The effect of ionic conditions on the conformations of supercoiled DNA. I. Sedimentation analysis

Potentials of a Plasma-Aerosol System for Wound Healing Advanced by Drug Introduction: An In Vitro Study

Cold plasmas have found their application in a wide range of biomedical fields by virtue of their high chemical reactivity. In the past decades, many attempts have been made to use cold plasmas in wound healing, and within this field, many studies have focused on plasma-induced cell proliferation mechanisms. In this work, one step further has been taken to demonstrate the advanced role of plasma in wound healing. To this end, the simultaneous ability of plasma to induce cell proliferation and permeabilize treated cells has been examined in the current study. The driving force was to advance the wound healing effect of plasma with drug delivery. On this subject, we demonstrate in vitro the healing effect of Ar, Ar+N₂ plasma, and their aerosol counterparts. A systematic study has been carried out to study the role of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in cell adhesion, signaling, differentiation, and proliferation. An additional investigation was also performed to study the permeabilization of cells and the delivery of the modeled drug carrier fluorescein isothiocyanate (FITC) labeled dextran into cells upon plasma treatment. Short 35 s plasma treatments were found to promote fibroblast adhesion, migration, signaling, proliferation, and differentiation by means of reactive oxygen and nitrogen species (RONS) created by plasma and deposited into the cell environment. The impact of the plasma downstream products NO₂^- and NO₃^- on the expressions of the focal adhesion's genes, syndecans, and collagens was observed to be prominent. On the other hand, the differentiation of fibroblasts to myofibroblasts was mainly initiated by ROS produced by the plasma. In addition, the ability of plasma to locally permeabilize fibroblast cells was demonstrated. During proliferative cell treatment, plasma can simultaneously induce cell membrane permeabilization (d ∼ 7.3 nm) by the species OH and H₂O₂. The choice for a plasma or a plasma-aerosol configuration thus allows the possibility to change the spatial chemistry of drug delivery molecules and thus to locally deliver drugs. Accordingly, this study offers a pivotal step toward plasma-assisted wound healing advanced by drug delivery.

RADIATION-INDUCED PLASMID DNA DAMAGE: EFFECT OF CONCENTRATION AND LENGTH

Plasmid DNA is commonly used as a simpler substitute for a cell in studies of early effects of ionizing radiation because it allows to determine yields of primary DNA lesions. Experimental studies often employ plasmids of different lengths, in different concentrations in the aqueous solution. Influence of these parameters on the heavy-ion induced yields of primary DNA damage has been studied, using plasmids pUC19 (2686 bp), pBR322 (4361 bp) and pKLAC2 (9107 bp) in 10 and 50 ng/μl concentration. Results demonstrate the impact of plasmid length, while no significant difference was observed between the two concentrations. The uncertainty of the results is discussed.

Periodic Motion of Sedimenting Flexible Knots

We study the dynamics of knotted deformable closed chains sedimenting in a viscous fluid. We show experimentally that trefoil and other torus knots often attain a remarkably regular horizontal toroidal structure while sedimenting, with a number of intertwined loops, oscillating periodically around each other. We then recover this motion numerically and find out that it is accompanied by a very slow rotation around the vertical symmetry axis. We analyze the dependence of the characteristic timescales on the chain flexibility and aspect ratio. It is observed in the experiments that this oscillating mode of the dynamics can spontaneously form even when starting from a qualitatively different initial configuration. In numerical simulations, the oscillating modes are usually present as transients or final stages of the evolution, depending on chain aspect ratio and flexibility, and the number of loops.

A model of lipid rearrangements during pore formation in the DPPC lipid bilayer

CONTEXT

The molecular bases of pore formation in the lipid bilayer remain unclear, as do the exact characteristics of their sizes and distributions. To understand this process, numerous studies have been performed on model lipid membranes including cell-sized giant unilamellar vesicles (GUV). The effect of an electric field on DPPC GUV depends on the lipid membrane state: in the liquid crystalline phase the created pores have a cylinder-like shape, whereas in the gel phase a crack has been observed.

OBJECTIVE

The aim of the study was to investigate the geometry of pores created in a lipid bilayer in gel and liquid crystalline phases in reference to literature experimental data.

METHODS

A mathematical model of the pore in a DPPC lipid bilayer developed based on the law of conservation of mass and the assumption of constant volume of lipid molecules, independent of their conformation, allows for analysis of pore shape and accompanying molecular rearrangements.

RESULTS

The membrane area occupied by the pore of a cylinder-like shape is greater than the membrane area occupied by lipid molecules creating the pore structure (before pore appearance). Creation of such pores requires more space, which can be achieved by conformational changes of lipid chains toward a more compact state. This process is impossible for a membrane in the most compact, gel phase.

DISCUSSION AND CONCLUSIONS

We show that the geometry of the pores formed in the lipid bilayer in the gel phase must be different from the cylinder shape formed in the lipid bilayer in a liquid crystalline state, confirming experimental studies. Furthermore, we characterize the occurrence of the 'buffer' zone surrounding pores in the liquid crystalline phase as a mechanism of separation of neighbouring pores.

Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation

Topological constraints, such as those associated with DNA supercoiling, play an integral role in genomic regulation and organization in living systems. However, physical understanding of the principles that underlie DNA organization at biologically relevant length scales remains a formidable challenge. We develop a coarse-grained simulation approach for predicting equilibrium conformations of supercoiled DNA. Our methodology enables the study of supercoiled DNA molecules at greater length scales and supercoiling densities than previously explored by simulation. With this approach, we study the conformational transitions that arise due to supercoiling across the full range of supercoiling densities that are commonly explored by living systems. Simulations of ring DNA molecules with lengths at the scale of topological domains in the Escherichia coli chromosome (∼10 kilobases) reveal large-scale conformational transitions elicited by supercoiling. The conformational transitions result in three supercoiling conformational regimes that are governed by a competition among chiral coils, extended plectonemes, and branched hyper-supercoils. These results capture the nonmonotonic relationship of size versus degree of supercoiling observed in experimental sedimentation studies of supercoiled DNA, and our results provide a physical explanation of the conformational transitions underlying this behavior. The length scales and supercoiling regimes investigated here coincide with those relevant to transcription-coupled remodeling of supercoiled topological domains, and we discuss possible implications of these findings in terms of the interplay between transcription and topology in bacterial chromosome organization.

Enhanced purification of plasmid DNA isoforms by exploiting ionic strength effects during ultrafiltration

The solution structure of plasmid DNA is known to be a strong function of solution conditions due to intramolecular electrostatic interactions between the charged phosphate groups along the DNA backbone. The objective of this work was to determine whether it was possible to enhance the use of ultrafiltration for separation of different plasmid isoforms by proper selection of the solution ionic strength and ion type. Experiments were performed with a 3.0 kbp plasmid using composite regenerated cellulose ultrafiltration membranes. The transmission of the linear isoform was nearly independent of solution ionic strength, but increased significantly with increasing filtrate flux due to the elongation of the highly flexible plasmid in the converging flow field into the membrane pores. In contrast, the transmission of the open-circular and supercoiled plasmids both increased with increasing NaCl or MgCl2 concentration due to the change in plasmid size and conformational flexibility. The effect of ionic strength was greatest for the supercoiled plasmid, providing opportunities for enhanced purification of this therapeutically active isoform. This behavior was confirmed using experiments performed with binary mixtures of the different isoforms. These results clearly demonstrate the potential for enhancing the performance of membrane systems for plasmid DNA separations by proper selection of the ionic conditions.

Orientation of DNA Minicircles Balances Density and Topological Complexity in Kinetoplast DNA

Kinetoplast DNA (kDNA), a unique mitochondrial structure common to trypanosomatid parasites, contains thousands of DNA minicircles that are densely packed and can be topologically linked into a chain mail-like network. Experimental data indicate that every minicircle in the network is, on average, singly linked to three other minicircles (i.e., has mean valence 3) before replication and to six minicircles in the late stages of replication. The biophysical factors that determine the topology of the network and its changes during the cell cycle remain unknown. Using a mathematical modeling approach, we previously showed that volume confinement alone can drive the formation of the network and that it induces a linear relationship between mean valence and minicircle density. Our modeling also predicted a minicircle valence two orders of magnitude greater than that observed in kDNA. To determine the factors that contribute to this discrepancy we systematically analyzed the relationship between the topological properties of the network (i.e., minicircle density and mean valence) and its biophysical properties such as DNA bending, electrostatic repulsion, and minicircle relative position and orientation. Significantly, our results showed that most of the discrepancy between the theoretical and experimental observations can be accounted for by the orientation of the minicircles with volume exclusion due to electrostatic interactions and DNA bending playing smaller roles. Our results are in agreement with the three dimensional kDNA organization model, initially proposed by Delain and Riou, in which minicircles are oriented almost perpendicular to the horizontal plane of the kDNA disk. We suggest that while minicircle confinement drives the formation of kDNA networks, it is minicircle orientation that regulates the topological complexity of the network.

Sound packing DNA: packing open circular DNA with low-intensity ultrasound

Supercoiling DNA (folding DNA into a more compact molecule) from open circular forms requires significant bending energy. The double helix is coiled into a higher order helix form; thus it occupies a smaller footprint. Compact packing of DNA is essential to improve the efficiency of gene delivery, which has broad implications in biology and pharmaceutical research. Here we show that low-intensity pulsed ultrasound can pack open circular DNA into supercoil form. Plasmid DNA subjected to 5.4 mW/cm² intensity ultrasound showed significant (p-values <0.001) supercoiling compared to DNA without exposure to ultrasound. Radiation force induced from ultrasound and dragging force from the fluid are believed to be the main factors that cause supercoiling. This study provides the first evidence to show that low-intensity ultrasound can directly alter DNA topology. We anticipate our results to be a starting point for improved non-viral gene delivery.

Topological Behavior of Plasmid DNA

The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and genetics. Powerful techniques were developed to reveal a myriad of different structural conformations that change B-DNA as it is transcribed, replicated, and recombined and as sister chromosomes are moved into new daughter cell compartments during cell division. This article links the original discoveries of superhelical structure and molecular topology to non-B form DNA structure and contemporary biochemical and biophysical techniques. The emphasis is on the power of plasmids for studying DNA structure and function. The conditions that trigger the formation of alternative DNA structures such as left-handed Z-DNA, inter- and intra-molecular triplexes, triple-stranded DNA, and linked catenanes and hemicatenanes are explained. The DNA dynamics and topological issues are detailed for stalled replication forks and for torsional and structural changes on DNA in front of and behind a transcription complex and a replisome. The complex and interconnected roles of topoisomerases and abundant small nucleoid association proteins are explained. And methods are described for comparing in vivo and in vitro reactions to probe and understand the temporal pathways of DNA and chromosome chemistry that occur inside living cells.

Surface charge effects on the 2D conformation of supercoiled DNA

We have adsorbed plasmid pUc19 DNA on a supported bilayer. By varying the fraction of cationic lipids in the membrane, we have tuned the surface charge. Plasmid conformations were imaged by Atomic Force Microscopy (AFM). We performed two sets of experiments: deposition from salt free solution on charged bilayers and deposition from salty solutions on neutral bilayers. Both sets show similar trends: at low surface charge density or low bulk salt concentration, the internal electrostatic repulsion forces plasmids to adopt completely opened structures, while at high surface charge density or higher bulk salt concentration, usual supercoiled plectonemes are observed. We experimentally demonstrate the equivalence of surface screening by mobile interfacial charges and bulk screening from salt ions. At low to medium screening, the electrostatic repulsion at plasmid crossings is predominant, leading to a number of crossovers decreasing linearly with the characteristic screening length. We compare our data with an analytical 2D-equilibrated model developed recently for the system and extract the DNA effective charge density when strands are adsorbed at the surface.

Sedimentation of knotted polymers

We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show that the sedimentation coefficient s, related to the terminal velocity of the knotted polymers, increases linearly with the average crossing number n(c) of the corresponding ideal knot. This provides direct computational confirmation of this relation, postulated on the basis of sedimentation experiments by Rybenkov et al. [J. Mol. Biol. 267, 299 (1997)]. Such a relation was previously shown to hold with simulations for knot electrophoresis. We also show that there is an accurate linear dependence of s on the inverse of the radius of gyration R(g)(-1), more specifically with the inverse of the R(g) component that is perpendicular to the direction along which the polymer sediments. When the polymer sediments in a slab, the walls affect the results appreciably. However, R(g)(-1) remains to a good precision linearly dependent on n(c). Therefore, R(g)(-1) is a good measure of a knot's complexity.

Dynamics and control of the two-pulse protocol in electroporation: numerical exploration

Externally applied voltages can create transient, non-selective pores in a cell's membrane, a phenomenon known as electroporation. Electroporation has reduced toxicity, is easy to perform, and does not induce the immune system. Therefore, the technique has a wide range of biological and medical applications. Previous experiments show that a two-pulse protocol, which consists of a fast, large-magnitude pulse and a slow, small-magnitude pulse, can increase the efficiency of drug delivery such as gene electrotransfer. In this work, we investigate the dynamics and control of the two-pulse protocol using a macroscopic model of electroporation. Numerical simulations show that there exists a range of pore radii that cannot be sustained using the conventional, open-loop, two-pulse protocol. As a result, one may need to use pores that are significantly larger than the sizes of the targeted molecules. Moreover, it is not possible to know the rate of delivery a priori. To ensure accurate drug delivery and avoid potential damage to the cell's membrane, we explore feedback mechanisms to eliminate the gap in sustainable pore radii and thus to precisely control the electroporation process. Numerical simulations show that a straightforward feedback algorithm can achieve robust control effects. Moreover, the control algorithm is effective without knowledge of the model and thus has the potential to be implemented in experiments.

Properties of knotted ring polymers. II. Transport properties

We have calculated the hydrodynamic radius R(h) and intrinsic viscosity [eta] of both lattice self-avoiding rings and lattice theta-state rings that are confined to specific knot states by our path-integration technique. We observe that naive scaling arguments based on the equilibrium polymer size fail for both the hydrodynamic radius and the intrinsic viscosity, at least over accessible chain lengths. (However, we do conjecture that scaling laws will nevertheless prevail at sufficiently large N.) This failure is attributed to a "double" cross-over. One cross-over effect is the transition from delocalized to localized knotting: in short chains, the knot is distributed throughout the chain, while in long chains it becomes localized in only a portion of the chain. This transition occurs slowly with increasing N. The other cross-over, superimposed upon the first, is the so-called "draining" effect, in which transport properties maintain dependence on local structure out to very large N. The hydrodynamic mobility of knotted rings of the same length and backbone structure is correlated with the average crossing number X of the knots. The same correlation between mobility and knot complexity X has been observed for the gel-electrophoretic mobility of cyclic DNA molecules.

Preparation of DNA and nucleoprotein samples for AFM imaging

Sample preparation techniques allowing reliable and reproducible imaging of DNA with various structures, topologies and complexes with proteins are reviewed. The major emphasis is given to methods utilizing chemical functionalization of mica, enabling preparation of the surfaces with required characteristics. The methods are illustrated by examples of imaging of different DNA structures. Special attention is given to the possibility of AFM to image the dynamics of DNA at the nanoscale. The capabilities of time-lapse AFM in aqueous solutions are illustrated by imaging of dynamic processes as transitions of local alternative structures (transition of DNA between H and B forms). The application of AFM to studies of protein-DNA complexes is illustrated by a few examples of imaging site-specific complexes, as well as such systems as chromatin. The time-lapse AFM studies of protein-DNA complexes including very recent advances with the use of high-speed AFM are reviewed.

Dynamics of an electrostatically charged elastic rod in fluid

We investigate the effects of electrostatic and steric repulsion on the dynamics of a pre-twisted charged elastic rod immersed in a viscous incompressible fluid. Equations of motion of the rod include the fluid–structure interaction, rod elasticity and a combination of two interactions that prevent self-contact, namely the electrostatic interaction and hard-core repulsion. The governing equations are solved using the generalized immersed-boundary method. We find that after perturbation, a pre-twisted minicircle collapses into a compact supercoiled configuration. The collapse proceeds along a complex trajectory that may pass near several unstable equilibrium configurations, before it settles in a locally stable equilibrium. The dwell time near an unstable equilibrium can be up to several microseconds. Both the final configuration and the transition path are sensitive to the initial excess link, ionic strength of the solvent and the initial perturbation.

Effect of crowding on the conformation of interwound DNA strands from neutron scattering measurements and Monte Carlo simulations

With a view to determining the distance between the two opposing duplexes in supercoiled DNA, we have measured small angle neutron scattering from pHSG298 plasmid (2675 base pairs) dispersed in saline solutions. Experiments were carried out under full and zero average DNA neutron scattering contrast using hydrogenated plasmid and a 1:1 mixture of hydrogenated and perdeuterated plasmid, respectively. In the condition of zero average contrast, the scattering intensity is directly proportional to the single DNA molecule scattering function (form factor), irrespective of the DNA concentration and without complications from intermolecular interference. The form factors are interpreted with Monte Carlo computer simulation. For this purpose, the many body problem of a dense DNA solution was reduced to the one of a single DNA molecule in a congested state by confinement in a cylindrical potential. It was observed that the interduplex distance decreases with increasing concentration of salt as well as plasmid. Therefore, besides ionic strength, DNA crowding is shown to be important in controlling the interwound structure and site juxtaposition of distal segments of supercoiled DNA. This first study exploiting zero average DNA contrast has been made possible by the availability of perdeuterated plasmid.

Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity

Agarose-gel electrophoresis has been used for more than thirty years to characterize the linking-number (Lk) distribution of closed-circular DNA molecules. Although the physical basis of this technique remains poorly understood, the gel-electrophoretic behavior of covalently closed DNAs has been used to determine the local unwinding of DNA by proteins and small-molecule ligands, characterize supercoiling-dependent conformational transitions in duplex DNA, and to measure helical-repeat changes due to shifts in temperature and ionic strength. Those results have been analyzed by assuming that the absolute mobility of a particular topoisomer is mainly a function of the integral number of superhelical turns, and thus a slowly varying function of plasmid molecular weight. In examining the mobilities of Lk topoisomers for a series of plasmids that differ incrementally in size over more than one helical turn, we found that the size-dependent agarose-gel mobility of individual topoisomers with identical values of Lk (but different values of the excess linking number, DeltaLk) vary dramatically over a duplex turn. Our results suggest that a simple semi-empirical relationship holds between the electrophoretic mobility of linking-number topoisomers and their average writhe in solution.

Determining protein-induced DNA bending in force-extension experiments: theoretical analysis

Computer simulations were used to investigate the possibility of determining protein-induced DNA bend angles by measuring the extension of a single DNA molecule. Analysis of the equilibrium sets of DNA conformations showed that shortening of DNA extension by a single protein-induced DNA bend can be as large as 35 nm. The shortening has a maximum value at the extending force of approximately 0.1 pN. At this force, the DNA extension experiences very large fluctuations that dramatically complicate the measurement. Using Brownian dynamics simulation of a DNA molecule extended by force, we were able to estimate the observation time needed to obtain the desired accuracy of the extension measurement. Also, the simulation revealed large fluctuations of the force, acting on the attached magnetic bead from the stretched DNA molecule.

Internal dynamics of superhelical DNA

We present the first data on the temporal kinetics of monomer mean square displacements in DNA circles with defined degrees of superhelicity. The segmental dynamics of specifically labeled DNA plasmids with superhelical densities between 0 and -0.016 was assessed by fluorescence correlation spectroscopy. Introduction of superhelicity leads to progressively faster dynamics in the long time regime corresponding to the coil diffusion as observed previously by Langowski et al. [Biopolymers 34, 639 (1994)10.1002/bip.360340506], but also in the short time range corresponding to the segmental motion within the DNA coil.

Modeling electroporation in a single cell

Electroporation uses electric pulses to promote delivery of DNA and drugs into cells. This study presents a model of electroporation in a spherical cell exposed to an electric field. The model determines transmembrane potential, number of pores, and distribution of pore radii as functions of time and position on the cell surface. For a 1-ms, 40 kV/m pulse, electroporation consists of three stages: charging of the cell membrane (0-0.51 micros), creation of pores (0.51-1.43 micros), and evolution of pore radii (1.43 micros to 1 ms). This pulse creates approximately 341,000 pores, of which 97.8% are small ( approximately 1 nm radius) and 2.2% are large. The average radius of large pores is 22.8 +/- 18.7 nm, although some pores grow to 419 nm. The highest pore density occurs on the depolarized and hyperpolarized poles but the largest pores are on the border of the electroporated regions of the cell. Despite their much smaller number, large pores comprise 95.3% of the total pore area and contribute 66% to the increased cell conductance. For stronger pulses, pore area and cell conductance increase, but these increases are due to the creation of small pores; the number and size of large pores do not increase.

Brownian dynamics simulation of knot diffusion along a stretched DNA molecule

Manipulation of individual DNA molecules by optical tweezers has made it possible to tie these molecules into knots. After stretching the DNA molecules the knots become highly localized. In their recent study, Quake and co-authors investigated diffusion of such knots along stretched DNA molecules. We used these data to test the accuracy of a Brownian dynamics simulation of DNA bending motion. We simulated stretched DNA molecules with knots 3(1), 4(1), and 7(1), and determined their diffusion coefficients. Comparison of the simulated and experimental results shows that Brownian dynamics simulation is capable of predicting the rates of large-scale DNA rearrangements within a factor of 2.

The mechanism of naked DNA uptake and expression

The administration of naked nucleic acids into animals is increasingly being used as a research tool to elucidate mechanisms of gene expression and the role of genes and their cognate proteins in the pathogenesis of disease in animal models (Herweijer and Wolff, 2003; Hodges and Scheule, 2003). It is also being used in several human clinical trials for genetic vaccines, Duchenne muscular dystrophy, peripheral limb ischemia, and cardiac ischemia (Davis et al., 1996; Romero et al., 2002; Tsurumi et al., 1997). Naked DNA is an attractive non-viral vector because of its inherent simplicity and because it can easily be produced in bacteria and manipulated using standard recombinant DNA techniques. It shows very little dissemination and transfection at distant sites following delivery and can be readministered multiple times into mammals (including primates) without inducing an antibody response against itself (i.e., no anti-DNA antibodies generated) (Jiao et al., 1992). Also, contrary to common belief, long-term foreign gene expression from naked plasmid DNA (pDNA) is possible even without chromosome integration if the target cell is postmitotic (as in muscle) or slowly mitotic (as in hepatocytes) and if an immune reaction against the foreign protein is not generated (Herweijer et al., 2001; Miao et al., 2000; Wolff et al., 1992; Zhang et al., 2004). With the advent of intravascular and electroporation techniques, its major restriction--poor expression levels--is no longer limiting and levels of foreign gene expression in vivo are approaching what can be achieved with viral vectors. Direct in vivo gene transfer with naked DNA was first demonstrated when efficient transfection of myofibers was observed following injection of mRNA or pDNA into skeletal muscle (Wolff et al., 1990). It was an unanticipated finding in that the use of naked nucleic acids was the control for experiments designed to assess the ability of cationic lipids to mediate expression in vivo. Subsequent studies also found foreign gene expression after direct injection in other tissues such as heart, thyroid, skin, and liver (Acsadi et al., 1991; Hengge et al., 1996; Kitsis and Leinwand, 1992; Li et al., 1997; Sikes and O'Malley 1994; Yang and Huang, 1996). However, the efficiency of gene transfer into skeletal muscle and these other tissues by direct injection is relatively low and variable, especially in larger animals such as nonhuman primates (Jiao et al., 1992). After our laboratory had developed novel transfection complexes of pDNA and amphipathic compounds and proteins, we sought to deliver them to hepatocytes in vivo via an intravascular route into the portal vein. Our control for these experiments was naked pDNA and we were once again surprised that this control group had the highest expression levels (Budker et al., 1996; Zhang et al., 1997). High levels of expression were achieved by the rapid injection of naked pDNA in relatively large volumes via the portal vein, the hepatic vein, and the bile duct in mice and rats. The procedure also proved effective in larger animals such as dogs and nonhuman primates (Eastman et al., 2002; Zhang et al., 1997). The next major advance was the demonstration that high levels of expression could also be achieved in hepatocytes in mice by the rapid injection of naked DNA in large volumes simply into the tail vein (Liu et al., 1999; Zhang et al., 1999). This hydrodynamic tail vein (HTV) procedure is proving to be a very useful research tool not only for gene expression studies, but also more recently for the delivery of small interfering RNA (siRNA) (Lewis et al., 2002; McCaffrey et al., 2002). The intravascular delivery of naked pDNA to muscle cells is also attractive particularly since many muscle groups would have to be targeted for intrinsic muscle disorders such as Duchenne muscular dystrophy. High levels of gene expression were first achieved by the rapid injection of naked DNA in large volumes via an artery route with both blood inflow and outflow blocked surgically (Budker et al., 1998; Zhang et al., 2001). Intravenous routes have also been shown to be effective (Hagstrom et al., 2004; Liang et al., 2004; Liu et al., 2001). For limb muscles, the ability to use a peripheral limb vein for injection and a proximal, external tourniquet to block blood flow renders the procedure to be clinically viable. This review concerns itself with the mechanism by which naked DNA is taken up by cells in vivo. A greater understanding of the mechanisms involved in the uptake and expression of naked DNA, and thus connections between postulated mechanisms and expression levels, is emphasized. Inquiries into the mechanism not only aid these practical efforts, but are also interesting on their own account with relevance to viral transduction and cellular processes. The delivery to hepatocytes is first discussed given the greater information available for this process, and then uptake by myofibers is discussed.

Cyclization of short DNA fragments and bending fluctuations of the double helix

Cloutier and Widom [Cloutier, T. E. & Widom, J. (2004) Mol. Cell 14, 355-362] recently reported that the cyclization efficiency of short DNA fragments, about 100 bp in length, exceeds theoretical expectations by three orders of magnitude. In an effort to resolve this discrepancy, we tried modifying the theory. We investigated how the distribution of the angles between adjacent base pairs of the double helix affects the cyclization efficiency. We found that only the incorporation of sharp kinks in the angle distribution provides the desired increase of the cyclization efficiency. We did not find a model, however, that fits all cyclization data for DNA fragments of different lengths. Therefore, we carefully reinvestigated the cyclization of 100-bp DNA fragments experimentally and found their cyclization efficiency to be in remarkable agreement with the traditional model of DNA bending. We also found an explanation for the discrepancy between our results and those of Cloutier and Widom.

Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans

The RecFOR pathway has been shown to be essential for DNA repair through the process of homologous recombination in bacteria and, recently, to be important in the recovery of stalled replication forks following UV irradiation. RecO, along with RecR, RecF, RecQ and RecJ, is a principal actor in this fundamental DNA repair pathway. Here we present the three-dimensional structure of a member of the RecO family. The crystal structure of Deinococcus radiodurans RecO (drRecO) reveals possible binding sites for DNA and for the RecO-binding proteins within its three discrete structural regions: an N-terminal oligonucleotide/oligosaccharide-binding domain, a helical bundle and a zinc-finger motif. Furthermore, drRecO was found to form a stable complex with RecR and to bind both single- and double-stranded DNA. Mutational analysis confirmed the existence of multiple DNA-binding sites within the protein.

DNA-loop formation on nucleosomes shown by in situ scanning force microscopy of supercoiled DNA

The flexibility of the chromatin structure, necessary for the processing of the genomic DNA, is controlled by a number of factors where flexibility and mobility of the nucleosomes is essential. Here, the influence of DNA supercoiling on the structure of single nucleosomes is investigated. Circular supercoiled plasmid DNA sub-saturated with histones was visualized by scanning force microscopy (SFM) in aqueous solution. SFM-imaging compared with topological analysis indicates instability of nucleosomes when the salt concentration is raised from 10 mM to 100 mM NaCl. Nucleosomes were observed after the deposition to the used scanning surface, i.e. mica coated with polylysine. On the images, the nucleosomes appear with a high probability in end-loops near the apices of the superhelices. In 100 mM NaCl but not in 10 mM NaCl, a significant number of complexes present the nucleosomes on superhelical crossings mainly located adjacent to an end-loop. The morphology of these structures and statistical analysis suggest that DNA loops were formed on the histone octamers, where the loop size distribution shows a pronounced peak at 50 nm. Recently, the formation and diffusion of loops on octamers has been discussed as a mechanism of translocations of nucleosomes along DNA. The presented data likely confirm the occurrence of loops, which may be stabilized by supercoiling. Analysis of the structure of regular nucleosomes not located on crossings indicates that reducing the salt concentration leads to more conformations, where DNA is partially unwrapped from the distal ends of the octamer.

Computational analysis of DNA gyrase action

DNA gyrase introduces negative supercoiling into circular DNA by catalyzing the passage of one DNA segment through another. The efficiency of the reaction is many times higher than that of other topological transformations. We analyze, by a computer simulation, the reaction selectivity for a model of DNA gyrase action that assumes existence of a free loop between the G- and T- DNA segments participating in the reaction. A popular model of this type assumed that the selectivity can be provided by the conformation of the DNA segment wrapped around the enzyme into the right-handed helix turn (G-segment). We simulated the distribution of the reaction products for this model. Equilibrium sets of DNA conformations with one segment of the double helix wrapped around the enzyme were constructed. From these sets we selected conformations that had a second segment properly juxtaposed with the first one. Assuming that the juxtapositions result in the strand-passing reaction, we calculated the reaction products for all these conformations. The results show that different products have to be formed if the enzyme acts according to the model. This conclusion can be extended for any model with a free loop between the G- and T-segments. An alternative model that is consistent with the major experimental observations and the computational analysis, is suggested.

Structural basis for cooperative DNA binding by CAP and lac repressor

Catabolite gene activator protein (CAP) and lac repressor (LR) are celebrated transcription-regulating proteins that bind to DNA cooperatively forming a ternary complex with the promoter loop. Here we present a multiscale model of the ternary complex derived from crystal structures of the proteins and a continuous structure of the DNA loop built using the theory of elasticity. We predict that the loop is underwound in the binary complex with the LR, whereas in the ternary complex with the LR and CAP, the loop is overwound and extended due to an upstream relocation of a DNA binding hand of LR. The computed relocation distance matches the experimental observations and the energy balance of the system explains the cooperativity effect. Using the multiscale approach, we build an all-atom model of the ternary complex that suggests a series of further experimental investigations.

Finite-element analysis of the displacement of closed DNA loops under torsional stress

Closed DNA loops that contain intrinsic curvature occur in biologically important structures that are formed by bringing together proteins attached at distinct sites. Such loops constitute topological domains that are characterized by a linking number Delta Lk. We calculate, using finite-element analysis, the structural changes induced by small changes in this linking number, Delta Lk. Because of the intrinsic curvature, the slightest change in linking number induces writhe and the loop begins to fold in space. We previously studied the case in which the initial curvature is uniformly distributed along the DNA rod. We found that there are two different folding modes, depending on the amount of intrinsic curvature and the Poisson ratio, a quantity that measures the ratio of bending stiffness to torsional rigidity. For combinations of the Poisson ratio and curvature that lie below a critical curve, called the Fickel curve, the folding is monotonic in the sense that the writhe uniformly increases as Delta Lk increases, until self-contact occurs. For combinations below this curve, the folding is non-monotonic in the sense that as Delta Lk increases the writhe first increases, then decreases back to essentially zero, and then increases uniformly until self-contact occurs. The folding behaviour and the self-contact points in the two folding modes are completely different. In this paper we first review this previous work. We then extend those results to more-complex situations in which the curvature is initially distributed non-uniformly along the DNA rod. We show that the location of the Fickel curve depends upon both the extent of the initial curvature and upon its distribution along the rod. We also show that two DNAs with the same total intrinsic curvature will fold differently depending upon the distribution of that curvature along the DNA axis, and upon the point of the loop at which the applied rotation or change in Delta Lk is introduced.

Model of creation and evolution of stable electropores for DNA delivery

Electroporation, in which electric pulses create transient pores in the cell membrane, is becoming an important technique for gene therapy. To enable entry of supercoiled DNA into cells, the pores should have sufficiently large radii (>10 nm), remain open long enough for the DNA chain to enter the cell (milliseconds), and should not cause membrane rupture. This study presents a model that can predict such macropores. The distinctive features of this model are the coupling of individual pores through membrane tension and the electrical force on the pores, which is applicable to pores of any size. The model is used to explore the process of pore creation and evolution and to determine the number and size of pores as a function of the pulse magnitude and duration. Next, our electroporation model is combined with a heuristic model of DNA uptake and used to predict the dependence of DNA uptake on pulsing parameters. Finally, the model is used to examine the mechanism of a two-pulse protocol, which was proposed specifically for gene delivery. The comparison between experimental results and the model suggests that this model is well-suited for the investigation of electroporation-mediated DNA delivery.

Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution

The conformations of supercoiled (sc) DNA and linear DNA bound to polylysine (PL)-coated mica were investigated by scanning force microscopy (SFM) in solution. From the polymer statistical analysis of linear DNA, we could distinguish between re-arrangements or trapping of the DNA on the surface. Conditions of re-arrangements to an almost equilibrated state can be achieved at appropriate PL surface concentrations. We could show that the ability of re-arrangements depends on the salt concentration of the adsorption/imaging buffer. Comparing the statistical analysis of the linear DNA with SFM images of scDNA suggested that irregular scDNA conformations are formed under conditions of trapping, whereas plectonemic structures are favoured under conditions of surface re-arrangements. Salt-dependent changes in the scDNA conformation over the range of 10-100 mM NaCl, as characterised by the parameters writhe and the superhelix radius r, are observable only under conditions that enable surface re-arrangements. The measured values of writhe suggest that the scDNA loses approximately one-half of the supercoils during the binding to the surface. At the same time r increases systematically with decreasing writhe, thus the scDNA topology remains determined by the constraints on supercoiling during the binding to PL-coated mica.

Intersegmental interactions in supercoiled DNA: atomic force microscope study

Intersegmental interactions in DNA facilitated by the neutralization of electrostatic repulsion was studied as a function of salt concentration and DNA supercoiling. DNA samples with defined superhelical densities were deposited onto aminopropyl mica at different ionic conditions and imaged in air after drying of the samples. Similar to hydrodynamic data, we did not observe a collapse of supercoiled DNA, as proposed earlier by cryo-EM studies. Instead, the formation of the contacts between DNA helices within supercoiled loops with no visible space between the duplexes was observed. The length of such close contacts increased upon increasing NaCl concentration. DNA supercoiling was a critical factor for the stabilization of intersegmental contacts. Implications of the observed effect for understanding DNA compaction in the cell and for regulation DNA transactions via interaction of distantly separated DNA regions are discussed.

Liquid crystal formation in supercoiled DNA solutions

The critical concentrations pertaining to the liquid crystal formation of pUC18 plasmid in saline solutions were obtained from (31)P nuclear magnetic resonance, polarized light microscopy, and phase equilibrium experiments. The transition is strongly first order with a broad gap between the isotropic and anisotropic phase. The critical boundaries are strongly and reversibly dependent on temperature and weakly dependent on ionic strength. With polarized light microscopy on magnetically oriented samples, the liquid crystalline phase is assigned cholesteric with a pitch on the order of 4 microm. Preliminary results show that at higher concentrations a true crystal is formed. The isotropic-cholesteric transition is interpreted with lyotropic liquid crystal theory including the effects of charge, orientation entropy, and excluded volume effects. It was found that the molecular free energy associated with the topology of the superhelix is of paramount importance in controlling the width of the phase gap. The theoretical results compare favorably with the critical boundary pertaining to the disappearance of the isotropic phase, but they fail to predict the low concentration at which the anisotropic phase first appears.

Dimensions of plectonemically supercoiled DNA

With a view to determine the configuration and regularity of plectonemically supercoiled DNA, we have measured the small angle neutron scattering from pUC18 plasmid in saline solutions. Furthermore, we have derived the mathematical expression for the single chain scattering function (form factor) of a superhelical structure, including the longitudinal and transverse interference over the plectonemic pitch and radius, respectively. It was found that an interwound configuration describes the data well, provided interactions among supercoils are accounted for in the second virial approximation. The opening angle was observed to be relatively constant and close to 58 degrees, but it was necessary to include a significant distribution in radius and pitch. For diluted supercoils with vanishing mutual interaction, the derived structural results agree with independent measurements, including the distribution in linking number deficit as determined by gel electrophoresis. With increasing plasmid concentration, prior and covering the transition to the liquid-crystalline phase, the radius and pitch are seen to decrease significantly. The latter observation shows that compaction of negatively supercoiled DNA by confinement results in a decrease in writhing number at the cost of a positive twist exerted on the DNA duplex. It is our conjecture that the free energy associated with this excess twist is of paramount importance in controlling the critical boundaries pertaining to the transition to the anisotropic, liquid-crystalline phase.

Monte Carlo simulations of supercoiled DNAs confined to a plane

Recent advances in atomic force microscopy (AFM) have enabled researchers to obtain images of supercoiled DNAs deposited on mica surfaces in buffered aqueous milieux. Confining a supercoiled DNA to a plane greatly restricts its configurational freedom, and could conceivably alter certain structural properties, such as its twist and writhe. A program that was originally written to perform Monte Carlo simulations of supercoiled DNAs in solution was modified to include a surface potential. This potential flattens the DNAs to simulate the effect of deposition on a surface. We have simulated transfers of a 3760-basepair supercoiled DNA from solution to a surface in both 161 and 10 mM ionic strength. In both cases, the geometric and thermodynamic properties of the supercoiled DNAs on the surface differ significantly from the corresponding quantities in solution. At 161 mM ionic strength, the writhe/twist ratio is 1.20-1.33 times larger for DNAs on the surface than for DNAs in solution and significant differences in the radii of gyration are also observed. Simulated surface structures in 161 mM ionic strength closely resemble those observed by AFM. Simulated surface structures in 10 mM ionic strength are similar to a minority of the structures observed by AFM, but differ from the majority of such structures for unknown reasons. In 161 mM ionic strength, the internal energy (excluding the surface potential) decreases substantially as the DNA is confined to the surface. Evidently, supercoiled DNAs in solution are typically deformed farther from the minimum energy configuration than are the corresponding surface-confined DNAs. Nevertheless, the work (Delta A(int)) done on the internal coordinates, which include uniform rotations at constant configuration, during the transfer is positive and 2.6-fold larger than the decrease in internal energy. The corresponding entropy change is negative, and its contribution to Delta A(int) is positive and exceeds the decrease in internal energy by 3.6 fold. The work done on the internal coordinates during the solution-to-surface transfer is directed primarily toward reducing their entropy. Evidently, the number of configurations available to the more deformed solution DNA is vastly greater than for the less deformed surface-confined DNA.

Time-lapse imaging of conformational changes in supercoiled DNA by scanning force microscopy

Most of the scanning force microscopy (SFM) images of supercoiled DNA on untreated mica thus far reported have not shown tight plectonemic structure seen by electron microscopy, but instead less coiled molecules and sometimes a partly "condensed" state with intimate chain-chain interactions. By observing time-lapse images of conformational changes of DNA induced by decreasing ionic strength of imaging buffer in solution SFM, we could show that the process of water rinsing, an indispensable step for preparation of dried samples, may be responsible for some of the conformational anomalies in the images previously reported. We have studied several protocols to observe supercoiled DNA molecules by SFM and discuss the merits and the demerits. Images obtained following uranyl acetate treatment may be ideal for the detection of DNA damage, as the supercoiled and nicked forms are easily distinguishable.

RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription

We report that RapA, an Escherichia coli RNA polymerase (RNAP)-associated homolog of SWI2/SNF2, is capable of dramatic activation of RNA synthesis. The RapA-mediated transcriptional activation in vitro depends on supercoiled DNA and high salt concentrations, a condition that is likely to render the DNA superhelix tightly compacted. Moreover, RapA activates transcription by stimulating RNAP recycling. Mutational analyses indicate that the ATPase activity of RapA is essential for its function as a transcriptional activator, and a rapA null mutant exhibits a growth defect on nutrient plates containing high salt concentrations in vivo. Thus, RapA acts as a general transcription factor and an integral component of the transcription machinery. The mode of action of RapA in remodeling posttranscription or posttermination complexes is discussed.

Analysis of genetic control elements in eukaryotes: transcriptional activity or nuclear hitchhiking?

A common way to analyse basal and stimulated activity of eukaryotic genetic control elements, such as promoters and enhancers, is to introduce them into cells via DNA vectors containing an easily assayable reporter gene. Activity is then studied by measurement of transiently produced mRNA or reporter protein. In such assays, it is assumed that the variable measured is proportional to the transcriptional activity of the control element under investigation. Here we question the validity of this generally accepted assumption. Specifically, recent observations indicate that control elements, in addition to modulating transgene transcription, can facilitate the nuclear uptake of their carrier plasmids. This process is mediated by transcription factors or other nuclear proteins harbouring nuclear localisation signals, which bind to the control elements in the cytoplasm and transport the DNA into the nucleus through the protein nuclear import machinery. As the number of mRNA transcripts produced for an epi-chromosomally expressed transgene is directly related to its copy number inside the nucleus, such transport activity may lead to substantial overestimation of the transcriptional potency of the control element(s) studied.

Electron and scanning force microscopy studies of alterations in supercoiled DNA tertiary structure

The configuration of supercoiled DNA (scDNA) was investigated by electron microscopy and scanning force microscopy. Changes in configuration were induced by varying monovalent/divalent salt concentrations and manifested by variation in the number of nodes (crossings of double helical segments). A decrease in the concentration of monovalent cations from 50 mM to approximately 1 mM resulted in a significant change of apparent configuration of negatively supercoiled DNA from a plectonemic form with virtually approximately 15 nodes (the value expected for molecules of approximately 3000 bp) to one or two nodes. This result was in good agreement with values calculated using an elastic rod model of DNA and salt concentration in the range of 5-50 mM. The effect did not depend on the identity of the monovalent cation (Na(+), K(+)) or the nature of the support used for electron microscopy imaging (glow-discharged carbon film, polylysine film). At very low salt concentrations, a single denatured region several hundred base-pairs in length was often detected. Similarly, at low concentrations of divalent cations (Mg(2+), Ca(2+), Zn(2+)), scDNA was apparently relaxed, although the effect was slightly dependent on the nature of the cation. Positively supercoiled DNA behaved in a manner different from that of its negative counterpart when the ion concentration was varied. As expected for these molecules, an increase in salt concentration resulted in an apparent relaxation; however, a decrease in salt concentration also led to an apparent relaxation manifested by a slight decrease in the number of nodes. Scanning force microscopy imaging of negatively scDNA molecules deposited onto a mica surface under various salt conditions also revealed an apparent relaxation of scDNA molecules. However, due to weak interactions with the mica surface in the presence of a mixture of mono/divalent cations, the effect occurred under conditions differing from those used for electron microscopy. We conclude that the observed changes in scDNA configuration are inherent to the DNA structure and do not reflect artifacts arising from the method(s) of sample preparation.