, the conventional PK and intracellular PK and PD of non-viral gene delivery systems are discussed, together with a new concept, referred to as controlled intracellular disposition, which integrates these factors to gain a better understanding of gene expression in the nucleus. The importance of optimizing the system from a transcriptional point of view in the nucleus is also discussed. These new concepts must be integrated to develop an optimized non-viral gene delivery system.

Asialoganglioside enhances the efficiency of gene transfection mediated by cationic liposomes with a cationic cholesterol derivative

We investigated the transfection efficiency mediated by asialoganglioside-containing cationic liposomes. Previously we reported that monosialoganglioside GM(1) (GM(1a)) enhanced transfection efficiency. In this study, we investigated the effects of sialic acid in gangliosides on transfection efficiency. Two mammalian culture cell lines HeLa and HepG2 were transfected with luciferase plasmids (pGL3) using cationic liposomes which contain monosialoganglioside GM(1) (GM(1a)) or its asialic counterpart, asialoganglioside GM(1) (GA(1)). Both GM(1a) and GA(1) enhanced the efficiency of transfection mediated by cationic liposomes, and GA(1) exhibited higher efficiency than GM(1a) in both cell lines. Transfection efficiency of ganglioside-containing liposomes was also assessed by the effects of antisense oligonucleotides (AS-ODN) for bcl-2 gene, which suppresses apoptotic cell death. Western blotting analysis revealed that the expression of Bcl-2 was decreased by AS-ODN, and the reduction of protein expression in cells treated with GA(1)-containing liposomes was more remarkable than that with GM(1a)-containing liposomes. Furthermore, the induction rate of apoptosis was higher in cells treated with AS-ODN with GA(1)-containing liposomes. Together with the results obtained by luciferase assay mentioned above, the removal of sialic acid from ganglioside causes the enhancement of efficiency of transfection mediated by cationic liposomes.

Visualization of intracellular trafficking of exogenous DNA delivered by cationic liposomes

To visualize the intracellular trafficking of exogenous DNAs delivered by cationic liposomes, rhodamine-labeled DNAs were transfected into NIH3T3 cells and observed by confocal laser microscopy. After 0.5- to 1-h incubations, the DNAs reached the nucleus with a much higher frequency than that expected from the cell division rate. This result suggests that DNAs can enter the nucleus in the presence of the nuclear membrane. Interestingly, some DNAs appeared to extend through the nuclear membrane in the aggregated form which were much larger than the nuclear pore complex. The DNAs which have passed through the nuclear membrane were stained with SYTO 24, a DNA labeling reagent. The stained part may be "naked" DNA that is free of lipids or proteins. This observation indicates that a complex containing DNA fuses with the nuclear membrane and then naked DNA is released into the nucleus.