Condensation of DNA by multivalent cations: experimental studies of condensation kinetics

Long ssRNA undergoes continuous compaction in the presence of polyvalent cations

In the presence of polyvalent cations, long double-stranded DNA (dsDNA) in dilute solution undergoes a single-molecule, first-order, phase transition ("condensation"), a phenomenon that has been documented and analyzed by many years of experimental and theoretical studies. There has been no systematic effort, however, to determine whether long single-stranded RNA (ssRNA) shows an analogous behavior. In this study, using dynamic light scattering, analytical ultracentrifugation, and gel electrophoresis, we examine the effects of increasing polyvalent cation concentrations on the effective size of long ssRNAs ranging from 3000 to 12,000 nucleotides. Our results indicate that ssRNA does not undergo a discontinuous condensation as does dsDNA but rather a "continuous" decrease in size with increasing polyvalent cation concentration. And, instead of the 10-fold decrease in size shown by long dsDNA, we document a 50% decrease, as demonstrated for a range of lengths and sequences of ssRNA.

The HIV-1 nucleocapsid chaperone protein forms locally compacted globules on long double-stranded DNA

The nucleocapsid (NC) protein plays key roles in Human Immunodeficiency Virus 1 (HIV-1) replication, notably by condensing and protecting the viral RNA genome and by chaperoning its reverse transcription into double-stranded DNA (dsDNA). Recent findings suggest that integration of viral dsDNA into the host genome, and hence productive infection, is linked to a small subpopulation of viral complexes where reverse transcription was completed within the intact capsid. Therefore, the synthesized dsDNA has to be tightly compacted, most likely by NC, to prevent breaking of the capsid in these complexes. To investigate NC’s ability to compact viral dsDNA, we here characterize the compaction of single dsDNA molecules under unsaturated NC binding conditions using nanofluidic channels. Compaction is shown to result from accumulation of NC at one or few compaction sites, which leads to small dsDNA condensates. NC preferentially initiates compaction at flexible regions along the dsDNA, such as AT-rich regions and DNA ends. Upon further NC binding, these condensates develop into a globular state containing the whole dsDNA molecule. These findings support NC’s role in viral dsDNA compaction within the mature HIV-1 capsid and suggest a possible scenario for the gradual dsDNA decondensation upon capsid uncoating and NC loss.

Nanoparticles for protein delivery in planta

Delivery of proteins into walled plant cells remains a challenge with few tractable solutions. Recent advances in biomacromolecule delivery using nanotechnology may evince methods to be exploited for protein delivery. While protein delivery remains no small feat, even in mammalian systems, the ability for nanoparticles to penetrate the cell wall and be decorated with a plethora of functional moieties makes them ideal protein vehicles in plants. As advances in protein biotechnology accelerate, so does the need for commensurate delivery systems. However, the road to nanoparticle-mediated protein delivery is fraught with challenges in regard to cell wall penetration, intracellular delivery, endosomal escape, and nanoparticle chemistry and design. The dearth of literature surrounding protein delivery in walled plant cells hints at the challenge of this problem but also indicates vast opportunity for innovations in plant-tailored nanotechnology.

α-Tocopherol-ascorbic acid hybrid antioxidant based cationic amphiphile for gene delivery: Design, synthesis and transfection

Natural antioxidants and vitamins have potential to protect biological systems from peroxidative damage induced by peroxyl radicals, α-tocopherol (Vitamin E, lipid soluble) and ascorbic acid (vitamin C, water soluble), well known natural antioxidant molecules. In the present study we described the synthesis and biological evaluation of hybrid of these two natural antioxidants with each other via ammonium di-ethylether linker, Toc-As in gene delivery. Two control cationic lipids N14-As and Toc-NOH are designed in such a way that one is with ascorbic acid moiety and no tocopherol moiety; another is with tocopherol moiety and no ascorbic acid moiety respectively. All the three cationic lipids can form self-assembled aggregates. The antioxidant efficiencies of the three lipids were compared with free ascorbic acid. The cationic lipids (Toc-As, N14-As and Toc-NOH) were formulated individually with a well-known fusogenic co-lipid DOPE and characterization studies such as DNA binding, heparin displacement, size, charge, circular dichroism were performed. The biological characterization studies such as cell viability assay and in vitro transfection studies were carried out with the above formulations in HepG2, Neuro-2a, CHO andHEK-293T cell lines. The three formulations showed their transfection efficiencies with highest in Toc-As, moderate inN14-As and least in Toc-NOH. Interestingly, the transfection efficiency observed with the antioxidant based conjugated lipid Toc-As is found to be approximately two and half fold higher than the commercially available lipofectamine 2000 at 4:1 charge ratio in Hep G2 cell lines. In the other cell lines studied the efficiency of Toc-As is found to be either higher or similarly active compared to lipofectamine 2000. The physicochemical characterization results show that Toc-As lipid is showing maximum antioxidant potency, strong binding with pDNA, least size and optimal zeta potential. It is also found to be least toxic in all the cell lines studied especially in Neuro-2a cell lines when compared to other two lipids. In summary, the designed antioxidant lipid can be exploited as a delivering system for treating ROS related diseases such as malignancy, brain stroke, etc.

Effect of Counterion Valence on Conformational Behavior of Spherical Polyelectrolyte Brushes Confined between Two Parallel Walls

We study the conformational behavior of spherical polyelectrolyte brushes in the presence of monovalent and trivalent counterions in a confined environment. The confinement is exerted by two parallel walls on the brushes. The enhancement of the confinement induces the extension of grafted chains. For the monovalent case, the increase of the charge fraction leads to extended brush conformation for different slit width (distance between two walls) but collapsed brush in the presence of trivalent counterions is observed. The confinement does not affect electrostatic correlation between trivalent counterions and charged monomers. However, it was found that narrow slit width contributes to stronger electrostatic correlation for the monovalent case. This is because more monovalent counterions are inside the brush at strong confinement, but almost all trivalent counterions are trapped into the brush independently of the slit width. The diffusion of counterions under the confinement is related to the electrostatic correlation. Our simulations also reveal that the brush thickness depends on the slit width nonlinearly.

Interfering with DNA High-Order Structures using Chiral Ruthenium(II) Complexes

In this work, it was found that DNA can undergo B-Z transformational changes and compaction in the presence of DNA intercalators such as ruthenium(II) polypyridyl complexes. The link between B-Z transition and condensation is weak but can be strengthened under certain circumstances with slight alterations to the structures of the ruthenium(II) complexes. Here, following on from previous research, this work reports a series of ruthenium(II) complexes with imidazophenanthroline ligands, which vary in size and planarity. The complexes exhibit distinct effects on DNA structures, ranging from little impact to the transformation of DNA secondary structures to the formation of higher-order DNA structures. Further studies on DNA morphological changes induced by chiral ruthenium(II) complexes are observed by atomic force microscopy and transmission electron microscopy.

Spermine Condenses DNA, but Not RNA Duplexes

Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA and some RNAs, such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA, and compare our findings with predictions of molecular-dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence containing a mixture of 14 GC pairs and 11 AU pairs resists condensation relative to DNA of an equivalent sequence or to 25 bp poly(rA):poly(rU) RNA. A comparison of wide-angle x-ray scattering profiles with simulation results suggests that spermine is sequestered deep within the major groove of mixed-sequence RNA. This prevents condensation by limiting opportunities to bridge to other molecules and stabilizes the RNA by locking it into a particular conformation. In contrast, for DNA, simulations suggest that spermine binds externally to the duplex, offering opportunities for intermolecular interaction. The goal of this study is to explain how RNA can remain soluble and available for interaction with other molecules in the cell despite the presence of spermine at concentrations high enough to precipitate DNA.

C 3-symmetric opioid scaffolds are pH-responsive DNA condensation agents

Herein we report the synthesis of tripodal C₃-symmetric opioid scaffolds as high-affinity condensation agents of duplex DNA. Condensation was achieved on both supercoiled and canonical B-DNA structures and identified by agarose electrophoresis, viscosity, turbidity and atomic force microscopy (AFM) measurements. Structurally, the requirement of a tris-opioid scaffold for condensation is demonstrated as both di- (C₂-symmetric) and mono-substituted (C₁-symmetric) mesitylene-linked opioid derivatives poorly coordinate dsDNA. Condensation, observed by toroidal and globule AFM aggregation, arises from surface-binding ionic interactions between protonated, cationic, tertiary amine groups on the opioid skeleton and the phosphate nucleic acid backbone. Indeed, by converting the 6-hydroxyl group of C₃-morphine (MC3) to methoxy substituents in C₃-heterocodeine (HC3) and C₃-oripavine (OC3) molecules, dsDNA compaction is retained thus negating the possibility of phosphate—hydroxyl surface-binding. Tripodal opioid condensation was identified as pH dependent and strongly influenced by ionic strength with further evidence of cationic amine-phosphate backbone coordination arising from thermal melting analysis and circular dichroism spectroscopy, with compaction also witnessed on synthetic dsDNA co-polymers poly[d(A-T)₂] and poly[d(G-C)₂]. On-chip microfluidic analysis of DNA condensed by C₃-agents provided concentration-dependent protection (inhibition) to site-selective excision by type II restriction enzymes: BamHI, HindIII, SalI and EcoRI, but not to the endonuclease DNase I.

A Simple Zn2+ Complex-Based Composite System for Efficient Gene Delivery

Metal complexes might become a new type of promising gene delivery systems because of their low cytotoxicity, structural diversity, controllable aqua- and lipo-solubility, and appropriate density and distribution of positive charges. In this study, Zn2+ complexes (1-10) formed with a series of ligands contained benzimidazole(bzim)were prepared and characterized. They were observed to have different affinities for DNA, dependent on their numbers of positive charges, bzim groups, and coordination structures around Zn2+. The binding induced DNA to condensate into spherical nanoparticles with ~ 50 nm in diameter. The cell transfection efficiency of the DNA nanoparticles was poor, although they were low toxic. The sequential addition of the cell-penetrating peptide (CPP) TAT(48-60) and polyethylene glycol (PEG) resulted in the large DNA condensates (~ 100 nm in diameter) and the increased cellular uptake. The clathrin-mediated endocytosis was found to be a key cellular uptake pathway of the nanoparticles formed with or without TAT(48-60) or/and PEG. The DNA nanoparticles with TAT(48-60) and PEG was found to have the cell transfection efficiency up to 20% of the commercial carrier Lipofect. These results indicated that a simple Zn2+-bzim complex-based composite system can be developed for efficient and low toxic gene delivery through the combination with PEG and CPPs such as TAT.

Substitution-inert trinuclear platinum complexes efficiently condense/aggregate nucleic acids and inhibit enzymatic activity

The trinuclear platinum complexes (TriplatinNC-A [{Pt(NH3 )3 }2 -μ-{trans-Pt(NH3 )2 (NH2 (CH2 )6 NH2 )2 }](6+) , and TriplatinNC [{trans-Pt(NH3 )2 (NH2 (CH2 )6 NH3 (+) )}2 -μ-{trans-Pt(NH3 )2 (NH2 (CH2 )6 NH2 )2 }](8+) ) are biologically active agents that bind to DNA through noncovalent (hydrogen bonding, electrostatic) interactions. Herein, we show that TriplatinNC condenses DNA with a much higher potency than conventional DNA condensing agents. Both complexes induce aggregation of small transfer RNA molecules, and TriplatinNC in particular completely inhibits DNA transcription at lower concentrations than naturally occurring spermine. Topoisomerase I-mediated relaxation of supercoiled DNA was inhibited by TriplatinNC-A and TriplatinNC at concentrations which were 60 times and 250 times lower than that of spermine. The mechanisms for the biological activity of TriplatinNC-A and TriplatinNC may be associated with their ability to condense/aggregate nucleic acids with consequent inhibitory effects on crucial enzymatic activities.

Photosensitive polyamines for high-performance photocontrol of DNA higher-order structure

Polyamines are small, ubiquitous, positively charged molecules that play an essential role in numerous biological processes such as DNA packaging, gene regulation, neuron activity, and cell proliferation. Here, we synthesize the first series of photosensitive polyamines (PPAs) and demonstrate their ability to photoreversibly control nanoscale DNA higher-order structure with high efficiency. We show with fluorescence microscopy imaging that the efficiency of the PPAs as DNA-compacting agents is directly correlated to their molecular charge. Micromolar concentration of the most efficient molecule described here, a PPA containing three charges at neutral pH, compacts DNA molecules from a few kilobase pairs to a few hundred kilobase pairs, while subsequent 3 min UV illuminations at 365 nm triggers complete unfolding of DNA molecules. Additional application of blue light (440 nm for 3 min) induces the refolding of DNA into the compact state. Atomic force microscopy reveals that the compaction involves a global folding of the whole DNA molecule, whereas UV-induced unfolding is a modification initiated from the periphery of the compacted DNA, resulting in the occurrence of intermediate flower-like structures prior to the fully unfolded state.

Adsorption behaviors of DNA/cation complexes on amino and silica chip surfaces: a dual polarization interferometry study

The adsorption of DNA/Ca(2+), DNA/Cu(2+), and DNA/Co(NH3)6(3+) complexes on amino and silica chip surfaces were investigated using dual polarization interferometry. A more compact DNA/cation complex layer formed on the amino chip surface compared with that on the silica chip surface at the same cation condition. The real-time mass, thickness, and density changes were monitored during the adsorption process. The overall results show that the approaching complexes can cause the conformation rearrangement of the preadsorbed complexes and the preadsorbed complexes affect the deposition pattern of the approaching complexes during the adsorption of DNA/Ca(2+) and DNA/Cu(2+) complexes on both chip surfaces. The relatively strong electrostatic repulsion between the approaching and adsorbed complexes results in multiple mass loading rate changes and loose attachment of the approaching complexes. The weak repulsion between the DNA/Co(NH3)6(3+) complexes cannot induce this kind of conformation rearrangement. Thus, no multiple mass loading rate changes were observed. Meanwhile, the preadsorbed DNA/Co(NH3)6(3+) complex can also affect the deposition pattern of the approaching complex because of the geometric resistance. Therefore, this study will help better understand the conformation change and deposition pattern of complexes with different charge conditions during the adsorption process on the solid-liquid interface.

Free terminal amines in DNA-binding peptides alter the product distribution from guanine radicals produced by single electron oxidation

PURPOSE

Electron deficient guanine radical species are major intermediates produced in DNA by the direct effect of ionizing irradiation. There is evidence that they react with amine groups in closely bound ligands to form covalent crosslinks. Crosslink formation is very poorly characterized in terms of quantitative rate and yield data. We sought to address this issue by using oligo-arginine ligands to model the close association of DNA and its binding proteins in chromatin.

MATERIALS AND METHODS

Guanine radicals were prepared in plasmid DNA by single electron oxidation. The product distribution derived from them was assayed by strand break formation after four different post-irradiation incubations.

RESULTS

We compared the yields of DNA damage produced in the presence of four ligands in which neither, one, or both of the amino and carboxylate termini were blocked with amides. Free carboxylate groups were unreactive. Significantly higher yields of heat labile sites were observed when the amino terminus was unblocked. The rate of the reaction was characterized by diluting the unblocked amino group with its amide blocked derivative.

CONCLUSION

These observations provide a means to develop quantitative estimates for the yields in which these labile sites are formed in chromatin by exposure to ionizing irradiation.

Deciphering the structure of DNA toroids

Toroids are small donut shaped organizational units within sperm chromatin and viruses containing DNA and protein. Investigators first characterized the dimensions of toroids created in vitro, in viruses and in decondensed sperm chromatin using transmission electron and atomic force microscopy. More recent measurements, performed using cryo-electron microscopy, have allowed experimenters to observe the hexagonal organization of DNA within viruses, and toroids created from DNA and cobalt hexammine. However, it has been difficult to obtain information about the assembly of DNA into a toroid, its structure and the biomechanical forces involved because of the limitations of these techniques. Similarly, biophysical studies of toroids utilizing techniques such as circular dichroism or light scattering are difficult to perform and interpret because toroids created using bulk DNA can aggregate and precipitate out of solution even at very low concentrations. The development of optical and magnetic traps has allowed experimenters to manipulate single DNA molecules within microfluidic, multichannel flow cells and measure the structural changes they undergo as they are transformed into toroids. During the past few years investigators have demonstrated that toroids consist of loops of DNA. They have observed the stepwise incorporation of these loops into a toroid that is not in contact with charged surfaces, which might affect its formation. The condensation of a constrained DNA molecule into a toroid was observed to significantly increase its tension, which reduced the size of the DNA loops that form the toroid. This structural information is important for understanding how genomic DNA is assembled and organized within the sperm cell and viruses. In this perspective we discuss what is known about the structure and formation of toroids, what has been learned recently using single molecule techniques and what remaining questions have the potential to be answered using these emerging technologies.

DNA condensations on mica surfaces induced collaboratively by alcohol and hexammine cobalt

We performed systematic studies of λ-DNA condensation on mica surfaces induced by alcohol and hexammine cobalt (III) [Co(NH(3))(6)(3+)] using atomic force microscopy (AFM). The critical condensation concentration for [Co(NH(3))(6)(3+)] was found to be about 10 microM; the DNA molecules extended freely on mica when the concentration was below the critical value. The morphology of condensed DNA became more compact with increasing concentration. At about 500 microM [Co(NH(3))(6)(3+)] concentration, no condensation patterns could be observed due to charge inversion of the compact structures resulting in failure of adhesion to the positively charged surfaces. The critical concentration for alcohol was about 15% (v/v). At this concentration, a few intramolecular loops could be observed in the AFM images. With increasing ethanol concentration the condensation pattern became more complicated ranging from flower-like to pancake-like. When the solution contained both alcohol and hexammine cobalt (III), DNA condensation patterns could be observed even when the concentrations of the two condensation agents were lower than their critical values. We observed this phenomenon by adding mixtures of 10% alcohol and 8 microM hexammine cobalt (III) to DNA solutions. The condensation patterns were more compact than those of the condensation agents separately. Typical toroids were found at an appropriate alcohol and hexammine cobalt (III) concentration. The collaborative condensation phenomenon was analyzed by electrostatic interaction and charge neutralization.

Single-molecule stretching studies of RNA chaperones

RNA chaperone proteins play significant roles in diverse biological contexts. The most widely studied RNA chaperones are the retroviral nucleocapsid proteins (NC), also referred to as nucleic acid (NA) chaperones. Surprisingly, the biophysical properties of the NC proteins vary significantly for different viruses, and it appears that HIV-1 NC has optimal NA chaperone activity. In this review we discuss the physical nature of the NA chaperone activity of NC. We conclude that the optimal NA chaperone must saturate NA binding, leading to strong NA aggregation and slight destabilization of all NA duplexes. Finally, rapid kinetics of the chaperone protein interaction with NA is another primary component of its NA chaperone activity. We discuss these characteristics of HIV-1 NC and compare them with those of other NA binding proteins and ligands that exhibit only some characteristics of NA chaperone activity, as studied by single molecule DNA stretching.

Visualizing the formation and collapse of DNA toroids

In living organisms, DNA is generally confined into very small volumes. In most viruses, positively charged multivalent ions assist the condensation of DNA into tightly packed toroidal structures. Interestingly, such cations can also induce the spontaneous formation of DNA toroids in vitro. To resolve the condensation dynamics and stability of DNA toroids, we use a combination of optical tweezers and fluorescence imaging to visualize in real-time spermine-induced (de)condensation in single DNA molecules. By actively controlling the DNA extension, we are able to follow (de)condensation under tension with high temporal and spatial resolution. We show that both processes occur in a quantized manner, caused by individual DNA loops added onto or removed from a toroidal condensate that is much smaller than previously observed in similar experiments. Finally, we present an analytical model that qualitatively captures the experimentally observed features, including an apparent force plateau.

Polyelectrolyte condensation in bulk, at surfaces, and under confinement

In this review we discuss recent results from computer simulations based on coarse-grained polyion models representing aqueous solutions of polyelectrolytes. The focus will be directed to the conformation of the polyions and, in particular, their condensation in bulk, induced by multivalent ions and oppositely charged polyelectrolytes, at responsive surfaces and under confinement.

DNA release dynamics from bioreducible poly(amido amine) polyplexes

The DNA release dynamics of bioreducible poly(amido amine) polyplexes were studied in real time by atomic force microscopy (AFM). DNA release is triggered by a depolymerization of high-molecular-weight polycations into low-molecular-weight oligocations that occurs by means of the thiol and disulfide exchange reaction mechanism. AFM images were captured in a simulated physiological reducing environment that used dithiothreitol. Distinctive stages of disassembly are common among various polyplexes that have different disulfide content, molecular weight, and polymer architecture, while the DNA release rate depends upon the disulfide content. In the first stage, polyplexes evolve from metastable structures into the more stable toroid structure upon the depolymerization. In the second stage, toroids either aggregate or fuse into larger toroids. In the last stage, DNA wormlike chains and loops are held by a central compact core. The results confirm the prospect of bioreducible poly(amido amine)s as controlled DNA delivery vectors. The study offers new physical insights into the DNA release pathway including intermediate structures that have a high degree of structural heterogeneity and disassembly induced particle growth. The study identifies disassembly induced colloidal and morphological instability as an important issue to be addressed.

Characterization of condensed plasmid DNA models for studying the direct effect of ionizing radiation

We have examined the changes in physical properties of aqueous solutions of the plasmid pUC18 that take place on the addition of the cationic oligopeptide penta-arginine. An increase in sedimentation rate and static light scattering, and changes in the nucleic acid CD spectrum all suggest that this ligand acts to condense the plasmid. Dynamic light scattering suggests the hydrodynamic radii of the condensate particles are a few micrometers, ca. 50-fold larger than that of the monomeric plasmid. Condensation of the plasmid also produces a ca. 100-fold decrease in the strand break yield produced by gamma irradiation. This extensive protection against reactive intermediates in the bulk of the solution implies that condensed plasmid DNA may offer a model system with which to study the direct effect of ionizing radiation (ionization of the DNA itself). The use of peptide ligands as condensing agents in this application is attractive because the derivatives of several amino acids (particularly tryptophan and tyrosine) have been shown to modify the radiation chemistry of DNA extensively.

Watching DNA condensation induced by poly(amido amine) dendrimers with time-resolved cryo-TEM

The condensation of DNA by poly(amido amine) dendrimers of generation 1, 2, and 4 has been followed by time-resolved cryogenic transmission electron microscopy (cryo-TEM). The recorded images show that significant morphological rearrangement occurs for DNA condensed with the lower generation dendrimers leading to the formation of toroidal aggregates. Higher charge density dendrimers, on the other hand, give rise to globular aggregates, where no transient morphologies are observed. We suggest that the dendrimers in this case are kinetically trapped as soon as they bind to the DNA strand.

Cationic peptides containing tyrosine protect against radiation-induced oxidative DNA damage

PURPOSE

To examine the effect of the amino acid tyrosine on oxidatively or direct-type damaged DNA damage when it is present in a DNA binding ligand.

MATERIALS AND METHODS

We made use of tetralysine ligands to ensure binding to DNA and to condense the DNA, and simulated direct-type damage by using gamma irradiation in the presence of thiocyanate ions. These ligands contained an additional C terminal amino acid. Phenylalanine was used as a control for tyrosine. These ligands were used in conjuction with a plasmid substrate to quantify strand break yields. Base damage yields were estimated by measuring the strand break yield after incubation of the plasmid with the bacterial base excision repair enzyme formamidopyrimidine-DNA N-glycosylase (FPG).

RESULTS

When the condensing ligand contains an additional tyrosine or tryptophan residue, the plasmid is protected against the effects of a single electron oxidation, as assayed by sensitivity to a base excision repair enzyme. This protection is significantly greater in condensed plasmid where the amino acid residues are in close proximity to the DNA, and can be observed even when only a small fraction of the ligand contains tyrosine.

CONCLUSIONS

Bound tyrosine residues located in close proximity to DNA are capable of reversing oxidative DNA damage far more efficiently than when present unbound in the bulk solution. This suggests that tyrosine residues in DNA binding proteins may participate in the repair of DNA that has been oxidatively damaged by ionizing radiation.

Photo-assisted gene delivery using light-responsive catanionic vesicles

Photoresponsive catanionic vesicles have been developed as a novel gene delivery vector combining enhanced cellular uptake with phototriggered release of vesicle payload following entry into cells. Vesicles with diameters ranging from 50 to 200 nm [measured using cryo-transmission electron microscopy (TEM) and light-scattering techniques] form spontaneously, following mixing of positively charged azobenzene-containing surfactant and negatively charged alkyl surfactant species. Fluorescent probe measurements showed that the catanionic vesicles at a cation/anion ratio of 7:3 formed at surfactant concentrations as low as 10 microM of the azobenzene surfactant under visible light (with the azobenzene surfactant species principally in the trans configuration), while 50-60 microM of the azobenzene surfactant is required to form vesicles under UV illumination (with the azobenzene surfactant species principally in the cis configuration). At intermediate surfactant concentrations (ca. 15-45 microM) under visible light conditions, transport of DNA-vesicle complexes occurred past the cell membrane of murine fibroblast NIH 3T3 cells through endocytosis. Subsequent UV illumination induced rupture of the vesicles and release of uncomplexed DNA into the cell interiors, where it was capable of passing through the nuclear membrane and thereby contributing to enhanced expression. Single-molecule fluorescent images of T4-DNA demonstrated that the formation of vesicles with a net positive charge led to compaction of DNA molecules via complex formation within a few seconds, while UV-induced disruption of the vesicle-DNA complexes led to DNA re-expansion to the elongated-coil state, also within a few seconds. Transfection experiments with eGFP DNA revealed that photoresponsive catanionic vesicles are more effectively taken up by cells compared to otherwise identical alkyl (i.e., nonazobenzene-containing and thus nonlight-responsive) catanionic vesicles, presumably because of pi-pi stacking interactions that enhance bilayer rigidity in the photoresponsive vesicles. Subsequent UV illumination following endocytosis leads to further dramatic enhancements in the transfection efficiencies, demonstrating that vector unpacking and release of DNA from the carrier complex can be the limiting step in the overall process of gene delivery.

Atomic force microscopy and surface-enhanced Raman scattering detection of DNA based on DNA-nanoparticle complexes

We report a simple method for the label-free detection of double-stranded DNA using surface-enhanced Raman scattering (SERS). We prepared cetyltrimethylammonium bromide (CTAB)-capped silver nanoparticles and a DNA-nanoparticle complex by adding silver nanoparticles to lambda-DNA solutions. In the present study, the utilization of CTAB-capped silver nanoparticles facilitates the electrostatic interaction between DNA molecules and silver nanoparticles; at the same time, the introduction of DNA avoids adding aggregating agent for the formation of nanoparticle aggregates to obtain large enhancement of DNA, because the DNA acts as both the probe molecules and aggregating agent of Ag nanoparticles. Atomic force microscopy (AFM) studies show that the morphology of DNA-Ag nanoparticle complexes seems to be determined by the concentrations of the DNA and the nanoparticles. Surface-enhanced Raman scattering (SERS) studies show that the morphology of the complexes plays a significant role in the intensity of SERS signals of DNA, and the best signal enhancement of DNA can be obtained by fine-tuning the experimental parameters. The SERS spectrum affords important structural information about the bases, phosphate backbone, and the conformation of DNA after mixing the DNA solutions with the Ag sol.

Confinement of DNA in water-in-oil microemulsions

The study of systems that allow DNA condensation in confined environments is an important task in producing cell-mimicking microreactors capable of biochemical activities. The water droplets formed in water-in-oil emulsions are potentially good candidates for such microcompartments. The anionic surfactant AOT was used here to stabilize the droplets. We have studied in detail the DNA distribution and the structural modifications of these microemulsion drops by varying the concentration and molecular weight of DNA and using various techniques such as light, X-ray, and neutron scattering, electrical conductivity, and surface tension. DNA induces the formation of large drops into which it is internalized. The size of these drops depends on the amount of DNA dissolved in water as well as on its molecular weight. The local DNA concentration is very high (>100 mg/mL). The large drops coexist with small empty drops (not containing DNA), similar to those found in the DNA-free microemulsion.

Applied chemistry of natural DNA

Recently, natural DNA has emerged as an appealing biomacromolecule for functional materials. It is abundant and renewable, and possesses the well known double helix structure that promises many unique properties difficult to find in other polymers. Natural DNA has been applied in electronic, optical and biomaterials, as a catalyst for enantioselective reactions, and as a material for cleaning the environment. Most of the applications are based on combining DNA with other chemicals or nanoparticles by electrostatic binding, intercalation or groove binding. In this critical review article, recent developments in utilizing natural DNA are reviewed by focusing on three basic properties of DNA: the electrostatic property as a polyelectrolyte, selective affinity for small molecules, and biocompatibility (128 references).

Influence of decavanadate clusters on the rheological properties of gelatin

The influence of polyoxovanadate clusters ([H(2)V(10)O(28)](4-)) on the thermo-reversible gelation of porcine skin gelatin solution (type A, M w approximately 40 000 g.mol (-1), pH = 3.4 << isoelectric point (IEP) approximately 8) has been investigated as a function of temperature and vanadate concentration by combining rheology and microcalorimetry. This work shows that the rheological properties of the system depend on electrostatic interactions between [H(2)V(10)O(28)](4-) and positively charged gelatin chains. In a first stage, we describe the renaturation of the gelatin triple helices in the presence of decavanadate clusters. We reveal that, when gelatin chains are in coil conformation (30 degrees C < T < 50 degrees C), the inorganic clusters act as physical cross-linkers that govern the visco-elastic properties of the mixture with an exponential dependence of the (G', G'') modulus with the vanadate concentration. Below 30 degrees C, we show that gelatin triple helix nucleation is slightly favored by the presence of vanadate, but above a helix concentration of 0.012 g.cm (-3), G' is fully governed by the helix concentration. During the melting process, we reveal the non-fully reversible behavior of the vanadate/gelatin rheological properties and the stabilization of gelatin triple helices due to vanadate species until 50 degrees C. This non-reversible character has also been observed in the same experimental conditions with collagen/vanadate solutions. This is the first time that such a stabilization of triple helices has been reported in the case of gelatin hydrogels chemically cross-linked or not. We propose to analyze these results by considering that triple helix aggregates should persist because of decavanadate bridging, that the nucleation of an extended triple helix network may induce a strong modification of the vanadate cross-linker distribution in the system, or both, thus promoting the formation of thermally stable vanadate/gelatin micro-gels in the dangling end of the triple helices.

Retroviral nucleocapsid proteins display nonequivalent levels of nucleic acid chaperone activity

Human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) is a nucleic acid chaperone that facilitates the remodeling of nucleic acids during various steps of the viral life cycle. Two main features of NC's chaperone activity are its abilities to aggregate and to destabilize nucleic acids. These functions are associated with NC's highly basic character and with its zinc finger domains, respectively. While the chaperone activity of HIV-1 NC has been extensively studied, less is known about the chaperone activities of other retroviral NCs. In this work, complementary experimental approaches were used to characterize and compare the chaperone activities of NC proteins from four different retroviruses: HIV-1, Moloney murine leukemia virus (MLV), Rous sarcoma virus (RSV), and human T-cell lymphotropic virus type 1 (HTLV-1). The different NCs exhibited significant differences in their overall chaperone activities, as demonstrated by gel shift annealing assays, decreasing in the order HIV-1 approximately RSV > MLV >> HTLV-1. In addition, whereas HIV-1, RSV, and MLV NCs are effective aggregating agents, HTLV-1 NC, which exhibits poor overall chaperone activity, is unable to aggregate nucleic acids. Measurements of equilibrium binding to single- and double-stranded oligonucleotides suggested that all four NC proteins have moderate duplex destabilization capabilities. Single-molecule DNA-stretching studies revealed striking differences in the kinetics of nucleic acid dissociation between the NC proteins, showing excellent correlation between nucleic acid dissociation kinetics and overall chaperone activity.

Characterization of the nanostructure of complexes formed by a redox-active cationic lipid and DNA

We report characterization of the nanostructures of complexes formed between the redox-active lipid bis(n-ferrocenylundecyl)dimethylammonium bromide (BFDMA) and DNA using small-angle neutron scattering (SANS) and cryogenic transmission electron microscopy (cryo-TEM). A particular focus was directed to the influence of lipid oxidation state (where reduced BFDMA has a net charge of +1 and oxidized BFDMA has a charge of +3) on the nanostructures of the solution aggregates formed. Complexes were characterized over a range of charge ratios of reduced BFDMA to DNA (1.1:1, 2.75:1, and 4:1) in solutions of 1 mM Li2SO4. For these complexes, a single peak in the SANS data at 1.2 nm(-1) indicated that a nanostructure with a periodicity of 5.2 nm was present, similar to that observed with complexes of the classical lipids DODAB/DOPE and DNA (multilamellar spacing of 7.0 nm). The absence of additional Bragg peaks in all the SANS data indicated that the periodicity did not extend over large distances. Both inverse Fourier transform analysis and form factor fitting suggested formation of a multilamellar vesicle. These results were confirmed by cryo-TEM images in which multilamellar complexes with diameters between 50 and 150 nm were observed with no more than seven lamellae per aggregate. In contrast to complexes of reduced BFDMA and DNA, Bragg peaks were absent in SANS spectra of complexes formed by oxidized BFDMA and DNA at all charge ratios investigated. The low-q behavior of the SANS data obtained using oxidized BFDMA and DNA complexes suggested that large, loose aggregates were formed, consistent with complementary cryo-TEM images showing predominantly loose disordered aggregates. Some highly ordered spongelike and cubic phase nanostructures were also detected in cryo-TEM images. We conclude that control of BFDMA oxidation state can be used to manipulate the nanostructures of lipid-DNA complexes formed using BFDMA.

Lipoplexes formed by DNA and ferrocenyl lipids: effect of lipid oxidation state on size, internal dynamics, and zeta-potential

The effect of lipid oxidation state on the physical properties of complexes formed by plasmid DNA and the redox-active lipid bis-(11-ferrocenylundecyl)dimethylammonium bromide (BFDMA) is reported. With increasing concentration of BFDMA, the hydrodynamic sizes of complexes formed by BFDMA and DNA (in the presence of 1 mM Li(2)SO(4)) pass through a maximum and the zeta-potential changes monotonically from -40 mV to +40 mV. In contrast, complexes formed by oxidized BFDMA and DNA exhibit a minimum in size and maintain a negative zeta-potential with increasing concentration of BFDMA. Angle-dependent dynamic light scattering measurements also reveal the presence of relaxation processes within complexes formed by DNA and oxidized BFDMA that are absent for complexes formed by DNA and reduced BFDMA. These results, when combined, reveal that the amphiphilic nature of reduced BFDMA leads to lipoplexes with physical properties resembling those formed by classical cationic lipids, whereas the interaction of oxidized BFDMA with DNA is similar to that of nonamphiphilic cationic molecules bearing multiple charges (e.g., spermidine). In particular, the negative zeta-potential and measurable presence of DNA chain dynamics within complexes formed by oxidized BFDMA and DNA indicate that these complexes are loosely packed with excess charge due to DNA in their outer regions. These results, when combined with additional measurements performed in OptiMEM reduced-serum cell culture medium, lead to the proposition that the strong dependence of transfection efficiency on the oxidation state of BFDMA, as reported previously, is largely a reflection of the substantial change in the zeta-potentials of these complexes with changes in the oxidation state of BFDMA.

Langevin dynamics of semiflexible polyelectrolytes: rod-toroid-globule-coil structures and counterion distribution

We have investigated the nature of counterion condensation on uniformly charged semiflexible polyelectrolyte chains and the concomitant configurations by monitoring the role of chain stiffness, chain length, counterion valency, and the strength of electrostatic interaction. The counterion condensation is seen to follow the adsorption process and the effective polymer charge increases with chain stiffness. Size and shape, as calculated through the radius of gyration, effective persistence length, and hydrodynamic radius, are studied. Stable coil-like, globular, folded-chain, toroidal, and rodlike configurations are possible at suitable combinations of values of chain stiffness, chain length, electrostatic interaction strength, and the valency of counterion. For high strengths of electrostatic interactions, sufficiently stiff polyelectrolytes form toroids in the presence of multivalent counterions, whereas flexible polyelectrolytes form disordered globules. The kinetic features of the nucleation and growth of toroids are monitored. Several metastable structures are found to frustrate the formation of toroids. The generic pathway involves the nucleation of one primary loop somewhere along the chain contour, followed by a growth process where the rest of the chain is folded continuously on top of the primary loop. The dependence of the average radii of toroids on the chain length is found to be roughly linear, in disagreement with existing scaling arguments.

Dynamic and static light scattering analysis of DNA ejection from the phage lambda

With the aid of time-resolved dynamic light scattering (DLS) and static light scattering (SLS), we have analyzed the ejection kinetics from the bacterial virus bacteriophage (or phage) lambda , triggered in vitro by its receptor. We have used DLS to investigate the kinetics in such a system. Furthermore, we have shown that both SLS and DLS can be interchangeably used to study the process of phage DNA release. DLS is superior to SLS in that it also allows the change in the light scattering arising from each of the components in the system to be monitored under conditions such that the relaxation times are separable. With help of these two methods we present a model explaining the reason for the observed decrease in the scattering intensity accompanying DNA ejection from phage. We emphasize that ejection from phage capsid occurs through a very long tail (which is nearly three times longer than the capsid diameter), which significantly separates ejected DNA from the scattering volume of the capsid. The scattering intensity recorded during the DNA ejection process is the result of a change in the form factor of the phage particle, i.e., the change in the interference effects between the phage capsid and the DNA confined in the phage particle. When the DNA molecule is completely ejected it remains in the proximity of the phage for some time, thus contributing to the scattering signal as it diffuses away from the phage capsid, into the scattering volume and returns to its unperturbed chain conformation in bulk solution. The free DNA chain does not contribute to the scattered intensity, when measured at a large angle, due to the DNA form factor and the low concentration. Although the final diffusion-controlled step can lead to overestimation of the real ejection time, we can still use both scattering methods to estimate the initial DNA ejection rates, which are mainly dependent on the pressure-driven DNA ejection from the phage, allowing studies of the effects of various parameters affecting the ejection.

Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte

A statistical mechanical model is presented which explicitly accounts for the fluctuations, the electrostatic, and the excluded volume correlations for ions bound to a polyelectrolyte such as DNA. The method can be employed to treat a wide range of ionic conditions including multivalent ions. The microscopic framework of the theory permits the use of realistic finite length and grooved structural model for the polyelectrolyte and modeling of the finite size of the bound ions. Test against Monte Carlo simulations suggests that the theory can give accurate predictions for the ion distribution and the thermodynamic properties. For multivalent ions, the theory makes improved predictions as compared with the mean-field approach. Moreover, for long polyelectrolyte and dilute salt concentration, the theory predicts ion binding properties that agree with the counterion condensation theory.

Polyelectrolytes in solutions with multivalent salt. Effects of flexibility and contour length

It has been experimentally observed that trivalent ions are capable of promoting compaction of semi-flexible polyelectrolyte chains. In this work we perform Monte Carlo simulations on single chain model systems with varying chain size and stiffness and evaluate the action of multivalent salt on the chain conformation. It is observed that longer chains tend to achieve relatively more compact conformations than shorter ones, and the dimensions of the collapsed structures do not significantly vary with contour length. The influence of contour length and intrinsic stiffness in the process of ion condensation is studied by analysis of the ion-ion nearest-neighbor distribution. The general trend is an increase of the degree of ion condensation as the chain length increases, in accordance with experimental evidence. A decreased importance of end-effects and, especially, larger volume charge densities are responsible for such behavior. The influence of chain stiffness is nontrivial, and depends on salt concentration. The results emphasize the complex nature of ion-correlation phenomena in flexible or semi-flexible chains and call for the development of more sophisticated analytical theories.

Copolymers of poly-L-lysine with serine and tryptophan form stable DNA vectors: implications for receptor-mediated gene transfer

Inefficient gene transfer and poor stability in physiological medium are important shortcomings for receptor-mediated gene transfer vectors. Here, we evaluate vectors formulated with random copolymers of L-lysine/L-serine (3:1) and L-lysine/L-tryptophan (4:1), focusing on both their biophysical and functional characterization. By means of dynamic light scattering (DLS) and transmission electron microscopy (TEM), we demonstrate that poly-L-lysine (pK), poly-L-lysine-L-tryptophan (pKW) and poly-L-lysine-L-serine (pKS) are able to form compacted, small particles when mixed with plasmid DNA in the absence of salt. Upon dilution in physiological medium, copolymers of both lys/ser and lys/trp do not aggregate, in contrast with poly-L-lysine DNA complexes as determined by scattering, DLS and TEM measurements. Tight packing, as demonstrated by resistance to heparin, SDS and trypsin treatments, is also featured in tryptophan-containing complexes. Successful receptor-mediated endocytosis gene transfer using galactosylated copolymers into cells expressing the asiagloglycoprotein receptor correlated with lack of aggregation. Particles obtained using galactosylated poly-L-lysine-L-tryptophan (Gal-pKW) copolymer demonstrated specific receptor-mediated gene transfer since reporter gene activity dropped in the presence of an excess ligand in the culture medium during transfection. Although copolymers of galactosylated poly-L-lysine-L-serine (Gal-pKS) do not aggregate in the presence of salt, they are not able to internalize in a specific receptor-mediated endocytosis fashion. The introduction of bulky aromatic/hydrophobic (tryptophan) or hydrophillic (serine) moieties into the positively charged vectors allows the compacted particles to disperse into salt-containing medium avoiding salt-induced aggregation. Moreover, tryptophan-containing particles are able to mediate specific gene transfer via receptor-mediated endocytosis.