Lipoplex formulation of superior efficacy exhibits high surface activity and fusogenicity, and readily releases DNA

Lipoplexes containing a mixture of cationic phospholipids dioleoylethylphosphatidylcholine (EDOPC) and dilauroylethylphosphatidylcholine (EDLPC) are known to be far more efficient agents in transfection of cultured primary endothelial cells than are lipoplexes containing either lipid alone. The large magnitude of the synergy permits comparison of the physical and physico-chemical properties of lipoplexes that have very different transfection efficiencies, but minor chemical differences. Here we report that the superior transfection efficiency of the EDLPC/EDOPC lipoplexes correlates with higher surface activity, higher affinity to interact and mix with negatively charged membrane-mimicking liposomes, and with considerably more efficient DNA release relative to the EDOPC lipoplexes. Observations on cultured cells agree with the results obtained with model systems; confocal microscopy of transfected human umbilical artery endothelial cells (HUAEC) demonstrated more extensive DNA release into the cytoplasm and nucleoplasm for the EDLPC/EDOPC lipoplexes than for EDOPC lipoplexes; electron microscopy of cells fixed and embedded directly on the culture dish revealed contact of EDLPC/EDOPC lipoplexes with various cellular membranes, including those of the endoplasmic reticulum, mitochondria and nucleus. The sequence of events outlining efficient lipofection is discussed based on the presented data.     

一种靶向性阳离子多肽载体的表达纯化

目的：原核表达靶向性阳离子多肽(KH)20-EGF,并对其DNA包装能力进行检验。方法：构建pET28a-(KH)20-EGF 原核表达载体。进行酶切和测序鉴定。转化BL21（DE3）后,经过IPTG诱导表达和NTA树脂纯化得到粗提蛋白产物,SDS-PAGE和Western blot鉴定后,将蛋白与质粒DNA混合,用于凝胶阻滞实验分析。结果：重组(KH)20-EGF的产量约为300μg/L。SDS-PAGE和Western blot表明该蛋白的凝胶迁移有些滞后;凝胶阻滞试验发现(KH)20-EGF对质粒DNA的迁移有阻滞作用。结论：成功表达非病毒载体(KH)20-EGF并确认其DNA包装能力。     

Cooperativity in the binding of the cationic biocide polyhexamethylene biguanide to nucleic acids

The interaction between the broad-spectrum antimicrobial agent, polyhexamethylene biguanide (PHMB), and various nucleic acids was investigated. Titration of either single- or double-stranded 100-bp DNA, or mixed-molecular weight marker DNA, or tRNA with PHMB caused precipitation of a complex between nucleic acid and PHMB in which the nucleotide/biguanide ratio was always close to unity. Binding of PHMB was highly cooperative, with apparent Hill coefficients 10.3-14.6. When a fluorescent derivative of PHMB was titrated with increasing amounts of nucleic acid, all four forms of nucleic acid caused strong polarisation of fluorescence, demonstrating the association with PHMB. The intensity and broad-spectrum binding of PHMB to all forms of nucleic acid has significant implications for the mechanism of action of this biocide.     

Cell Biological and Biophysical Aspects of Lipid-mediated Gene Delivery

Cationic lipids are conceptually and methodologically simple tools to deliver nucleic acids into the cells. Strategies based on cationic lipids are viable alternatives to viral vectors and are becoming increasingly popular owing to their minimal toxicity. The first-generation cationic lipids were built around the quaternary nitrogen primarily for binding and condensing DNA. A large number of lipids with variations in the hydrophobic and hydrophilic region were generated with excellent transfection efficiencies in vitro. These cationic lipids had reduced efficiencies when tested for gene delivery in vivo. Efforts in the last decade delineated the cell biological basis of the cationic lipid gene delivery to a significant detail. The application of techniques such as small angle X-ray spectroscopy (SAXS) and fluorescence microscopy, helped in linking the physical properties of lipid:DNA complex (lipoplex) with its intracellular fate. This biological knowledge has been incorporated in the design of the second-generation cationic lipids. Lipid-peptide conjugates (peptoids) are effective strategies to overcome the various cellular barriers along with the lipoplex formulations methodologies. In this context, cationic lipid-mediated gene delivery is considerably benefited by the methodologies of liposome-mediated drug delivery. Lipid mediated gene delivery has an intrinsic advantage of being a biomimetic platform on which considerable variations could be built to develop efficient in vivo gene delivery protocols.     

Liposome complexation efficiency monitored by FRET: effect of charge ratio,helper lipid and plasmid size

Cationic lipid/DNA complexes (lipoplexes) are promising vehicles for DNA vaccines or gene therapy. In these systems, transfection efficiency is highly related to lipoplex charge ratio, since lipoplexes with charge ratios (±) lower than electroneutrality have most DNA uncovered by the liposomes, and thus are unprotected from enzyme degradation. However, a large excess of cationic lipids is undesirable because of eventual cytotoxicity. The aim of this work was to determine the minimum charge ratio from which all DNA molecules are complexed by the liposomes varying the lipid formulation and plasmid size, using a new FRET (fluorescence resonance energy transfer) methodology. The similarity of FRET results, fluorescence intensity data and fluorescence decays of several charge ratios above (±) ≥ 4 or 5 confirmed that once all DNA is covered by the liposomes, additional lipid molecules do not affect the lipoplex multilamellar repeat distance. It was also verified by FRET that the presence of helper lipid reduces the amount of cationic lipid required for DNA protection but does not affect the lipoplex multilamellar repeat distance. This distance varies with the plasmid size when supercoiled plasmid is used, being apparently larger when longer plasmids are used. Our study indicates that, despite the complexity of these systems not being totally described by our model, FRET is an informative technique in lipoplex characterization.     

Peptide nucleic acids and the origin of life

The possibilities of pseudo-peptide-DNA mimics like PNA (peptide nucleic acid) having a role for the prebiotic origin of life prior to an RNA world is discussed on the basis of literature data showing that this type of molecules might have formed on the primitive earth (or other places in the universe), as well as data indicating the possibilities of template-directed PNA chemical replication and ligation. In particular, the merits of an achiral prebiotic genetic material is discussed.     

Binding ability of a thymine-functionalized oligolysine towards nucleic acids

In this Letter, we investigated the binding properties towards nucleic acids of a thymine-functionalized oligolysine, composed of nucleobase-bearing amino acid moieties and underivatized l-lysine residues alternate in the backbone. The basic nucleopeptide proved to be well soluble in water and able to interact with both DNA and RNA, as suggested by circular dichroism, UV and surface plasmon resonance studies performed on the thymine-containing oligomer with both adenine-containing DNA (dA₁₂) and RNA (rA₁₂ and poly rA) molecules. In both cases the thymine-functionalized oligolysine was proven to form complexes characterized by a 1:1 T/A stoichiometric ratio, as evidenced by CD titration. UV melting experiments revealed that the complex formed between the homothymine oligolysine and rA₁₂ RNA was more stable than the complex with dA₁₂ DNA probably due to the additional H-bonding of the 2′-OH groups in RNA, that reinforces the overall interaction with the nucleopeptide. Finally, human serum stability assays were conducted on the thymine-bearing nucleopeptide which showed a half-life of 45 min.     

Plasmid DNA activates murine macrophages to induce inflammatory cytokines in a CpG motif-independent manner by complex formation with cationic liposomes

Plasmid DNA (pDNA) is very important in non-viral gene therapy and DNA vaccination. Unmethylated CpG motifs in bacterial DNA, but not in vertebrate DNA, are known to trigger an inflammatory response, which inhibits gene expression while improving immunological consequences. In this report, we investigated the cytokine secretion induced by pDNA/cationic liposome complexes using murine macrophages. Naked CpG DNA induced tumor necrosis factor-alpha (TNF-alpha) secretion from the macrophages, but DNA without CpG motif did not, demonstrating that the cytokine induction was mediated by CpG motifs. pDNA complexed with cationic liposomes, but not the cationic liposomes alone, produced a significant amount of TNF-alpha from the macrophages. Surprisingly, methylated pDNA and calf thymus DNA complexed with the cationic liposomes were also able to induce TNF-alpha production, indicating that these responses were not dependent on CpG motifs. Taken together, the present study demonstrated that for the first time DNA can stimulate murine macrophages in a CpG motif-independent manner when it is complexed with the cationic liposomes.     

Evaluation and optimization of DNA delivery into gliosarcoma 9L cells by a cholesterol-based cationic liposome

This paper reports results concerning the transfection of gliosarcoma cells 9L using an original cholesterol-based cationic liposome as carrier. This cationic liposome was prepared from triethyl aminopropane carbamoyl cholesterol (TEAPC-Chol) and a helper lipid, dioleoyl phosphatidyl ethanolamine (DOPE). The used concentration of liposome was not cytotoxic as revealed by the MTT test. TEAPC-Chol/DOPE liposomes allowed the plasmids encoding reporter genes to enter the nucleus as observed both by electron microscopy and functionality tests using fluorescence detection of green fluorescent protein (GFP) and luminometric measurements of luciferase activity. By changing the cationic lipid/DNA molar charge ratio, optimal conditions were determined. Further, improvement of the transfection level has been obtained by either precondensing plasmid DNA with poly-l-lysine or by adding polyethylene glycol (PEG) in the transfection medium. The optimal conditions determined are different depending on whether the transfection is made with cells in culture or with tumors induced by subcutaneous (s.c.) injection of cells in Nude mice. For in vivo assays, a simple method to overcome the interference of haemoglobin with the chemiluminescence intensity of luciferase has been used. These results would be useful for gaining knowledge about the potential for the cationic liposome TEAPC-Chol/DOPE to transfect brain tumors efficiently.     

Study of Plasma Induced Chemistry by DC Discharges in CO<Subscript>2</Subscript>/N<Subscript>2</Subscript>/H<Subscript>2</Subscript>O Mixtures Above a Water Surface

The chemistry induced by atmospheric pressure DC discharges above a water surface in CO(2)/N(2)/H(2)O mixtures was investigated. The gaseous mixtures studied represent a model prebiotic atmosphere of the Earth. The most remarkable changes in the chemical composition of the treated gas were the decomposition of CO(2) and the production of CO. The concentration of CO increased logarithmically with the increasing input energy density and an increasing initial concentration of CO(2) in the gas. The highest achieved concentration of CO was 4.0 +/- 0.6 vol. %. The production of CO was crucial for the synthesis of organic species, since reactions of CO with some reactive species generated in the plasma, e. g. H* or N* radicals, were probably the starting point in this synthesis. The presence of organic species (including the tentative identification of some amino acids) was demonstrated by the analysis of solid and liquid samples by high-performance liquid chromatography, infrared absorption spectroscopy and proton-transfer-reaction mass spectrometry. Formation of organic species in a completely inorganic CO(2)/N(2)/H(2)O atmosphere is a significant finding for the theory of the origins of life.     

Origin of life: Consideration of alternatives to proteins and nucleic acids

Summary Starting with relatively simple, non-hydrolyzable compounds in aqueous solution, entirely spontaneous condensations give rise to polymers that contain purines, pyrimidines, amino acids, coenzymes, lipid components and even phosphate. The presence of certain lipid micelles allows significant product formation at millimolar substrate concentrations. The first step involves formation of a Michael adduct from--unsaturated carbonyl compounds and various nucleophiles. Polymerization of these adducts occurs via sequential Knoevenagel condensations. All reactions take place readily at temperatures below 45°. The polymers can act as macromolecular catalysts as evidenced by hydrolytic activity. The purines and pyrimidines in the polymers appear to be capable of both base pairing and stacking interactions with ribonucleic acids. Specific examples of potential alternatives to base pairing are presented. These results are discussed from the standpoint of the spontaneous development of reproducing molecules. Proteins and nucleic acids may be evolutionary developments which have displaced earlier biopolymers.     

Towards a universally adaptable method for quantitative extraction of high-purity nucleic acids from soil

A universally adaptable protocol for quantitative extraction of high-purity nucleic acids from soil is presented. A major problem regarding the extraction of nucleic acids from soil is the presence of humic substances, which interfere with the extraction process itself and in subsequent analytical manipulations. By the approach described here, the humic compounds are precipitated prior to cell lysis with Al(2)(SO(4))(3), and thus eliminated prior to the nucleic acid extraction. The protocol allows for removing of a considerable content and range of humic acids and should therefore be applicable for a wide spectrum of soil types. Accordingly, reproducible results in analyses of different soil types are made possible, inclusively for quantitative comparisons.     

Medicinal chemistry of plasmid DNA with peptide nucleic acids: A new strategy for gene therapy

Summary In this chapter, we describe an approach using a peptide nucleic acid (PNA) clamp to directly and irreversibly modify plasmid DNA, without affecting either its supercoiled conformation or its ability to be efficiently transcribed. This strategy enables investigators to functionalize their gene of interest by direct coupling of ligands (fluorophores, peptide, proteins, sugars or oligonucleotides) to plasmid DNA. This approach provides versatile tools to study the mechanisms of gene delivery and to circumvent some of the main obstacles of synthetic gene delivery systems, such as specific targeting and efficient delivery. The proof-of-principal of PNA-dependent gene chemistry (PDGC) was demonstrated with a fluorescently labeled PNA that allowed generation of a highly fluorescent preparation of plasmid DNA that was functionally and conformationally intact. Fluorescent-PNA/DNA was used to identify critical parameters involved in naked DNA and non-viral gene delivery technology. The greatest potential of PDGC lies in the ability to attach specific ligands (e.g., peptides, proteins) to the plasmid DNA in order to overcome cellular barriers of non-viral gene delivery systems. In this regard, specific examples of ligands coupled to DNA are described and their effect on increasing the efficacy of gene therapy is presented     

Observation of DNA-polymer condensate formation in real time at a molecular level

Dynamic real time assembly of toroidal and rod-like DNA condensates has been visualised using atomic force microscopy. Imaging has been conducted in an aqueous environment allowing the visualisation of hydrated, pegylated-polymer DNA condensates undergoing dynamic structural movement and conformational change. A major hurdle in the field of gene delivery is cellular transfection and the subsequent transfer of condensed genetic material to the cell nucleus. An increased understanding of the process of DNA condensation will aid the development and optimisation of gene delivery vectors.     

Phylogenomics reveal a robust fungal tree of life

Our understanding of the tree of life (TOL) is still fragmentary. Until recently, molecular phylogeneticists have built trees based on ribosomal RNA sequences and selected protein sequences, which, however, usually suffered from lack of support for the deeper branches and inconsistencies probably due to limited subsampling of the entire genome. Now, phylogenetic hypotheses can be based on the analysis of full genomes. We used available complete genome data as well as the eukaryote orthologous group (KOG) proteins to reconstruct with confidence basal branches of the fungal TOL. Phylogenetic analysis of a core of 531 KOGs shared among 21 fungal genomes, three animal genomes and one plant genome showed a single tree with high support resulting from four different methods of phylogenetic reconstruction. The single tree that we inferred from our dataset showed excellent nodal support for each branch, suggesting that it reflects the true phylogenetic relationships of the species involved.     

On the Origins of a Crowded Cytoplasm

Contemporary cells show a highly crowded macromolecular content, the processes which originated this state being largely unknown. We propose that a driving force leading to the crowded cellular state could be the increase in growth rate produced by an enhanced cytoplasmic protein concentration. Briefly, in a diluted scenario, an increase in protein concentration has two opposing effects on growth rate. The favorable effect is the increase in the activity per unit volume of the component proteins and the disadvantageous effect is the concomitant increase in the protein mass per unit volume which has to be produced. In this work we show that the first effect is quantitatively more important, resulting in an overall increase in growth rate. This result was obtained with a model of E. coli and using nonmechanistic physiological arguments. The proposed driving force operates even at low protein concentrations, where the nonspecific interactions of macromolecular crowding are not significant, and could be as ancient as the first protocells. Experimental measurement of this cytoplasmic protein concentration effect in present organisms is hindered by the prevailing nonspecific interactions, product of long-term evolution. However, chemical/biochemical systems, built up to mimic properties of living cells, could be an adequate tool to test this effect. [Reviewing Editor: Dr. Antony Dean]     

Expression, purification and characterization of TAT-high mobility group box-1A peptide as a carrier of nucleic acids

High mobility group box 1 (HMGB1) is an abundant nuclear protein that binds to double-stranded DNA. HMGB1 is composed of high mobility (HMG) box A, box B, and C-terminal acidic regions. In this study, a recombinant TAT linked HMGB1 box A (rTAT-HMGB1A) peptide was expressed, purified, and characterized as a carrier of nucleic acids. The HMGB1A cDNA was amplified by PCR, and cloned into the pET21a expression vector with the TAT domain located at the N-terminus. The rTAT-HMGB1A peptide was overexpressed and purified using Nickel affinity chromatography. A recombinant HMGB1A (rHMGB1A) peptide without the TAT domain was also overexpressed and purified as a control. In gel retardation assays, both the rHMGB1A and rTAT-HMGB1A peptides formed complexes with DNA equally well. However, transfection assays showed that the rTAT-HMGB1A peptide had a higher gene transfer efficiency than rHMGB1A. Finally, rTAT-HMGB1A had no cytotoxicity to HEK 293 cells suggesting that rTAT-HMGB1A may be useful as a non-toxic gene delivery carrier.     

Purification and cDNA cloning of maize HMGd reveal a novel plant chromosomal HMG-box protein with sequence similarity to HMGa

We have purified the chromosomal high mobility group (HMG) protein HMGd from maize suspension culture cells, determined the N-terminal amino acid (aa) sequence, and isolated the corresponding cDNA. Sequence analysis showed that the cDNA encoded a protein of 126 aa residues with a theoretical mass of 14 104 Da. The protein contains an HMG-box DNA-binding domain and a short acidic C-terminal tail. HMGd is in approx. 65% of its residues identical to maize HMGa, whereas it is only approx. 46% identical to maize HMGcl/2. The differences to the previously reported HMG proteins in aa sequence, in overall charge and in protein size indicate that we have identified a third type of plant chromosomal HMG-box protein belonging to the HMG1 protein family. Immunoblot analysis with a HMGd antiserum reveals that HMGd is expressed in all tissues tested.     

The peptide nucleic acids (PNAs): a new generation of probes for genetic and cytogenetic analyses

Peptide nucleic acids (PNAs) are synthetic homologs of nucleic acids in which the phosphate-sugar polynucleotide backbone is replaced by a flexible pseudo-peptide polymer to which the nucleobases are linked. This structure gives PNAs the capacity to hybridize with high affinity and specificity to complementary sequences of DNA and RNA, and also confers remarkable resistance to DNAses and proteinases. The unique physico-chemical characteristics of PNAs have led to the development of a wide range of biological assays. Several exciting new applications of PNA technology have been published recently in genetics and cytogenetics. Also, PNA-based hybridization technology is developing rapidly within the field of in situ fluorescence hybridization, pointing out the great potential of PNA probes for chromosomal investigations.