The observation of the local ordering characteristics of spermidine-condensed DNA: atomic force microscopy and polarizing microscopy studies

Unveiling Sticholysin II and plasmid DNA interaction: Implications for developing non-viral vectors

Non-viral gene delivery systems offer significant potential for gene therapy due to their versatility, safety, and cost advantages over viral vectors. However, their effectiveness can be hindered by the challenge of efficiently releasing the genetic cargo from endosomes to prevent degradation in lysosomes. To overcome this obstacle, functional components can be incorporated into these systems. Sticholysin II (StII) is one of the pore-forming proteins derived from the sea anemone Stichodactyla helianthus, known for its high ability to permeabilize cellular and model membranes. In this study, we aimed to investigate the interaction between StII, and a model plasmid (pDNA) as an initial step towards designing an improved vector with enhanced endosomal escape capability. The electrophoretic mobility shift assay (EMSA) confirmed the formation of complexes between StII and pDNA. Computational predictions identified specific residues involved in the StII-DNA interaction interface, highlighting the importance of electrostatic interactions and hydrogen bonds in mediating the binding. Atomic force microscopy (AFM) of StII-pDNA complexes revealed the presence of nodular fiber and toroid shapes. These complexes were found to have a predominantly micrometer size, as confirmed by dynamic light scattering (DLS) measurements. Despite increase in the overall charge, the complexes formed at the evaluated nitrogen-to-phosphorus (N/P) ratios still maintained a negative charge. Moreover, StII retained its pore-forming capacity regardless of its binding to the complexes. These findings suggest that the potential ability of StII to permeabilize endosomal membranes could be largely maintained when combined with nucleic acid delivery systems. Additionally, the still remaining negative charge of the complexes would enable the association of another positively charged component to compact pDNA. However, to minimize non-specific cytotoxic effects, it is advisable to explore methods to regulate the protein's activity in response to the microenvironment.

Covalent Conjugation of Carbon Dots with Plasmid and DNA Condensation Thereafter: Realistic Insights into the Condensate Morphology, Energetics, and Photophysics

The use of carbon quantum dots (CDs) as trackable nanocarriers for plasmid and gene as hybrid DNA condensates has gained momentum, as evident from the significant recent research efforts. However, the in-depth morphology of the condensates, the energetics of the condensation process, and the photophysical aspects of the CD are not well understood and often disregarded. Herein, for the first time, we covalently attached linearized pUC19 with citric acid and cysteamine-derived CD through the reaction of the surface amine groups of CDs with the 5'-phospho-methyl imidazolide derivative of the plasmid to obtain a 1:1 CD-pUC19 covalent conjugate. The CD-pUC19 conjugates were further transformed into DNA condensates with spermine that displayed a toroidal morphology with a diameter of ∼200 nm involving ∼2-5 CD-pUC19 conjugates in a single condensate. While the interaction of pristine CD to spermine was exothermic, the binding of the CD-pUC19 conjugate with spermine was endothermic and primarily entropy-driven. The condensed plasmid displayed severe conformational stress and deviation from the B-form due to the compact packing of the DNA but better transfection ability than the pristine CD. The CDs in the condensates tend to come close to each other at the core that results in their shielding from excitation. However, this does not prevent them from emanating reactive oxygen species on visible light exposure that compromises the decondensation process and cell viability at higher exposure times, calling for utmost caution in establishing them as nonviral transfecting agents universally.

A Comprehensive Biophysical Analysis of the Effect of DNA Binding Drugs on Protamine-induced DNA Condensation

DNA condensation is a ubiquitous phenomenon in biology, yet the physical basis for it has remained elusive. Here, we have explored the mechanism of DNA condensation through the protamine-DNA interaction, and by examining on it the influence of DNA binding drugs. We observed that the DNA condensation is accompanied by B to Ψ-DNA transition as a result of DNA base pair distortions due to protamine binding, bringing about the formation of toroidal structure through coil-globule transition. The binding energetics suggested that electrostatic energy, bending energy and hydration energy must play crucial roles in DNA condensation. EtBr intercalation interferes with the protamine-DNA interaction, challenging the distortion of the DNA helix and separation of DNA base pairs by protamine. Thus, EtBr, by competing directly with protamine, resists the phenomenon of DNA condensation. On the contrary, netropsin impedes the DNA condensation by an allosteric mechanism, by resisting the probable DNA major groove bending by protamine. In summary, we demonstrate that drugs with distinct binding modes use different mechanism to interfere with DNA condensation.

Versatile Analysis of DNA-Biomolecule Interactions in Solution by Hydrodynamic Separation and Single Molecule Detection

DNA can interact with a wide array of molecules with a range of binding affinities, stoichiometry, and size-scales. We present a sensitive, quantitative, and versatile platform for sensing and evaluating these diverse DNA-biomolecule interactions and DNA conformational changes in free solution. Single molecule free solution hydrodynamic separation utilizes differences in hydrodynamic mobility to separate bound DNA-biomolecule complexes from unbound DNA and determine the associated size change that results from binding. Single molecule detection enables highly quantitative analysis of the fraction of DNA in the bound and unbound state to characterize binding behavior including affinity, stoichiometry, and cooperativity. A stacked injection scheme increases throughput to enable practical analysis of DNA-biomolecule interactions using only picoliters of sample per measurement. To demonstrate analysis of DNA-protein interactions on a local scale, we investigate binding of the E. coli single stranded binding protein to two DNA oligos both individually and in direct competition. We show that stoichiometry and cooperativity is a function of DNA length and verify these differences in binding characteristics through direct competition. To demonstrate analysis of DNA-small molecule interactions and global conformational changes, we also assess DNA condensation with the polyamine spermidine. We use hydrodynamic mobility to evaluate the size of spermidine-condensed DNA and single molecule burst analysis to evaluate DNA packing within the condensed globules relative to free-coiled DNA. This platform thus presents a versatile tool capable of quantitative and sensitive evaluation of diverse biomolecular interactions, complex properties, and binding characteristics.

Promotion of homology-directed DNA repair by polyamines

Polyamines, often elevated in cancer cells, have been shown to promote cell growth and proliferation. Whether polyamines regulate other cell functions remains unclear. Here, we explore whether and how polyamines affect genome integrity. When DNA double-strand break (DSB) is induced in hair follicles by ionizing radiation, reduction of cellular polyamines augments dystrophic changes with delayed regeneration. Mechanistically, polyamines facilitate homologous recombination-mediated DSB repair without affecting repair via non-homologous DNA end-joining and single-strand DNA annealing. Biochemical reconstitution and functional analyses demonstrate that polyamines enhance the DNA strand exchange activity of RAD51 recombinase. The effect of polyamines on RAD51 stems from their ability to enhance the capture of homologous duplex DNA and synaptic complex formation by the RAD51-ssDNA nucleoprotein filament. Our work demonstrates a novel function of polyamines in the maintenance of genome integrity via homology-directed DNA repair.

The maintenance polyamines homeostasis is important for cell growth, and several cancers harbor elevated levels of polyamines that may contribute to sustained proliferative potential. Here the authors demonstrate that polyamines participate in DNA double-strand break repair through the stimulation of RAD51-mediated homologous DNA pairing and strand exchange.

Double domain polyethylenimine-based nanoparticles for integrin receptor mediated delivery of plasmid DNA

The objective of the present study is to conjugate L-thyroxine PEI derivative onto another PEI to compensate the amine content of the whole structure which has been utilized for the ligand conjugation. Since α_vβ₃ integrin receptors are over-expressed on cancer cells and there is binding site for L-thyroxine on these receptors, PEI conjugation by L-thyroxine along with restoring the PEI amine content might be an efficient strategy for targeted delivery using polymeric nanoparticles. The results demonstrated the ability of the PEI conjugate in the formation of nanoparticles with the size of around 210 nm with higher buffering capacity. The conjugated PEI derivative increased the transfection efficiency in the cell lines over-expressing integrin by up to two folds higher than unmodified PEI, whereas in the cell lines lacking the integrin receptors there was no ligand conjugation-associated difference in gene transfer ability. The specificity of transfection demonstrated the delivery of plasmid DNA through integrin receptors. Also, the results of in vivo imaging of the polyplexes revealed that ^99mTc-labeled PEI/plasmid DNA complexes accumulated in kidney and bladder 4 h post injection. Therefore, this PEI derivative could be considered as an efficient targeted delivery system for plasmid DNA.

Preparation, characterization, and transfection efficiency of low molecular weight polyethylenimine-based nanoparticles for delivery of the plasmid encoding CD200 gene

Various strategies have been utilized to improve both gene transfer efficiency and cell-induced toxicity of polyethylenimine (PEI), the most extensively investigated cationic polymeric vector. In this study, we sought to enhance transfection efficiency of low molecular weight PEI (LMW PEI) while maintaining its low toxicity by cross-linking LMW PEI via succinic acid linker. These modifications were designed to improve the hydrophilic–hydrophobic balance of the polymer, by enhancing the buffering capacity and maintaining low cytotoxic effects of the final conjugate. Decreased expression of CD200 in the central nervous system has been considered as one of the proposed mechanisms associated with neuroinflammation in multiple sclerosis; therefore, we selected plasmid-encoding CD200 gene for transfection using the modified PEI derivatives. Dynamic light scattering experiments demonstrated that the modified PEIs were able to condense plasmid DNA and form polyplexes with a size of approximately 130 nm. The highest level of CD200 expression was achieved at a carrier to plasmid ratio of 8, where the expression level was increased by 1.5 fold in the SH-SY5Y cell line, an in vitro model of neurodegenerative disorders. Furthermore, the results of in vivo imaging of the LMW PEI-based nanoparticles in the mouse model of multiple sclerosis revealed that fluorescently labeled plasmid encoding CD200 was distributed from the injection site to various tissues and organs including lymph nodes, liver, brain, and finally, kidneys. The nanoparticles also showed the ability to cross the blood–brain barrier and enter the periventricular area.

Cationic Liposomes Modified with Polyallylamine as a Gene Carrier: Preparation, Characterization and Transfection Efficiency Evaluation

Purpose: Cationic polymers and cationic liposomes have shown to be effective non-viral gene delivery vectors. In this study, we tried to improve the transfection efficiency by employing the advantages of both. Methods: For this purpose, modified polyallylamines (PAAs) were synthesized. These modifications were done through the reaction of PAA (15 KDa) with acrylate and 6-bromoalkanoic acid derivatives. Liposomes comprising of these cationic polymers and cationic lipid were prepared and extruded through polycarbonate filters to obtain desired size. Liposome-DNA nanocomplexes were prepared in three carrier to plasmid (C/P) ratios. Size, zeta potential and DNA condensation ability of each complex were characterized separately and finally transfection efficiency and cytotoxicity of prepared vectors were evaluated in Neuro2A cell line. Results: The results showed that mean particle size of all these nanocomplexes was lower than 266 nm with surface charge of 22.0 to 33.9 mV. Almost the same condensation pattern was observed in all vectors and complete condensation was occurred at C/P ratio of 1.5. The lipoplexes containing modified PAA 15 kDa with 10% hexyl acrylate showed the highest transfection efficacy and lowest cytotoxicity in C/P ratio of 0.5. Conclusion: In some cases nanocomplexes consisting of cationic liposome and modified PAA showed better transfection activity and lower cytotoxicity compared to PAA.

Selective condensation of DNA by aminoglycoside antibiotics

The condensing effect of aminoglycoside antibiotics on the structure of double-stranded DNA was examined. The selective condensation of DNA by small molecules is an interesting approach in biotechnology. Here, we present the interaction between calf thymus DNA and three types of antibiotic molecules: tobramycin, kanamycin, and neomycin. Several techniques were applied to study this effect. Atomic force microscopy, transmission electron microscopy images, and nuclear magnetic resonance spectra showed that the interaction of tobramycin with double-stranded DNA caused the rod, toroid, and sphere formation and very strong condensation of DNA strands, which was not observed in the case of other aminoglycosides used in the experiment. Studies on the mechanisms by which small molecules interact with DNA are important in understanding their functioning in cells, in designing new and efficient drugs, or in minimizing their adverse side effects. Specific interactions between tobramycin and DNA double helix was modeled using molecular dynamics simulations. Simulation study shows the aminoglycoside specificity to bend DNA double helix, shedding light on the origins of toroid formation. This phenomenon may lighten the ototoxicity or nephrotoxicity issues, but also other adverse reactions of aminoglycoside antibiotics in the human body.

Compaction of bacterial genomic DNA: clarifying the concepts

The unconstrained genomic DNA of bacteria forms a coil, whose volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to occupy the whole available volume when constrained to fit in the cell. Still, it has been known for more than half a century that the DNA is localized in a well-defined region of the cell, called the nucleoid, which occupies only 15% to 25% of the total volume. Although this problem has focused the attention of many scientists in recent decades, there is still no certainty concerning the mechanism that enables such a dramatic compaction. The goal of this Topical Review is to take stock of our knowledge on this question by listing all possible compaction mechanisms with the proclaimed desire to clarify the physical principles they are based upon and discuss them in the light of experimental results and the results of simulations based on coarse-grained models. In particular, the fundamental differences between ψ-condensation and segregative phase separation and between the condensation by small and long polycations are highlighted. This review suggests that the importance of certain mechanisms, like supercoiling and the architectural properties of DNA-bridging and DNA-bending nucleoid proteins, may have been overestimated, whereas other mechanisms, like segregative phase separation and the self-association of nucleoid proteins, as well as the possible role of the synergy of two or more mechanisms, may conversely deserve more attention.

DNA conformational changes induced by cationic gemini surfactants: the key to switching DNA compact structures into elongated forms

The extent of DNA decompaction induced by m-s-m gemini surfactants depend on the surfactant's tail length and on spacer's length.

Targeting double-stranded RNA with spermine, 1-naphthylacetyl spermine and spermidine: a comparative biophysical investigation

RNA targeting is an evolving new approach to anticancer therapeutics that requires identification of small molecules to selectively target specific RNA structures. In this report, the interaction of biogenic polyamines spermine, spermidine and the synthetic analogue 1-naphthylacetyl spermine with three double-stranded RNA polynucleotides--poly(I)·poly(C), poly(C)·poly(G), and poly(A)·poly(U)--has been described to understand the structural and thermodynamic basis of the binding and the comparative efficacy of the analogue over the natural polyamines. Circular dichroism spectroscopy, thermal melting experiments, and ethidium bromide displacement assay were used to characterize the interaction. Microcalorimetry studies were performed to deduce the energetics of the interaction and atomic force microscopy experiments done to gain insight into the interaction at the molecular level. The experiments demonstrated structural perturbations in the polynucleotides on binding of the polyamines. Thermal melting studies showed enhanced stabilization of RNA-polyamine complexes with increase in the total standard molar enthalpy of transition. The binding affinity was strongest for poly(I)·poly(C) as revealed by microcalorimetry results and varied as poly(I)·poly(C) > poly(C)·poly(G) > poly(A)·poly(U). The order of affinity for the polyamines was spermine >1-naphthylacetyl spermine > spermidine. Total enthalpy-entropy compensation and high standard molar heat capacity values characterized the interactions. The results of the study on the binding of polyamines to dsRNAs presented here have been compared to those reported earlier with dsDNAs. The present findings advance our knowledge on the mechanism of interaction of polyamines with RNA and may help in the search for analogues that can interfere with biogenic polyamine metabolism and function.

Conjugation of poly(amidoamine) dendrimers with various acrylates for improved delivery of plasmid encoding interleukin-12 gene

In this study, a small library of polyamidoamine (PAMAM) derivatives was prepared through the conjugation of its amines with various acrylates containing 5–21 carbon chain lengths at two different conjugation degrees, and the ability of the nano-sized PAMAM-based complexes to transfer the plasmid encoding interleukin-12 (IL-12) gene into the cells was studied. As the wide clinical application of the recombinant IL-12 protein has been limited due to several deaths reported following the systemic administration of the protein, local expression of the IL-12 gene inside the tumor target has been considered as an effective alternative strategy. The idea subjacent to this type of modification was to enhance transfection efficiency by the synergistic effects of endosome buffering via the PAMAM amines and the interaction with biological membranes caused by the hydrophobic moieties grafted on the PAMAM structure. Acrylate conjugation of primary amines on PAMAM structure enhanced transfection efficiency, with the highest level of IL-12 expression occurring with the conjugates containing five to nine carbon chains on their periphery at the grafting degree of 10%. The results obtained in this study suggest that combining the cationic nature of PAMAM along with modulating the hydrophobicity of the dendrimer to achieve an appropriate hydrophobic-hydrophilic balance yields the optimal carriers for non-viral gene delivery.

Nanostructure-induced DNA condensation

The control of the DNA condensation process is essential for compaction of DNA in chromatin, as well as for biological applications such as nonviral gene therapy. This review endeavours to reflect the progress of investigations on DNA condensation effects of nanostructure-based condensing agents (such as nanoparticles, nanotubes, cationic polymer and peptide agents) observed by using atomic force microscopy (AFM) and other techniques. The environmental effects on structural characteristics of nanostructure-induced DNA condensates are also discussed.

Assembly of single-stranded DNA onto HOPG surface at different temperature: atomic force microscopy study

Assembly of long single-stranded DNA (ssDNA) and short oligodeoxynucleotides onto bare highly oriented pyrolytic graphite (HOPG) at different temperature has been studied. It was indicated that both long ssDNA and oligodeoxynucleotides can sequentially form network, straight chains, and layer structures when the adsorption temperature was changed from room temperature, 37-55°C. High-resolution atomic force microscopy (AFM) imaging of the layer structures revealed that they are composed of parallel ssDNA chains with relatively higher height and tend to form patterns with three-fold symmetry. These new findings are significantly important for understanding assembly characterization of ssDNA. In addition, this assembly method for ssDNA is expected to be used for preparation of DNA structures in biosensing and DNA-based nanodevices.

Intrinsic dynamics of DNA-polymer complexes: a mechanism for DNA release

The transfer of genetic material into cells using nonviral vectors offers unique potential for therapeutics; however, the efficacy of delivery depends upon a poorly understood, multistep pathway, limiting the prospects for successful gene delivery. Mechanistic insight into DNA association and release has been hampered by a lack of atomic resolution structural and dynamic information for DNA-polymer complexes (polyplexes). Here, we report a dendrimer-based polyplex system containing poly(ethyleneglycol) (PEG) arms that is suitable for atomic-level characterization by solution NMR spectroscopy. NMR chemical shift, line width, and proton transverse relaxation rate measurements reveal that free and dendrimer-bound polyplex DNA exchange rapidly relative to the NMR time scale (<millisecond). The dendrimers retain a high degree of mobility in the polyplex, whereas the DNA shows restrained mobility, suggesting that the polyplex is a highly dynamic complex with a rapidly exchanging dendrimer atmosphere around a more rigid DNA framework.

Critical behavior of megabase-size DNA toward the transition into a compact state

We studied the changes in the higher-order structure of a megabase-size DNA (S120-1 DNA) under different spermidine (SPD) concentrations through single-molecule observations using fluorescence microscopy (FM) and atomic force microscopy (AFM). We examined the difference between the folding transitions in S120-1 DNA and sub-megabase-size DNA, T4 DNA (166 kbp). From FM observations, it is found that S120-1 DNA exhibits intra-chain segregation as the intermediate state of transition, in contrast to the all-or-none nature of the transition on T4 DNA. Large S120-1 DNA exhibits a folding transition at lower concentrations of SPD than T4 DNA. AFM observations showed that DNA segments become aligned in parallel on a two-dimensional surface as the SPD concentration increases and that highly intense parallel alignment is achieved just before the compaction. S120-1 DNA requires one-tenth the SPD concentration as that required by T4 DNA to achieve the same degree of parallel ordering. We theoretically discuss the cause of the parallel ordering near the transition into a fully compact state on a two-dimensional surface, and argue that such parallel ordering disappears in bulk solution.

Biomolecular Triconjugates Formed between Gold, Protamine, and Nucleic Acid: Comparative Characterization on the Nanoscale

DNA and RNA micro- and nanoparticles are increasingly being used for gene and siRNA drug delivery and a variety of other applications in bionanotechnology. On the nanoscale, these entities represent unique challenges from a physicochemical characterization perspective. Here, nucleic acid conjugates with protamine and gold nanoparticles (GNP) were characterized comparatively in the nanorange of concentration by UV/Vis NanoDrop spectroscopy, fluorimetry, and gel electrophoresis. Given the intense interest in splice-site switching oligomers (SSOs), we utilized a human tumor cell culture system (HeLa pLuc-705), in which SSO-directed splicing repair upregulates luciferase expression, in order to investigate bioactivity of the bionanoconjugates. Process parameters important for bioactivity were investigated, and the bimolecular nanoconjugates were confirmed by shifts in the dynamic laser light scatter (DLLS), UV/Vis spectrum, gel electrophoresis, or sedimentation pattern. The data presented herein may be useful in the future development of pharmaceutical and biotechnology formulations, processes, and analyses concerning protein, DNA, or RNA bionanoconjugates.

Characterizing DNA condensation and conformational changes in organic solvents

Organic solvents offer a new approach to formulate DNA into novel structures suitable for gene delivery. In this study, we examined the in situ behavior of DNA in N, N-dimethylformamide (DMF) at low concentration via laser light scattering (LLS), TEM, UV absorbance and Zeta potential analysis. Results revealed that, in DMF, a 21bp oligonucleotide remained intact, while calf thymus DNA and supercoiled plasmid DNA were condensed and denatured. During condensation and denaturation, the size was decreased by a factor of 8–10, with calf thymus DNA forming spherical globules while plasmid DNA exhibited a toroid-like conformation. In the condensed state, DNA molecules were still able to release the counterions to be negatively charged, indicating that the condensation was mainly driven by the excluded volume interactions. The condensation induced by DMF was reversible for plasmid DNA but not for calf thymus DNA. When plasmid DNA was removed from DMF and resuspended in an aqueous solution, the DNA was quickly regained a double stranded configuration. These findings provide further insight into the behavior and condensation mechanism of DNA in an organic solvent and may aid in developing more efficient non-viral gene delivery systems.

Method to improve DNA condensation efficiency by alkali treatment

The improvement of DNA's bioactivities by altering their structure is meaningful for their biological applications, ranging from DNA condensation study to gene therapeutic research. In this study, we treated the plasmid DNA with alkali and investigated the structure and the condensation efficiency of the alkali-treated DNA. We noticed that the alkali treatment could significantly increase the DNA condensation efficiency with spermidine and polyethylenimine (PEI). In addition, due to the improved interactions between the alkali-treated DNA and PEI, gene transfection experiments could be performed in the presence of less PEI. This research can contribute to the creation of a universal method to enhance the interaction between DNA and gene delivery vectors by alkali treatment, and should have significant potential in the field of gene therapy.

Patterning of 293T fibroblasts on a mica surface

Controllable cell growth on the defined areas of surfaces is important for potential applications in biosensor fabrication and tissue engineering. In this study, controllable cell growth was achieved by culturing 293 T fibroblast cells on a mica surface which had been patterned with collagen strips by a microcontact printing (microCP) technique. The collagen area was designed to support cell adhesion and the native mica surface was designed to repel cell adhesion. Consequently, the resulting cell patterns should follow the micro-patterns of the collagen. X-ray photoelectron spectroscopy (XPS), water contact angle (WCA) measurement, atomic-force microscope (AFM) observation, and force-curve measurement were used to monitor property changes before and after the collagen adsorption process. Further data showed that the patterned cells were of good viability and able to perform a gene-transfection experiment in vitro. This technique should be of potential applications in the fields of biosensor fabrication and tissue engineering.

Polymorphism of the SOD1-DNA aggregation species can be modulated by DNA

Proteinaceous aggregates rich in copper, zinc superoxide dismutase (SOD1) have been found in both in vivo and in vitro models. We have shown that double-stranded DNA that acts as a template accelerates the in vitro formation of wild-type SOD1 aggregates. Here, we examined the polymorphism of templated-SOD1 aggregates generated in vitro upon association with DNA under different conditions. Electron microscopy imaging indicates that this polymorphism is capable of being manipulated by the shapes, structures, and doses of the DNAs tested. The nanometer- and micrometer-scale aggregates formed under acidic conditions and under neutral conditions containing ascorbate fall into three classes: aggregate monomers, oligomeric aggregates, and macroaggregates. The aggregate monomers observed at given DNA doses exhibit a polymorphism that is markedly corresponded to the coiled shapes of linear DNA and structures of plasmid DNA. On the other hand, the regularly branched structures observed under both atomic force microscopy and optical microscope indicate that the DNAs tested are simultaneously condensed into a nanoparticle with a specific morphology during SOD1 aggregation, revealing that SOD1 aggregation and DNA condensation are two concurrent phenomena. The results might provide the basis of therapeutic approaches to suppress the formation of toxic protein oligomers or aggregates by screening the toxicity of the protein aggregates with various sizes and morphologies.

Peptide-functionalized poly(ethylene glycol) star polymers: DNA delivery vehicles with multivalent molecular architecture

Exploring the development of nonviral nucleic acid delivery vectors with progressive, specific, and novel designs in molecular architecture is a fundamental way to investigate how aspects of chemical and physical structure impact the transfection process. In this study, macromolecules comprised of a four-arm star poly(ethylene glycol) and termini modified with one of five different heparin binding peptides have been investigated for their ability to bind, compact, and deliver DNA to mammalian cells in vitro. These new delivery vectors combine a PEG-derived stabilizing moiety with peptides that exhibit unique cell-surface binding ability in a molecular architecture that permits multivalent presentation of the cationic peptides. Five peptide sequences of varying heparin binding affinity were studied; each was found to sufficiently bind heparin for biological application. Additionally, the macromolecules were able to bind and compact DNA into particles of proper size for endocytosis. In biological studies, the PEG-star peptides displayed a range of toxicity and transfection efficiency dependent on the peptide identity. The vectors equipped with peptides of highest heparin binding affinity were found to bind DNA tightly, increase levels of cellular internalization, and display the most promising transfection qualities. Our results suggest heparin binding peptides with specific sequences hold more potential than nonspecific cationic polymers to optimize transfection efficiency while maintaining cell viability. Furthermore, the built-in multivalency of these macromolecules may allow simultaneous binding of both DNA at the core of the polyplex and heparan sulfate on the surface of the cell. This scheme may facilitate a bridging transport mechanism, tethering DNA to the surface of the cell and subsequently ushering therapeutic nucleic acids into the cell. This multivalent star shape is therefore a promising architectural feature that may be exploited in the design of future polycationic gene delivery vectors.

A luminescent beta-cyclodextrin-based Ru(phen)3 complex as DNA compactor, enzyme inhibitor, and translocation tracer

A beta-cyclodextrin-based Ru(phen)(3) complex (1) has been synthesized and exhibits good luminescent behavior. Atomic force microscopic and scanning electron microscopic studies show that 1 can induce the aggregation of originally circular DNA to toroidal or spherical shapes. The morphology of these DNA aggregates changes following a pathway of naked circular DNA --> toroid with gaps --> solid toroid --> spherical aggregate, depending on the different 1/DNA (w/w) ratios, and their average diameters vary from the nanometer to micrometer scale. Owing to its capability of inducing the aggregation of DNA, 1 can be used as an inhibitor for DNA topoisomerase and DNA cleavage enzymes. Further studies by means of fluorescence microscopy indicate that 1 can also efficiently trace the translocation of DNA into 293T cells (the human embryonic kidney cell line). These observations consequently establish 1 as not only a potential DNA carrier but also a fluorescent DNA probe.

Atomic force microscopy reveals the assembly of potential DNA “nanocarriers” by poly-l-ornithine

Atomic force microscopy (AFM) has been used to visualize the process of condensation of plasmid DNA by poly-L-ornithine on mica surface. AFM images reveal that the transition of negatively charged DNA to condensed nanoparticles on addition of increasing amounts of positively charged poly-L-ornithine (charge ratio (Z+/Z-) varied between 0.1 and 1) at a wide range of DNA concentrations (3-20 ng/microl) occurs through formation of several distinct morphologies. The nature of the complexes is strongly dependent on both the charge ratio and the DNA concentration. Initiation of condensation when the concentration of DNA is low (approximately 3-7 ng/microl) occurs possibly through formation of monomolecular complexes which are thick rod-like in shape. On the contrary, when condensation is carried out at DNA concentrations of 13-20 ng/microl, multimolecular structures are also formed even at low charge ratios. This difference in pathway seems to result in differences in the extent of condensation as well as size and aggregation of the nanoparticles formed at the high charge ratios. To the best of our knowledge, this is the first direct single molecule elucidation of the mechanism of DNA condensation by poly-L-ornithine. Cationic poly-aminoacids like poly-L-ornithine are known to be efficient in delivery of plasmid DNA containing therapeutic genes in a variety of mammalian cell lines by forming condensed "nanocarriers" with DNA. Single molecule insight into the mechanism by which such nanocarriers are packaged during the condensation process could be helpful in predicting efficacy of intracellular delivery and release of DNA from them and also provide important inputs for design of new gene delivery vectors.

Influence of charged surfaces on the morphology of DNA condensed with multivalent ions

DNA in solution can be condensed into dense aggregates by multivalent counterions. Here we investigate the effect of a nearby surface on the morphology of DNA condensates. We show that, contrary to what has often been assumed, interactions between DNA condensates and the surface can strongly influence the observed morphology. This limits the usefulness of surface probes such as atomic force microscopy for studying the morphology of condensates in bulk solution. Surprisingly, we find that the most negatively charged surface disturbs the condensate morphology most, suggesting that the microscopic mechanism resulting in DNA condensation is also responsible for the attractive force between DNA and the surface.

Influence of DNA condensation state on transfection efficiency in DNA/polymer complexes: an AFM and DLS comparative study

Atomic force microscopy (AFM) is used to describe the formation process of polymer/DNA complexes. Two main objectives of this research are presented. The first one is to apply AFM as an effective tool to analyse DNA molecules and different polycation/DNA complexes in order to evaluate their degree of condensation (size and shape). The other one is to search for a relationship between the condensation state of DNA and its transfection efficiency. In this study, linear methacrylate based polymers and globular SuperFect polymers are used in order to induce DNA condensation. Ternary complexes, composed of methacrylate based polymers and polyethylene glycol (PEG)-based copolymers, are also investigated. AFM allows us to confirm good condensation conditions and relate them (or not) to transfection efficiencies. These AFM results (obtained after drying in air) are compared with measurements deduced from Dynamic Light Scattering (DLS) experiments performed in water. This comparison allowed us to identify the structural modifications resulting from deposition on the mica surface.

A new approach to DNA bending by polyamines and its implication in DNA condensation

Polyamines are known to induce dynamical bending of DNA molecules. This mechanism is very important since many DNA binding proteins (DNAse, transcription factor, etc.) exert their action by their ability to bend DNA. We propose an analytical model which describes the dynamical bending of DNA by polyamine ions in highly diluted DNA solutions. The bending probability depends on the entropy loss of polyamines due to their localization. This localization is facilitated by the electrostatic repulsion between multivalent counterions condensed on DNA, which reduces the entropy loss in counterion localization. Therefore DNA bending by polyamines depends on the competition between monovalent counterions and polyamines. We find that the bending probability is weak for a low binding ratio of polyamines (i.e. number of bound polyamines per base pair), whereas a high bending probability can be reached at large polyamine binding ratio. In addition, we describe a new mechanism of DNA bending. It occurs with the help of thermal agitation, which initiates the bending and favours the polyamine localization. This model provides further insights into DNA bending by polyamines and its implication in DNA condensation. A qualitative estimation of the DNA bending probability is obtained by measuring the cleavage efficiency of DNA by bleomycin versus spermidine concentration. Indeed, a local helix distortion by polyamines results in an amplification of the double-strand cleavage by bleomycin. The measurement of the bleomycin amplification is performed by analysing images of DNA molecules with atomic force microscope. Some features of the dynamical bending indicate that condensation and bending are interrelated.