Thermodynamics of cation-induced DNA condensation

Multivalent counterions induced attraction between DNA polyelectrolytes

In this paper we study the electrostatic attraction between two parallel rodlike DNA polyelectrolytes induced by neutralizing multivalent counterions at the zero temperature limit. The counterions crystallize on the charged surfaces of DNA so that we can handle the system by using the Wigner crystal lattice model. We derived the 3D ground state configuration of counterions with minimized energy by use of the gradient descent method, and calculated the interaction between two DNA cylinders with divalent or trivalent counterions when they approach. The results show that the complex ground state configuration of counterions plays a key role in determining the caused attraction. The counterions form three-dimensional Wigner crystals on each cylinder at large separation. When the cylinders are brought together, some counterion lines will move towards the inner region and lead to strong attraction. The calculated interaction from our model is in good agreement with the simulation result, however, the single particle approximation considerably overestimates the attraction.

Counterions in the ground state partially condense in the intervening region of two approaching DNA cylinders and result in attraction.

Compaction of bacterial genomic DNA: clarifying the concepts

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

Local de-condensation of double-stranded DNA in oppositely charged polyelectrolyte as induced by spermidine

How polyamines such as spermidine cooperate with histone to condense and de-condense DNA during transcription has not been clarified. In this work, using the complex of DNA and poly(L-lysine) (PLL) at +/- ratio of 0.5 as a model of nucleosome, we monitored the de-condensation of DNA in the presence of spermidine. As revealed by the results from atomic force microscopy and time-resolved laser light scattering, spermidine was able to transform the spherical complex into a core-shelled structure, with the hard core being the DNA-PLL complex and the soft shell being DNA and spermidine. The soft shell evolved into a coiled DNA conformation with time. Such a local de-condensation process should be helpful in understanding the DNA transcription and cell division process in vivo.

Physical theory of ionomer aggregation in water

This article presents a physical theory for the aggregation of ionomer molecules in aqueous solution. To study this phenomenon, we consider a system of charged rigid rods with uniform surface charge immersed in water. The free-energy functional derived for this system consists of hydrophobic and direct electrostatic contributions as well as entropic terms. Energy minimization gives the stable aggregation number as a function of surface charge density, surface tension, geometric parameters, and density of rods in solution. We provide configuration diagrams of the system, which display the impact of the hydrophobic and electrostatic interaction strengths on the stabilization of finite-size bundles.

Helical structure determines different susceptibilities of dsDNA, dsRNA, and tsDNA to counterion-induced condensation

Recent studies of counterion-induced condensation of nucleic acid helices into aggregates produced several puzzling observations. For instance, trivalent cobalt hexamine ions condensed double-stranded (ds) DNA oligomers but not their more highly charged dsRNA counterparts. Divalent alkaline earth metal ions condensed triple-stranded (ts) DNA oligomers but not dsDNA. Here we show that these counterintuitive experimental results can be rationalized within the electrostatic zipper model of interactions between molecules with helical charge motifs. We report statistical mechanical calculations that reveal dramatic and nontrivial interplay between the effects of helical structure and thermal fluctuations on electrostatic interaction between oligomeric nucleic acids. Combining predictions for oligomeric and much longer helices, we also interpret recent experimental studies of the role of counterion charge, structure, and chemistry. We argue that an electrostatic zipper attraction might be a major or even dominant force in nucleic acid condensation.

Physics of DNA: unravelling hidden abilities encoded in the structure of ‘the most important molecule’

A comprehensive article “Structure and Interactions of Biological Helices”, published in 2007 in Reviews of Modern Physics, overviewed various aspects of the effect of DNA structure on DNA–DNA interactions in solution and related phenomena, with a thorough analysis of the theory of these effects. Here, an updated qualitative account of this area is presented without any sophisticated ‘algebra’. It overviews the basic principles of the structure-specific interactions between double-stranded DNA and focuses on the physics behind several related properties encoded in the structure of DNA. Among them are (i) DNA condensation and aptitude to pack into small compartments of cells or viral capcids, (ii) the structure of DNA mesophases, and (iii) the ability of homologous genes to recognize each other prior to recombination from a distance. Highlighted are some of latest developments of the theory, including the shape of the ‘recognition well’. The article ends with a brief discussion of the first experimental evidence of the protein-free homology recognition in a ‘test tube’.

ON-OFF switching of transcriptional activity of large DNA through a conformational transition in cooperation with phospholipid membrane

We report that structural transitions of DNA cause the ON-OFF switching of transcriptional activity in cooperation with phospholipid membrane in a reconstituted artificial cell. It has been shown that long DNA of more than 20-30 kilo base-pairs exhibits a discrete conformational transition between a coiled state and highly folded states in aqueous solution, depending on the presence of various condensing agents such as polyamine. Recently, we reported a conformational transition of long DNA through interplay with phospholipid membrane, from a folded state in aqueous phase to an extended coil state on a membrane surface, in a cell-sized water-in-oil microdroplet covered by phosphatidylethanolamine monolayer (Kato, A.; Shindo, E.; Sakaue, T.; Tsuji, A.; Yoshikawa, K. Biophys. J. 2009, 97, 1678-1686). In this study, to elucidate the effects of these conformational changes on the biologically important function of DNA, transcription, we investigated the transcriptional activity of DNA in a microdroplet. Transcriptional activity was evaluated at individual DNA molecule level by a method we developed, in which mRNA molecules are labeled with fluorescent oligonucleotide probes. Transcription proceeded on almost all of the DNA molecules with a coiled conformation in the aqueous phase. In the presence of a tetravalent amine, spermine, the DNA had a folded conformation, and transcription was completely inhibited. When the Mg(2+) concentration was increased, DNA was adsorbed onto the inner surface of the membrane and exhibited an extended conformation. The transcription experiments showed that this conformational transition recovered transcriptional activity; transcription occurred on DNA molecules that were on the membrane.

Conformational transition of giant DNA in a confined space surrounded by a phospholipid membrane

It has been established that a long DNA molecule exhibits a large discrete conformational change from a coiled state to a highly folded state in aqueous solution, depending on the presence of various condensing agents such as polyamines. In this study, T4 DNA labeled with fluorescent dyes was encapsulated in a cell-sized microdroplet covered with a phospholipid membrane to investigate the conformational behavior of a DNA molecule in such a confined space. Fluorescence microscopy showed that the presence of Mg(2+) induced the adsorption of DNA onto the membrane inner-surface of a droplet composed of phosphatidylethanolamine, while no adsorption was observed onto a phosphatidylcholine membrane. Under the presence of spermine (tetravalent amine), DNA had a folded conformation in the bulk solution. However, when these molecules were encapsulated in the microdroplet, DNA adsorbed onto the membrane surface accompanied by unfolding of its structure into an extended coil conformation under high concentrations of Mg(2+). In addition, DNA molecules trapped in large droplets tended not to be adsorbed on the membrane, i.e., no conformational transition occurred. A thermodynamic analysis suggests that the translational entropy loss of a DNA molecule that is accompanied by adsorption is a key factor in these phenomena under micrometer-scale confinement.

Molecular voids formed from effective attraction in submonolayer DNA deposited on Au(111)

The development of DNA-based biosensors requires a deep understanding of how DNA molecules adsorb and organize on solid state surfaces as well as the electronic properties of individual and aggregates of DNA molecules. Using scanning tunneling microscopy (STM) and atomic force microscopy (AFM), we have successfully characterized an attractive force driven molecular void formation for DNA chemically adsorbed on Au(111) as a function of strand length and deposition conditions. Here we report the observation of these void structures formed on the Au(111) surface by adsorption of both 45 and 90 base pair long, thiolated double-stranded DNA. We found that the average void diameter decreases when increasing the number of base pairs exposed to the surface. The critical determinant in the molecular void formation is the total charge delivered to the surface via the adsorption of the DNA strands and the related counterions, which can ultimately be quantified by the number of base pairs in each adsorbed DNA molecule. Complementary measurements involving STM and AFM suggest that an intact Au(111) surface area is preserved inside the void and is surrounded by a submonolayer of DNA molecules adsorbed on the surface. The discussion of the possible mechanisms for the void formation implies an effective attraction between the DNA molecules.

Metal Ions Protect DNA Against Strand Breakage Induced by Fast Neutrons

Single and double strand breaks (SSB and DSB) are induced by fast neutrons in plasmid (pBR322) DNA in 1 mM potassium phosphate buffer (pH 7.25). Increasing the concentration of monovalent (Na+, Cs+, Li+), divalent (Mg2+, Ca2+) and trivalent (Al3+, Co3+ (NH3)6) metal cations strongly decreases the yield of DSB. The extent of the observed protection depends on the valence of the cation. The production of SSB is only slightly decreased, except for Al3+ and Co3+ (NH3)6, whose effects are particularly large (complete protection at 1 and 0.1 mM respectively). Circular dichroism spectra show that Al3+ induces an important structural change of DNA at the ion concentration where the protection becomes total. This change is probably a condensation (collapse), as in the well-known case of Co3+ (NH3)6. Our results suggest two mechanisms of protection by metal ions: (i) the induction of structural changes of DNA, that render less accessible the critical sites of attack by OH. radicals; and (ii) the stabilization of the double helical regions between two close-set nicks on opposite strands, that hinders the effective double strand breakage of DNA.

DNA liquid-crystalline gel as adsorbent of carcinogenic agent

DNA liquid crystalline gel (LCG) has been newly prepared by a dialysis of concentrated DNA solutions into concentrated metal cation solutions. The condition for forming DNA LCG is examined by means of the insolubilization reaction. The shrinking ratio and the ratio of the thickness of LCG layer, delta, and the diameter of the dialysis tube, d0, do not depend on d0. The adsorption of one of carcinogenic agents, acridine orange is demonstrated. From the experimental results, the mechanism for forming DNALCG is discussed.

Fluorescence dynamics of DNA condensed by the molecular crowding agent poly(ethylene glycol)

Condensation of extended DNA into compact structures is encountered in a variety of situations, both natural and artificial. While condensation of DNA has been routinely carried out by the use of multivalent cations, cationic lipids, detergents, and polyvalent cationic polymers, the use of molecular crowding agents in condensing DNA is rather striking. In this work, we have studied the dynamics of plasmid DNA condensed in the presence of a molecular crowding agent, polyethylene glycol (PEG). Steady-state and time-resolved fluorescence of the recently established condensation-indicating DNA binder, YOYO-1 [G. Krishnamoorthy, G. Duportail, and Y. Mely (2002), Biochemistry 41, 15277-15287] was used in inferring the dynamic aspects of DNA condensates. It is shown that DNA condensed by PEG is more flexible and less compact when compared to DNA condensed by binding agents such as polyethyleneimine. The relevance of such differences in dynamics toward functional aspects of condensed DNA is discussed.

Condensation of DNA-actin polyelectrolyte mixtures driven by ions of different valences

Multivalent ions can induce condensation of like-charged polyelectrolytes into compact states, a process that requires different ion valences for different polyelectrolyte species. In this work we examine the condensation behavior in binary anionic polyelectrolyte mixtures consisting of DNA coils and F-actin rods in the presence of monovalent, divalent, and trivalent ions. As expected, monovalent ions do not condense either component and divalent ions selectively condense F-actin rods out of the polyelectrolyte mixture. For trivalent ions, however, we observe a microphase separation between the two polyelectrolytes into coexisting finite-sized F-actin bundles and DNA toroids. Further, by increasing the DNA volume fraction in the mixture, condensed F-actin bundles can be completely destabilized, leading to only DNA condensation within the mixture. We examine a number of possible causes and propose a model based on polyelectrolyte competition for ions.

Role of calcium in gene delivery

The treatment of genetic diseases using therapeutic gene transfer is considered to be a significant development. This development has brought with it certain limitations, and the process of overcoming these barriers has seen a drastic change in gene delivery. Many metal ions such as Mg2+, Mn2+, Ba2+ and, most importantly, Ca2+ have been demonstrated to have significant roles in gene delivery. Recently, calcium phosphate alone, or in combination with viral and nonviral vectors, was found to exert a positive effect on gene transfer when incorporated in the colloidal particulate system, which is an advancing approach to gene delivery. This review elaborates on various successful methods of using calcium in gene delivery.

DNA structural transitions induced by divalent metal ions in aqueous solutions

Using methods of IR spectroscopy, light scattering, gel-electrophoresis DNA structural transitions are studied under the action of Cu2+, Zn2+, Mn2+, Ca2+ and Mg2+ ions in aqueous solution. Cu2+, Zn2+, Mn2+ and Ca2+ ions bind both to DNA phosphate groups and bases while Mg2+ ions-only to phosphate groups of DNA. Upon interaction with divalent metal ions studied (except for Mg2+ ions) DNA undergoes structural transition into a compact form. DNA compaction is characterized by a drastic decrease in the volume occupied by DNA molecules with reversible formation of DNA dense particles of well-defined finite size and ordered morphology. The DNA secondary structure in condensed particles corresponds to the B-form family. The mechanism of DNA compaction under Mt2+ ion action is not dominated by electrostatics. The effectiveness of the divalent metal ions studied to induce DNA compaction correlates with the affinity of these ions for DNA nucleic bases: Cu2+>>Zn2+>Mn2+>Ca2+>>Mg2+. Mt2+ ion interaction with DNA bases (or Mt2+ chelation with a base and an oxygen of a phosphate group) may be responsible for DNA compaction. Mt2+ ion interaction with DNA bases can destabilize DNA causing bends and reducing its persistent length that will facilitate DNA compaction.

Direct observation of counterion organization in F-actin polyelectrolyte bundles

Attractions between like-charged polyelectrolytes have been observed in a variety of systems (W.M. Gelbart, R.F. Bruinsma, P.A. Pincus, V.A. Parsegian, Phys. Today 53, September issue, 38 (2000)). Recent biological examples include DNA, filamentous viruses, and F-actin. Theoretical investigations on idealized systems indicate that counterion correlations play a central role, but no experiments that specifically probe such correlations have been performed. Using synchrotron X-ray diffraction, we have directly observed the organization of multivalent ions on cytoskeletal filamentous actin (a well-defined biological polyelectrolyte) and found an unanticipated symmetry-breaking collective counterion mechanism for generating attractions. Surprisingly, the counterions do not form a lattice that simply follows actin's helical symmetry; rather, the counterions organize into "frozen" ripples parallel to the actin filaments and form structures reminiscent of charge density waves. Moreover, these 1D counterion charge density waves form a coupled mode with twist deformations of the oppositely charged actin filaments. This counterion organization is not sensitive to thermal fluctuations in temperature range accessible to protein-based polyelectrolyte systems. Moreover, the counterion density waves are "pinned" to the spatial periodicity of charges on the actin filament even if the global filament charge density is varied, indicating the importance of charge periodicity on the polyelectrolyte substrate.

Contribution of hydrophobicity to thermodynamics of ligand-DNA binding and DNA collapse

The importance of understanding the dynamics of DNA condensation is inherent in the biological significance of DNA packaging in cell nuclei, as well as for gene therapy applications. Specifically, the role of ligand hydrophobicity in DNA condensation has received little attention. Considering that only multivalent cations can induce true DNA condensation, previous studies exploring monovalent lipids have been unable to address this question. In this study we have elucidated the contribution of the hydrophobic effect to multivalent cation- and cationic lipid-DNA binding and DNA collapse by studying the thermodynamics of cobalt hexammine-, spermine-, and lipospermine-plasmid DNA binding at different temperatures. Comparable molar heat capacity changes (DeltaC(p)) associated with cobalt hexammine- and spermine-DNA binding (-23.39 cal/mol K and -17.98 cal/mol K, respectively) suggest that upon binding to DNA, there are insignificant changes in the hydration state of the methylene groups in spermine. In contrast, the acyl chain contribution to the DeltaC(p) of lipospermine-DNA binding (DeltaC(p ) = DeltaC(p lipospermine) - DeltaC(p spermine)) is significant (-220.94 cal/mol K). Although lipopermine induces DNA ordering into "tubular" suprastructures, such structures do not assume toroidal dimensions as observed for spermine-DNA complexes. We postulate that a steric barrier posed by the acyl chains in lipospermine precludes packaging of DNA into dimensions comparable to those found in nature.

Information content and complexity in the high-order organization of DNA

Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main polymorphs A, B, and Z, cruciforms, intrinsic curvature, and multistranded motifs. DNA secondary motifs are stabilized and regulated by the primary base sequence, contextual effects, environmental factors, as well as by high-order DNA packaging modes. The high-order modes are, in turn, affected by secondary structures and by the environment. This review is concerned with the flow of structural information among the hierarchical structural levels of DNA molecules, the intricate interplay between the various factors that affect these levels, and the regulation and physiological significance of DNA high-order structures.

Osmotic Observations on Chemically Cross-Linked DNA Gels in Physiological Salt Solutions

Neutralized DNA gels exhibit a reversible volume transition when CaCl2 is added to the surrounding aqueous NaCl solution. In this paper, a systematic study of the osmotic and mechanical properties of Na-DNA gels is presented to determine, qualitatively and quantitatively, the effect of Ca-Na exchange on the volume transition. It is found that in the absence of CaCl2 the DNA gels exhibit osmotic behavior similar to that of DNA solutions with reduced DNA concentration. At low CaCl2 concentration, the gel volume gradually decreases as the CaCl2 concentration increases. Below the volume transition, the concentration dependence of the osmotic pressure can be satisfactorily described by a Flory-Huggins-type equation. The Ca2+ ions primarily affect the third-order interaction term, which strongly increases upon the introduction of Ca2+ ions. The second-order interaction term only slightly depends on the CaCl2 concentration. It is demonstrated that DNA gels cross-linked in solutions containing CaCl2 exhibit reduced osmotic mixing pressure. The concentration dependence of the shear modulus of DNA gels can be described by a single power law. The scaling exponent is practically independent of the NaCl concentration and increases with increasing CaCl2 content.

Stabilization of DNA utilizing divalent cations and alcohol

A novel method for protection of DNA from high shear induced damage is presented. This method uses simple divalent cations and the lyophilizable alcohol, tert-butanol, to self-assemble DNA into condensed, shear-resistant forms. The DNA used in these studies was a 5600 BP plasmid DNA encoding a therapeutic gene. Various solvents and salts were used to identify optimal conditions to condense plasmid DNA. A stable formulation was identified with plasmid DNA condensed in a cosolvent solution containing 20% (v/v) tert-butanol and 1mM calcium chloride. The DNA was formulated at 100 microg/ml and condensed into rod and toroidal shapes that were approximately 50-300 nm in diameter. The rods were found to be kinetically stable for greater than 24h following their preparation. Condensation of the plasmid DNA in this manner results in nearly 100% of the plasmid DNA remaining intact after 1 min of high shear stress applied by a 50 W probe sonicator. Uncondensed control plasmid DNA is completely fragmented following 30s of identical sonication. It is believed that condensation of DNA in this manner will permit utilization of high shear-stress inducing processing techniques, such as lyophilization or spray-drying without resulting in damage to the DNA.

Interaction of double-stranded T4 DNA with cationic gel of poly(diallyldimethylammonium chloride)

Interaction between duplex T4 DNA and a slightly cross-linked cationic gel of poly(diallyldimethylammonium chloride) in aqueous media was studied by fluorescent microscopy. While short DNA chains such as plasmid DNAs penetrate into the gel and form a phase of polyelectrolyte complex with the cationic network, the genomic giant DNA chains of T4 phages form complexes only on local areas of the gel surface. The DNA/gel complex exhibited different characteristic morphologies depending on the conditions for preparing the complex, such as the DNA concentration, flux of the solution, and surface geometry of the gel: (1) In the interaction with the flat surface of film-type gel, compact round objects, which reflected a condensed state of single DNA chains, were observed. (2) In the interaction with partly dried gel, a characteristic pattern similar to propagating waves was formed on the gel surface. (3) When flux is generated for a concentrated DNA solution, long oriented fiberlike structures were formed, which consisted of ensembles of chains. The interaction with small pieces of mechanically decomposed gel leads to complete covering of their surface by the DNA.

Metal ion-induced lateral aggregation of filamentous viruses fd and M13

We report a detailed comparison between calculations of inter-filament interactions based on Monte-Carlo simulations and experimental features of lateral aggregation of bacteriophages fd and M13 induced by a number of divalent metal ions. The general findings are consistent with the polyelectrolyte nature of the virus filaments and confirm that the solution electrostatics account for most of the experimental features observed. One particularly interesting discovery is resolubilization for bundles of either fd or M13 viruses when the concentration of the bundle-inducing metal ion Mg(2+) or Ca(2+) is increased to large (>100 mM) values. In the range of Mg(2+) or Ca(2+) concentrations where large bundles of the virus filaments are formed, the optimal attractive interaction energy between the virus filaments is estimated to be on the order of 0.01 kT per net charge on the virus surface when a recent analytical prediction to the experimentally defined conditions of resolubilization is applied. We also observed qualitatively distinct behavior between the alkali-earth metal ions and the divalent transition metal ions in their action on the charged viruses. The understanding of metal ions-induced reversible aggregation based on solution electrostatics may lead to potential applications in molecular biology and medicine.

Unique condensation patterns of triplex DNA: physical aspects and physiological implications

Triple-stranded DNA structures can be formed in living cells, either by native DNA sequences or following the application of antigene strategies, in which triplex-forming oligonucleotides are targeted to the nucleus. Recent studies imply that triplex motifs may play a role in DNA transcription, recombination and condensation processes in vivo. Here we show that very short triple-stranded DNA motifs, but not double-stranded segments of a comparable length, self-assemble into highly condensed and ordered structures. The condensation process, studied by circular dichroism and polarized-light microscopy, occurs under conditions that mimic cellular environments in terms of ionic strength, ionic composition and crowding. We argue that the unique tendency of triplex DNA structures to self-assemble, a priori unexpected in light of the very short length and the large charge density of these motifs, reflects the presence of strong attractive interactions that result from enhanced ion correlations. The results provide, as such, a direct experimental link between charge density, attractive interactions between like-charge polymers and DNA packaging. Moreover, the observations strongly support the notion that triple-stranded DNA motifs may be involved in the regulation of chromosome organization in living cells.

Sequence recognition in the pairing of DNA duplexes

Pairing of DNA fragments with homologous sequences occurs in gene shuffling, DNA repair, and other vital processes. While chemical individuality of base pairs is hidden inside the double helix, x ray and NMR revealed sequence-dependent modulation of the structure of DNA backbone. Here we show that the resulting modulation of the DNA surface charge pattern enables duplexes longer than approximately 50 base pairs to recognize sequence homology electrostatically at a distance of up to several water layers. This may explain the local recognition observed in pairing of homologous chromosomes and the observed length dependence of homologous recombination.

Examination of the biophysical interaction between plasmid DNA and the polycations, polylysine and polyornithine, as a basis for their differential gene transfection in-vitro

The impetus to develop non-viral gene delivery vectors has led to examination of synthetic polycationic polymers as plasmid DNA (pDNA) condensing agents. Previous reports have highlighted superiority (up to x 10-fold) in the in-vitro transfection of pDNA complexes formed by poly-(L)-ornithine (PLO) compared to those formed with poly-(L)-lysine (PLL). The apparent basis for this consistent superiority of PLO complexes remains to be established. This comparative study investigates whether physico chemical differences in the supramolecular properties of polycation:pDNA complexes provide a basis for their observed differential gene transfection. Specifically, particle size distribution and zeta potential of the above complexes formulated over a wide range of polycation:pDNA ratios were found to be consistent with a condensed (150-200 nm) cationic ( + 30-40 mV) system but not influenced by the type of cationic polymer used. A spectrofluorimetric EtBr exclusion assay showed that polycation:pDNA complexes display different pDNA condensation behaviour, with PLO able to condense pDNA at a lower polycation mass compared to both polylysine isomers, and form complexes that were more resistant to disruption following challenge with anionic counter species, i.e. poly-(L)-aspartic acid and the glycosaminoglycan molecule. heparin. We conclude that particle size and surface potential as gross supramolecular properties of these complexes do not represent, at least in a non-biological system, the basis for the differential transfection behaviour observed between these condensing polymers. However, differences in the ability of the polylysine and polyornithine polymers to interact with pDNA and to stabilise the polymer-pDNA assembly could have profound effects upon the cellular and sub-cellular biological processing of pDNA molecules and contribute to the disparity in cell transfection efficiency observed between these complexes.

Atomic force microscopy analysis of intermediates in cobalt hexammine-induced DNA condensation

The packaging pathway of cobalt hexammine-induced DNA condensation on the surface of mica was examined by varying the concentration of Co(NH3)6(3+) in a dilute DNA solution and visualizing the condensates by atomic force microscopy (AFM). Images reveal that cobalt hexammine-induced DNA condensation on mica involves well-defined structures. At 30 microM Co(NH3)6(3+), prolate ellipsoid condensates composed of relatively shorter rods with linkages between them are formed. At 80 microM Co(NH3)6(3+), the condensed features include toroids with average diameter of approximately 240 nm as well as U-shaped and rod-like condensates with nodular appearances. The results imply that the condensates, whether toroids, U-shaped or rod-like structures have similar intermediate state which includes relatively shorter rod-like segments. The average size of the condensed toroids after incubated at room temperature for 5 h (approximately 240 nm) is much larger than that incubated for 0.5 h (approximately 100 nm). The results indicate that the condensation of DNA by Co(NH3)6(3+) is a kinetic-controlled process.

DNA condensation by multivalent cations

In the presence of multivalent cations, high molecular weight DNA undergoes a dramatic condensation to a compact, usually highly ordered toroidal structure. This review begins with an overview of DNA condensation: condensing agents, morphology, kinetics, and reversibility, and the minimum size required to form orderly condensates. It then summarizes the statistical mechanics of the collapse of stiff polymers, which shows why DNA condensation is abrupt and why toroids are favored structures. Various ways to estimate or measure intermolecular forces in DNA condensation are discussed, all of them agreeing that the free energy change per base pair is very small, on the order of 1% of thermal energy. Experimental evidence is surveyed showing that DNA condensation occurs when about 90% of its charge is neutralized by counterions. The various intermolecular forces whose interplay gives rise to DNA condensation are then reviewed. The entropy loss upon collapse of the expanded wormlike coil costs free energy, and stiffness sets limits on tight curvature. However, the dominant contributions seem to come from ions and water. Electrostatic repulsions must be overcome by high salt concentrations or by the correlated fluctuations of territorially bound multivalent cations. Hydration must be adjusted to allow a cooperative accommodation of the water structure surrounding surface groups on the DNA helices as they approach. Undulations of the DNA in its confined surroundings extend the range of the electrostatic forces. The condensing ions may also subtly modify the local structure of the double helix.

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

DNA in viruses and cells exists in highly condensed, tightly packaged states. We have undertaken an in vitro study of the kinetics of DNA condensation by the trivalent cation hexaammine cobalt (III) with the aim of formulating a quantitative, mechanistic model of the condensation process. Experimental approaches included total intensity and dynamic light scattering, electron microscopy, and differential sedimentation. We determined the average degree of condensation, the distribution of condensate sizes, and the fraction of uncondensed DNA as a function of reaction time for a range of [DNA] and [Co(NH(3))(3+)(6)]. We find the following: (1) DNA condensation occurs only above a critical [Co(NH(3))(3+)(6)] for a given DNA and salt concentration. At the onset of condensation, [Co(NH(3))(3+)(6)]/[DNA-phosphate] is close to the average value of 0.54, which reflects the 89-90% charge neutralization criterion for condensation. (2) The equilibrium weight average hydrodynamic radius <R(H) > of the condensates first decreases, then increases with increasing [Co(NH(3))(3+)(6)] as they undergo a transition from intramolecular (monomolecular) to intermolecular (multimolecular) condensation. However, <R(H) > is insensitive to [DNA]. (3) The uncondensed DNA fraction decays approximately exponentially with time. The equilibrium uncondensed DNA fraction and relaxation time decrease with increasing [Co(NH(3))(3+)(6)] but are insensitive to [DNA]. (4) The condensation rate in its early stages is insensitive to [DNA] but proportional to [Co(NH(3))(3+)(6)](xs) = [Co(NH(3))(3+)(6)] - [Co(NH(3))(3+)(6)](crit). (5) Data for low [DNA] and low [Co(NH(3))(3+)(6)] at early stages of condensation are most reliable for kinetic modeling since under these conditions there is minimal clumping and network formation among separate condensates. A mechanism with initial monomolecular nucleation and subsequent bimolecular association and unimolecular dissociation steps with rate constants that depend on the number of DNA molecules in the condensate, accounts reasonably well for these observations.

Stretching of single collapsed DNA molecules

The elastic response of single plasmid and lambda phage DNA molecules was probed using optical tweezers at concentrations of trivalent cations that provoked DNA condensation in bulk. For uncondensed plasmids, the persistence length, P, decreased with increasing spermidine concentration before reaching a limiting value 40 nm. When condensed plasmids were stretched, two types of behavior were observed: a stick-release pattern and a plateau at approximately 20 pN. These behaviors are attributed to unpacking from a condensed structure, such as coiled DNA. Similarly, condensing concentrations of hexaammine cobalt(III) (CoHex) and spermidine induced extensive changes in the low and high force elasticity of lambda DNA. The high force (5-15 pN) entropic elasticity showed worm-like chain (WLC) behavior, with P two- to fivefold lower than in low monovalent salt. At lower forces, a 14-pN plateau abruptly appeared. This corresponds to an intramolecular attraction of 0.083-0.33 kT/bp, consistent with osmotic stress measurements in bulk condensed DNA. The intramolecular attractive force with CoHex is larger than with spermidine, consistent with the greater efficiency with which CoHex condenses DNA in bulk. The transition from WLC behavior to condensation occurs at an extension about 85% of the contour length, permitting looping and nucleation of condensation. Approximately half as many base pairs are required to nucleate collapse in a stretched chain when CoHex is the condensing agent.

Thermodynamics of the conformational transition of biopolyelectrolytes: the case of specific affinity of counterions

A formal development of the Counterion Condensation theory (CC) of linear polyelectrolytes has been performed to include specific (chemical) affinity of condensed counterions, for polyelectrolyte charge density values larger than the critical value of condensation. It has been conventionally assumed that each condensed counterion exhibits an affinity free-energy difference for the polymer, (DeltaG(aff)). Moreover, the model assumes that the enthalpic and entropic contributions to DeltaG(aff), i.e., DeltaH(aff) and DeltaS(aff), are both independent of temperature, ionic strength and polymer concentration. Equations have been derived relative to the case of the thermally induced, ionic strength dependent, conformational transition of a biopolyelectrolyte between two conformations for which chemical affinity is supposed to take place. The experimental data of the intramolecular conformational transition of the ionic polysaccharide kappa-carrageenan in dimethylsulfoxide (DMSO) have been successfully compared with the theoretical predictions. This novel approach provides the enthalpic and entropic affinity values for both conformations, together with the corresponding thermodynamic functions of nonpolyelectrolytic origin pertaining to the biopolymer backbone change per se, i.e., DeltaH(n.pol) and DeltaS(n.pol), according to a treatment previously shown to be successful for lower values of the biopolyelectrolyte linear charge density. The ratio of DeltaH(n.pol) to DeltaS(n.pol) was found to be remarkably constant independent of the value of the dielectric constant of the solvent, from formamide to water to DMSO, pointing to the identity of the underlying conformational process.

Structural effects of cobalt-amine compounds on DNA condensation

Light scattering and electron microscopy have been used to investigate the structural effects of the trivalent complexes hexaammine cobalt (III) chloride (Cohex), tris(ethylenediamine) cobalt(III) chloride (Coen), and cobalt(III) sepulchrate chloride (Cosep) on DNA condensation. These cobalt-amine compounds have similar ligand coordination geometries but differ slightly in size. Their hydrophobicity is in the order Cosep > Coen > Cohex, according to the numbers of methylene groups in these ligands. All of these compounds effectively precipitate DNA at high concentrations; but despite a lower surface charge density, Cosep condenses DNA twice as effectively as Coen or Cohex. UV and CD measurements of the supernatants of cobalt-amine/DNA solutions reveal a preferential binding of Delta-Coen over Lambda-Coen to the precipitated DNA, but there is no chiral selectivity for Cosep. Competition experiments show that the binding strengths of these three cobalt-amine compounds to aggregated DNA are comparable. A charge neutralization of 88-90% is required for DNA condensation. Our data indicate that 1) electrostatic interaction is the main driving force for binding of multivalent cations to DNA; 2) DNA condensation is dependent on the structure of the condensing agent; and 3) the hydration pattern or polarization of water molecules on the surface of condensing agents plays an important role in DNA condensation and chiral recognition.

Surface-directed DNA condensation in the absence of soluble multivalent cations

Multivalent cations are known to condense DNA into higher ordered structures, including toroids and rods. Here we report that solid supports treated with monovalent or multivalent cationic silanes, followed by removal of soluble molecules, can condense DNA. The mechanism of this surface-directed condensation depends on surface-mobile silanes, which are apparently recruited to the condensation site. The yield and species of DNA aggregates can be controlled by selecting the type of functional groups on surfaces, DNA and salt concentrations. For plasmid DNA, the toroidal form can represent >70% of adsorbed structures.