Spermine-induced aggregation of DNA, nucleosome, and chromatin

The role of polyamine metabolism in cellular function and physiology

Polyamines are molecules with multiple amino groups that are essential for cellular function. The major polyamines are putrescine, spermidine, spermine, and cadaverine. Polyamines are important for posttranscriptional regulation, autophagy, programmed cell death, proliferation, redox homeostasis, and ion channel function. Their levels are tightly controlled. High levels of polyamines are associated with proliferative pathologies such as cancer, whereas low polyamine levels are observed in aging, and elevated polyamine turnover enhances oxidative stress. Polyamine metabolism is implicated in several pathophysiological processes in the nervous, immune, and cardiovascular systems. Currently, manipulating polyamine levels is under investigation as a potential preventive treatment for several pathologies, including aging, ischemia/reperfusion injury, pulmonary hypertension, and cancer. Although polyamines have been implicated in many intracellular mechanisms, our understanding of these processes remains incomplete and is a topic of ongoing investigation. Here, we discuss the regulation and cellular functions of polyamines, their role in physiology and pathology, and emphasize the current gaps in knowledge and potential future research directions.

Adsorption of semiflexible wormlike polymers to a bar and their double-chain complex formation

We theoretically study pairing (double-strand complexation) of semiflexible wormlike chains (WLC) due to their side-to-side attraction. Considering binding of two WLCs of high stiffness we start with the case of infinite stiffness of one chain which is replaced with a straight bar. A combination of the quantitative transfer matrix approach with scaling arguments in terms of trains, loops of different sizes, tails and supertrains allowed us to characterize all the regimes of semiflexible chain adsorption on a bar. In particular, we predict a self-similar monomer concentration profile c(r) ∝ r-10/3 near the bar (at distances r below the chain Kuhn length l) at the critical point for adsorption. Such localized critical profile leads to a sharp adsorption transition. Furthermore, we found that supertrains serve as the basic structural elements in WLC complexes leading to bridging, network formation and condensation of semiflexible polymers in dilute solutions. Polymer collapse (precipitation) and redissolution on increasing attraction strength are predicted in qualitative agreement with experiments on aqueous solutions of DNA and F-actin.

Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles

Due to the vast length scale inside the cell nucleus, multiscale models are required to understand chromatin folding, structure, and dynamics and how they regulate genomic activities such as DNA transcription, replication, and repair. We study the interactions and structure of condensed phases formed by the universal building block of chromatin, the nucleosome core particle (NCP), using bottom-up multiscale coarse-grained (CG) simulations with a model extracted from all-atom MD simulations. In the presence of the multivalent cations Mg(H2O)62+ or CoHex3+, we analyze the internal structures of the NCP aggregates and the contributions of histone tails and ions to the aggregation patterns. We then derive a "super" coarse-grained (SCG) NCP model to study the macroscopic scale phase separation of NCPs. The SCG simulations show the formation of NCP aggregates with Mg(H2O)62+ concentration-dependent densities and sizes. Variation of the CoHex3+ concentrations results in highly ordered lamellocolumnar and hexagonal columnar phases in agreement with experimental data. The results give detailed insights into nucleosome interactions and for understanding chromatin folding in the cell nucleus.

Electrostatic encoding of genome organization principles within single native nucleosomes

The eukaryotic genome, first packed into nucleosomes of about 150 bp around the histone core, is organized into euchromatin and heterochromatin, corresponding to the A and B compartments, respectively. Here, we asked if individual nucleosomes in vivo know where to go. That is, do mono-nucleosomes by themselves contain A/B compartment information, associated with transcription activity, in their biophysical properties? We purified native mono-nucleosomes to high monodispersity and used physiological concentrations of biological polyamines to determine their condensability. The chromosomal regions known to partition into A compartments have low condensability and vice versa. In silico chromatin polymer simulations using condensability as the only input showed that biophysical information needed to form compartments is all contained in single native nucleosomes and no other factors are needed. Condensability is also strongly anticorrelated with gene expression, and especially so near the promoter region and in a cell type dependent manner. Therefore, individual nucleosomes in the promoter know whether the gene is on or off, and that information is contained in their biophysical properties. Comparison with genetic and epigenetic features suggest that nucleosome condensability is a very meaningful axis onto which to project the high dimensional cellular chromatin state. Analysis of condensability using various condensing agents including those that are protein-based suggests that genome organization principle encoded into individual nucleosomes is electrostatic in nature. Polyamine depletion in mouse T cells, by either knocking out ornithine decarboxylase (ODC) or inhibiting ODC, results in hyperpolarized condensability, suggesting that when cells cannot rely on polyamines to translate biophysical properties of nucleosomes to control gene expression and 3D genome organization, they accentuate condensability contrast, which may explain dysfunction known to occur with polyamine deficiency.

Sequence-Dependent Orientational Coupling and Electrostatic Attraction in Cation-Mediated DNA-DNA Interactions

Condensation of DNA is vital for its biological functions and controlled nucleic acid assemblies. However, the mechanisms of DNA condensation are not fully understood due to the inability of experiments to access cation distributions and the complex interplay of energetic and entropic forces during assembly. By constructing free energy surfaces using exhaustive sampling and detailed analysis of cation distributions, we elucidate the mechanism of DNA condensation in different salt conditions and with different DNA sequences. We found that DNA condensation is facilitated by the correlated dynamics of the localized cations at the grooves of DNA helices. These dynamics are strongly dependent on the salt conditions and DNA sequences. In the presence of magnesium ions, major groove binding facilitates attraction. In contrast, in the presence of polyvalent cations, minor groove binding serves to create charge patterns, leading to condensation. Our findings present a novel advancement in the field and have broad implications for understanding and controlling nucleic acid complexes in vivo and in vitro.

Entropy of Charge Inversion in DNA including One-Loop Fluctuations

The entropy and charge distributions have been calculated for a simple model of polyelectrolytes attached to the surface of DNA using a field-theoretic method that includes fluctuations to the lowest one-loop order beyond mean-field theory. Experiments have revealed correlation-driven behavior of DNA in charged solutions, including charge inversion and condensation. In our model, the condensed polyelectrolytes are taken to be doubly charged dimers of length comparable to the distance between sites along the phosphate chains. Within this lattice gas model, each adsorption site is assumed to have either a vacancy or a positively charged dimer attached with the dimer oriented either parallel or perpendicular to the double-helix DNA chain. We find that the inclusion of the fluctuation terms decreases the entropy by ∼50% in the weak-binding regime. There, the bound dimer concentration is low because the dimers are repelled from the DNA molecule, which competes with the chemical potential driving them from the solution to the DNA surface. Surprisingly, this decrease in entropy due to correlations is so significant that it overcompensates for the entropy increase at the mean-field level, so that the total entropy is even lower than in the absence of interactions between lattice sites. As a bonus, we present a transparent exposition of the methods used that could be useful to students and others wishing to use this formulation to extend this calculation to more realistic models.

Dimensional Reduction for Single-Molecule Imaging of DNA and Nucleosome Condensation by Polyamines, HP1α and Ki-67

Macromolecules organize themselves into discrete membrane-less compartments. Mounting evidence has suggested that nucleosomes as well as DNA itself can undergo clustering or condensation to regulate genomic activity. Current in vitro condensation studies provide insight into the physical properties of condensates, such as surface tension and diffusion. However, methods that provide the resolution needed for complex kinetic studies of multicomponent condensation are desired. Here, we use a supported lipid bilayer platform in tandem with total internal reflection microscopy to observe the two-dimensional movement of DNA and nucleosomes at the single-molecule resolution. This dimensional reduction from three-dimensional studies allows us to observe the initial condensation events and dissolution of these early condensates in the presence of physiological condensing agents. Using polyamines, we observed that the initial condensation happens on a time scale of minutes while dissolution occurs within seconds upon charge inversion. Polyamine valency, DNA length, and GC content affect the threshold polyamine concentration for condensation. Protein-based nucleosome condensing agents, HP1α and Ki-67, have much lower threshold concentrations for condensation than charge-based condensing agents, with Ki-67 being the most effective, requiring as low as 100 pM for nucleosome condensation. In addition, we did not observe condensate dissolution even at the highest concentrations of HP1α and Ki-67 tested. We also introduce a two-color imaging scheme where nucleosomes of high density labeled in one color are used to demarcate condensate boundaries and identical nucleosomes of another color at low density can be tracked relative to the boundaries after Ki-67-mediated condensation. Our platform should enable the ultimate resolution of single molecules in condensation dynamics studies of chromatin components under defined physicochemical conditions.

Spermine enhances antiviral and anticancer responses by stabilizing DNA binding with the DNA sensor cGAS

Self-nonself discrimination is vital for the immune system to mount responses against pathogens while maintaining tolerance toward the host and innocuous commensals during homeostasis. Here, we investigated how indiscriminate DNA sensors, such as cyclic GMP-AMP synthase (cGAS), make this self-nonself distinction. Screening of a small-molecule library revealed that spermine, a well-known DNA condenser associated with viral DNA, markedly elevates cGAS activation. Mechanistically, spermine condenses DNA to enhance and stabilize cGAS-DNA binding, optimizing cGAS and downstream antiviral signaling. Spermine promotes condensation of viral, but not host nucleosome, DNA. Deletion of viral DNA-associated spermine, by propagating virus in spermine-deficient cells, reduced cGAS activation. Spermine depletion subsequently attenuated cGAS-mediated antiviral and anticancer immunity. Collectively, our results reveal a pathogenic DNA-associated molecular pattern that facilitates nonself recognition, linking metabolism and pathogen recognition.

Nucleosome destabilization by polyamines

The roles and molecular interactions of polyamines (PAs) in the nucleus are not fully understood. Here their effect on nucleosome stability, a key regulatory factor in eukaryotic gene control, is reported, as measured in agarose embedded nuclei of H2B-GFP expressor HeLa cells. Nucleosome stability was assessed by quantitative microscopy [1,2] in situ, in close to native state of chromatin, preserving the nucleosome constrained topology of the genomic DNA. A robust destabilizing effect was observed in the millimolar concentration range in the case of spermine, spermidine as well as putrescine, which was strongly pH and salt concentration-dependent, and remained significant also at neutral pH. The integrity of genomic DNA was not affected by PA treatment, excluding DNA break-elicited topological relaxation as a factor in destabilization. The binding of PAs to DNA was demonstrated by the displacement of ethidium bromide, both from deproteinized nuclear halos and from plasmid DNA. The possibility that DNA methylation patterns may be influenced by PA levels is contemplated in the context of gene expression and DNA methylation correlations identified in the NCI-60 panel-based CellMiner database: methylated loci in subsets of high-ODC1 cell lines and the dependence of PER3 DNA methylation on PA metabolism.

Products Generated by Amine-Catalyzed Strand Cleavage at Apurinic/Apyrimidinic Sites in DNA: New Insights from a Biomimetic Nucleoside Model System

Abasic sites are common in cellular and synthetic DNA. As a result, it is important to characterize the chemical fate of these lesions. Amine-catalyzed strand cleavage at abasic sites in DNA is an important process in which conversion of small amounts of the ring-opened abasic aldehyde residue to an iminium ion facilitates β-elimination of the 3'-phosphoryl group. This reaction generates a trans-α,β-unsaturated iminium ion on the 3'-terminus of the strand break as an obligate intermediate. The canonical product expected from amine-catalyzed cleavage at an AP site is the corresponding trans-α,β-unsaturated aldehyde sugar remnant resulting from hydrolysis of this iminium ion. Interestingly, a handful of studies have reported noncanonical 3'-sugar remnants generated by amine-catalyzed strand cleavage, but the formation and properties of these products are not well-understood. To address this knowledge gap, a nucleoside system was developed that enabled chemical characterization of the sugar remnants generated by amine-catalyzed β-elimination in the 2-deoxyribose system. The results predict that amine-catalyzed strand cleavage at an AP site under physiological conditions has the potential to reversibly generate noncanonical cleavage products including cis-alkenal, 3-thio-2,3-dideoxyribose, and 2-deoxyribose groups alongside the canonical trans-alkenal residue on the 3'-terminus of the strand break. Thus, the model reactions provide evidence that the products generated by amine-catalyzed strand cleavage at abasic sites in cellular DNA may be more complex that commonly thought, with trans-α,β-unsaturated iminium ion intermediates residing at the hub of interconverting product mixtures. The results expand the list of possible 3'-sugar remnants arising from amine-catalyzed cleavage of abasic sites in DNA that must be chemically or enzymatically removed for the completion of base excision repair and single-strand break repair in cells.

Unexpected Complexity in the Products Arising from NaOH-, Heat-, Amine-, and Glycosylase-Induced Strand Cleavage at an Abasic Site in DNA

Hydrolytic loss of nucleobases from the deoxyribose backbone of DNA is one of the most common unavoidable types of damage in synthetic and cellular DNA. The reaction generates abasic sites in DNA, and it is important to understand the properties of these lesions. The acidic nature of the α-protons of the ring-opened abasic aldehyde residue facilitates the β-elimination of the 3'-phosphoryl group. This reaction is expected to generate a DNA strand break with a phosphoryl group on the 5'-terminus and a trans-α,β-unsaturated aldehyde residue on the 3'-terminus; however, a handful of studies have identified noncanonical sugar remnants on the 3'-terminus, suggesting that the products arising from strand cleavage at apurinic/apyrimidinic sites in DNA may be more complex than commonly thought. We characterized the strand cleavage induced by the treatment of an abasic site-containing DNA oligonucleotide with heat, NaOH, piperidine, spermine, and the base excision repair glycosylases Fpg and Endo III. The results showed that under multiple conditions, cleavage at an abasic site in a DNA oligomer generated noncanonical sugar remnants including cis-α,β-unsaturated aldehyde, 2-deoxyribose, and 3-thio-2,3-dideoxyribose products on the 3'-terminus of the strand break.

Formation and Repair of an Interstrand DNA Cross-Link Arising from a Common Endogenous Lesion

Interstrand DNA cross-links (ICLs) are cytotoxic because they block the strand separation required for read-out and replication of the genetic information in duplex DNA. The unavoidable formation of ICLs in cellular DNA may contribute to aging, neurodegeneration, and cancer. Here, we describe the formation and properties of a structurally complex ICL derived from an apurinic/apyrimidinic (AP) site, which is one of the most common endogenous lesions in cellular DNA. The results characterize a cross-link arising from aza-Michael addition of the N²-amino group of a guanine residue to the electrophilic sugar remnant generated by spermine-mediated strand cleavage at an AP site in duplex DNA. An α,β-unsaturated iminium ion is the critical intermediate involved in ICL formation. Studies employing the bacteriophage φ29 polymerase provided evidence that this ICL can block critical DNA transactions that require strand separation. The results of biochemical studies suggest that this complex strand break/ICL might be repaired by a simple mechanism in which the 3'-exonuclease action of the enzyme apurinic/apyrimidinic endonuclease (APE1) unhooks the cross-link to initiate repair via the single-strand break repair pathway.

Aqueous Triple-Phase System in Microwell Array for Generating Uniform-Sized DNA Hydrogel Particles

DNA hydrogels are notable for their biocompatibility and ability to incorporate DNA information and computing properties into self-assembled micrometric structures. These hydrogels are assembled by the thermal gelation of DNA motifs, a process which requires a high salt concentration and yields polydisperse hydrogel particles, thereby limiting their application and physicochemical characterization. In this study, we demonstrate that single, uniform DNA hydrogel particles can form inside aqueous/aqueous two-phase systems (ATPSs) assembled in a microwell array. In this process, uniform dextran droplets are formed in a microwell array inside a microfluidic device. The dextran droplets, which contain DNA motifs, are isolated from each other by an immiscible PEG solution containing magnesium ions and spermine, which enables the DNA hydrogel to undergo gelation. Upon thermal annealing of the device, we observed the formation of an aqueous triple-phase system in which uniform DNA hydrogel particles (the innermost aqueous phase) resided at the interface of the aqueous two-phase system of dextran and PEG. We expect ATPS microdroplet arrays to be used to manufacture other hydrogel microparticles and DNA/dextran/PEG aqueous triple-phase systems to serve as a highly parallel model for artificial cells and membraneless organelles.

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

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

Counterion-Dependent Mechanisms of DNA Origami Nanostructure Stabilization Revealed by Atomistic Molecular Simulation

The DNA origami technique has proven to have tremendous potential for therapeutic and diagnostic applications like drug delivery, but the relatively low concentrations of cations in physiological fluids cause destabilization and degradation of DNA origami constructs preventing in vivo applications. To reveal the mechanisms behind DNA origami stabilization by cations, we performed atomistic molecular dynamics simulations of a DNA origami rectangle in aqueous solvent with varying concentrations of magnesium and sodium as well as polyamines like oligolysine and spermine. We explored the binding of these ions to DNA origami in detail and found that the mechanism of stabilization differs between ion types considerably. While sodium binds weakly and quickly exchanges with the solvent, magnesium and spermine bind close to the origami with spermine also located in between helices, stabilizing the crossovers characteristic for DNA origami and reducing repulsion of parallel helices. In contrast, oligolysine of length ten prevents helix repulsion by binding to adjacent helices with its flexible side chains, spanning the gap between the helices. Shorter oligolysine molecules with four subunits are weak stabilizers as they lack both the ability to connect helices and to prevent helix repulsion. This work thus shows how the binding modes of ions influence the stabilization of DNA origami nanostructures on a molecular level.

Like-charge polymer-membrane complexation mediated by multivalent cations: One-loop-dressed strong coupling theory

We probe the electrostatic mechanism driving adsorption of polyelectrolytes onto like-charged membranes upon the addition of tri- and tetravalent counterions to a bathing monovalent salt solution. We develop a one-loop-dressed strong coupling theory that treats the monovalent salt at the electrostatic one-loop level and the multivalent counterions within a strong-coupling approach. It is shown that the adhesive force of the multivalent counterions mediating the like-charge adsorption arises from their strong condensation at the charged membrane. The resulting interfacial counterion excess locally maximizes the screening ability of the electrolyte and minimizes the electrostatic polymer grand potential. This translates into an attractive force that pulls the polymer to the similarly charged membrane. We show that the high counterion valency enables this adsorption transition even at weakly charged membranes. Additionally, strongly charged membranes give rise to monovalent counterion-induced correlations and intensify the interfacial multivalent counterion condensation, strengthening the complexation of the polymer with the like-charged membrane, as well as triggering the orientational transition of the molecule prior to its adsorption. Finally, our theory provides two additional key features as evidenced by previous adsorption experiments: first, the critical counterion concentration for polymer adsorption decreases with the rise of the counterion valency and, second, the addition of monovalent salt enhances the screening of the membrane charges and suppresses monovalent counterion correlations close to the surface. This weakens the interfacial multivalent counterion condensation and results in the desorption of the polymer from the substrate.

Orientational transition and complexation of DNA with anionic membranes: Weak and intermediate electrostatic coupling

We characterize the role of charge correlations in the adsorption of a short, rodlike anionic polyelectrolyte onto a similarly charged membrane. Our theory reveals two different mechanisms driving the like-charge polyelectrolyte-membrane complexation: In weakly charged membranes, repulsive polyelectrolyte-membrane interactions lead to the interfacial depletion and a parallel orientation of the polyelectrolyte with respect to the membrane; while in the intermediate membrane charge regime, the interfacial counterion excess gives rise to an attractive "salt-induced" image force. This furthermore results in an orientational transition from a parallel to a perpendicular configuration and a subsequent short-ranged like-charge adsorption of the polyelectrolyte to the substrate. A further increase of the membrane charge engenders a charge inversion, originating from surface-induced ionic correlations, that act as a separate mechanism capable of triggering the like-charge polyelectrolyte-membrane complexation over an extended distance interval from the membrane surface. The emerging picture of this complexation phenomenon identifies the interfacial "salt-induced" image forces as a powerful control mechanism in polyelectrolyte-membrane complexation.

Peptide Sequence-Dependent Gene Expression of PEGylated Peptide/DNA Complexes

Oligolysine-based PEG-peptides with 15 or 20 amino acid residues including two cysteines were synthesized to formulate cross-linked polyplex micelles (PMs) incorporating luciferase-coding plasmid DNA (pDNA). Two cysteine residues were separately allocated at the C-terminal, center, or N-terminal of peptide moieties. Although TEM observation showed that all PEG-peptides condensed pDNA into rod-like or toroidal morphologies, the rod length distribution of PMs was affected by both the amino acid sequence and the peptide length of PEG-peptides. In comparison to the cysteine-uninstalled PEG-peptides, the cysteine-installed PEG-peptides exhibited a reductive environment-responsive pDNA release, which was observed in a gel retardation assay. From physicochemical characterizations, a relationship between the amino acid sequence and the in vitro gene expression efficacy of PMs in a cell-free protein synthesis system has been clearly demonstrated. Finally, the cell-based assay using HeLa cells has been tested, and the differences between both results of cell-free and cell-based systems are discussed.

Role of metallic core for the stability of virus-like particles in strongly coupled electrostatics

Electrostatic interactions play important roles in the formation and stability of viruses and virus-like particles (VLPs) through processes that often involve added, or naturally occurring, multivalent ions. Here, we investigate the electrostatic or osmotic pressure acting on the proteinaceous shell of a generic model of VLPs, comprising a charged outer shell and a metallic nanoparticle core, coated by a charged layer and bathed in an aqueous electrolyte solution. Motivated by the recent studies accentuating the role of multivalent ions for the stability of VLPs, we focus on the effects of multivalent cations and anions in an otherwise monovalent ionic solution. We perform extensive Monte-Carlo simulations based on appropriate Coulombic interactions that consistently take into account the effects of salt screening, the dielectric polarization of the metallic core, and the strong-coupling electrostatics due to multivalent ions. We specifically study the intricate roles these factors play in the electrostatic stability of the model VLPs. It is shown that while the insertion of a metallic nanoparticle by itself can produce negative, inward-directed, pressure on the outer shell, addition of only a small amount of multivalent counterions can robustly engender negative pressures, enhancing the VLP stability across a wide range of values for the system parameters.

Biochemical, Metabolomic, and Genetic Analyses of Dephospho Coenzyme A Kinase Involved in Coenzyme A Biosynthesis in the Human Enteric Parasite Entamoeba histolytica

Coenzyme A (CoA) is an essential cofactor for numerous cellular reactions in all living organisms. In the protozoan parasite Entamoeba histolytica, CoA is synthesized in a pathway consisting of four enzymes with dephospho-CoA kinase (DPCK) catalyzing the last step. However, the metabolic and physiological roles of E. histolytica DPCK remain elusive. In this study, we took biochemical, reverse genetic, and metabolomic approaches to elucidate role of DPCK in E. histolytica. The E. histolytica genome encodes two DPCK isotypes (EhDPCK1 and EhDPCK2). Epigenetic gene silencing of Ehdpck1 and Ehdpck2 caused significant reduction of DPCK activity, intracellular CoA concentrations, and also led to growth retardation in vitro, suggesting importance of DPCK for CoA synthesis and proliferation. Furthermore, metabolomic analysis showed that suppression of Ehdpck gene expression also caused decrease in the level of acetyl-CoA, and metabolites involved in amino acid, glycogen, hexosamine, nucleic acid metabolisms, chitin, and polyamine biosynthesis. The kinetic properties of E. histolytica and human DPCK showed remarkable differences, e.g., the Km values of E. histolytica and human DPCK were 58-114 and 5.2 μM toward dephospho-CoA and 15-20 and 192 μM for ATP, respectively. Phylogenetic analysis also supported the uniqueness of the amebic enzyme compared to the human counterpart. These biochemical, evolutionary features, and physiological importance of EhDPCKs indicate that EhDPCK represents the rational target for the development of anti-amebic agents.

Enhanced polymer capture speed and extended translocation time in pressure-solvation traps

The efficiency of nanopore-based biosequencing techniques requires fast anionic polymer capture by like-charged pores followed by a prolonged translocation process. We show that this condition can be achieved by setting a pressure-solvation trap. Polyvalent cation addition to the KCl solution triggers the like-charge polymer-pore attraction. The attraction speeds-up the pressure-driven polymer capture but also traps the molecule at the pore exit, reducing the polymer capture time and extending the polymer escape time by several orders of magnitude. By direct comparison with translocation experiments [D. P. Hoogerheide et al., ACS Nano 8, 7384 (2014)1936-085110.1021/nn5025829], we characterize as well the electrohydrodynamics of polymers transport in pressure-voltage traps. We derive scaling laws that can accurately reproduce the pressure dependence of the experimentally measured polymer translocation velocity and time. We also find that during polymer capture, the electrostatic barrier on the translocating molecule slows down the liquid flow. This prediction identifies the streaming current measurement as a potential way to probe electrostatic polymer-pore interactions.

Defining the Structure of a Protein-Spherical Nucleic Acid Conjugate and Its Counterionic Cloud

Protein-spherical nucleic acid conjugates (Pro-SNAs) are an emerging class of bioconjugates that have properties defined by their protein cores and dense shell of oligonucleotides. They have been used as building blocks in DNA-driven crystal engineering strategies and show promise as agents that can cross cell membranes and affect both protein and DNA-mediated processes inside cells. However, ionic environments surrounding proteins can influence their activity and conformational stability, and functionalizing proteins with DNA substantively changes the surrounding ionic environment in a nonuniform manner. Techniques typically used to determine protein structure fail to capture such irregular ionic distributions. Here, we determine the counterion radial distribution profile surrounding Pro-SNAs dispersed in RbCl with 1 nm resolution through in situ anomalous small-angle X-ray scattering (ASAXS) and classical density functional theory (DFT). SAXS analysis also reveals the radial extension of the DNA and the linker used to covalently attach the DNA to the protein surface. At the experimental salt concentration of 50 mM RbCl, Rb⁺ cations compensate ∼90% of the negative charge due to the DNA and linker. Above 75 mM, DFT calculations predict overcompensation of the DNA charge by Rb⁺. This study suggests a method for exploring Pro-SNA structure and function in different environments through predictions of ionic cloud densities as a function of salt concentration, DNA grafting density, and length. Overall, our study demonstrates that solution X-ray scattering combined with DFT can discern counterionic distribution and submolecular features of highly charged, complex nanoparticle constructs such as Pro-SNAs and related nucleic acid conjugate materials.

Single-molecule compaction of megabase-long chromatin molecules by multivalent cations

To gain insight into the conformational properties and compaction of megabase-long chromatin molecules, we reconstituted chromatin from T4 phage DNA (165 kb) and recombinant human histone octamers (HO). The unimolecular compaction, induced by divalent Mg2+ or tetravalent spermine4+ cations, studied by single-molecule fluorescence microscopy (FM) and dynamic light scattering (DLS) techniques, resulted in the formation of 250-400 nm chromatin condensates. The compaction on this scale of DNA size is comparable to that of chromatin topologically associated domains (TAD) in vivo. Variation of HO loading revealed a number of unique features related to the efficiency of chromatin compaction by multivalent cations, the mechanism of compaction, and the character of partly compact chromatin structures. The observations may be relevant for how DNA accessibility in chromatin is maintained. Compaction of saturated chromatin, in turn, is accompanied by an intra-chain segregation at the level of single chromatin molecules, suggesting an intriguing scenario of selective activation/deactivation of DNA as a result of chromatin fiber heterogeneity due to the nucleosome positioning. We suggest that this chromatin, reconstituted on megabase-long DNA because of its large size, is a useful model of eukaryotic chromatin.

Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA

Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3’ddR5p) at the 3’-terminus of the strand break. Interestingly, this strand scission process leaves an electrophilic α,β-unsaturated aldehyde residue embedded within the resulting nicked duplex. Here we present evidence that 3’ddR5p derivatives generated by spermine-catalyzed strand cleavage at Ap sites in duplex DNA can react with adenine residues on the opposing strand to generate a complex lesion consisting of an interstrand cross-link adjacent to a strand break. The cross-link blocks DNA replication by ϕ29 DNA polymerase, a highly processive polymerase enzyme that couples synthesis with strand displacement. This suggests that 3’ddR5p-derived cross-links have the potential to block critical cellular DNA transactions that require strand separation. LC-MS/MS methods developed herein provide powerful tools for studying the occurrence and properties of these cross-links in biochemical and biological systems.

Crystallization, Reentrant Melting, and Resolubilization of Virus Nanoparticles

Crystallization is a fundamental and ubiquitous process that is well understood in the case of atoms or small molecules, but its outcome is still hard to predict in the case of nanoparticles or macromolecular complexes. Controlling the organization of virus nanoparticles into a variety of 3D supramolecular architectures is often done by multivalent ions and is of great interest for biomedical applications such as drug or gene delivery and biosensing, as well as for bionanomaterials and catalysis. In this paper, we show that slow dialysis, over several hours, of wild-type Simian Virus 40 (wt SV40) nanoparticle solution against salt solutions containing MgCl₂, with or without added NaCl, results in wt SV40 nanoparticles arranged in a body cubic center crystal structure with Im3m space group, as a thermodynamic product, in coexistence with soluble wt SV40 nanoparticles. The nanoparticle crystals formed above a critical MgCl₂ concentrations. Reentrant melting and resolubilization of the virus nanoparticles took place when the MgCl₂ concentrations passed a second threshold. Using synchrotron solution X-ray scattering we determined the structures and the mass fraction of the soluble and crystal phases as a function of MgCl₂ and NaCl concentrations. A thermodynamic model, which balances the chemical potentials of the Mg²⁺ ions in each of the possible states, explains our observations. The model reveals the mechanism of both the crystallization and the reentrant melting and resolubilization and shows that counterion entropy is the main driving force for both processes.

The Influence of Ionic Environment and Histone Tails on Columnar Order of Nucleosome Core Particles

The nucleosome core particle (NCP) is the basic building block of chromatin. Nucleosome-nucleosome interactions are instrumental in chromatin compaction, and understanding NCP self-assembly is important for understanding chromatin structure and dynamics. Recombinant NCPs aggregated by multivalent cations form various ordered phases that can be studied by x-ray diffraction (small-angle x-ray scattering). In this work, the effects on the supramolecular structure of aggregated NCPs due to lysine histone H4 tail acetylations, histone H2A mutations (neutralizing the acidic patch of the histone octamer), and the removal of histone tails were investigated. The formation of ordered mainly hexagonal columnar NCP phases is in agreement with earlier studies; however, the highly homogeneous recombinant NCP systems used in this work display a more compact packing. The long-range order of the NCP columnar phase was found to be abolished or reduced by acetylation of the H4 tails, acidic patch neutralization, and removal of the H3 and H2B tails. Loss of nucleosome stacking upon removal of the H3 tails in combination with other tails was observed. In the absence of the H2A tails, the formation of an unknown highly ordered phase was observed.

Anomalous Protein-Protein Interactions in Multivalent Salt Solution

The stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom molecular dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental findings of "reentrant protein condensation", we observe an anomalous trend in the protein-protein potential of mean force with increasing electrolyte concentration in the order: (i) double-layer repulsion, (ii) ion-ion correlation attraction, (iii) overcharge repulsion, and in excess of 1:1 salt, (iv) non Coulombic attraction. To efficiently sample configurational space we explore hybrid continuum solvent models, applicable to many-protein systems, where weakly coupled ions are treated implicitly, while strongly coupled ones are treated explicitly. Good agreement is found with the primitive model of electrolytes, as well as with atomic models of protein and solvent.

Like-charge attraction and opposite-charge decomplexation between polymers and DNA molecules

We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test-charge theory [S. Buyukdagli et al., Phys. Rev. E 94, 042502 (2016)1539-375510.1103/PhysRevE.94.042502] to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for one-loop level electrostatic correlation effects such as the ionic cloud deformation around the strongly charged DNA molecule as well as image-charge forces induced by the low DNA permittivity. Our model can reproduce and explain various characteristics of the experimental phase diagrams for polymer solutions. First, the addition of polyvalent cations to the electrolyte solution results in the attraction of the negatively charged polymer by the DNA molecule. The glue of the like-charge attraction is the enhanced shielding of the polymer charges by the dense counterion layer at the DNA surface. Second, through the shielding of the DNA-induced electrostatic potential, mono- and polyvalent cations of large concentration both suppress the like-charge attraction. Within the same formalism, we also predict a new opposite-charge repulsion effect between the DNA molecule and a positively charged polymer. In the presence of polyvalent anions such as sulfate or phosphate, their repulsion by the DNA charges leads to the charge screening deficiency of the region around the DNA molecule. This translates into a repulsive force that results in the decomplexation of the polymer from DNA. This opposite-charge repulsion phenomenon can be verified by current experiments and the underlying mechanism can be beneficial to gene therapeutic applications where the control over polymer-DNA interactions is the key factor.

Magnesium chloride and polyamine can differentiate mouse embryonic stem cells into trophectoderm or endoderm

Magnesium chloride and polyamines stabilize DNA and chromatin. Furthermore, they can induce nucleosome aggregation and chromatin condensation in vitro. To determine the effects of elevating the cation concentrations in the nucleus of a living cell, we microinjected various concentrations of mono-, di- and polyvalent cation solutions into the nuclei of mouse embryonic stem (ES) cells and traced their fates. Here, we show that an elevation of either MgCl₂, spermidine or spermine concentration in the nucleus exerts a significant effect on mouse ES cells, and can differentiate a certain population of the cells into trophectoderm, a lineage that mouse ES cells do not normally generate, or endoderm. It is hypothesized that the cell differentiation was most probably caused by the condensation of chromatin including the Oct3/4 locus, which was induced by the elevated concentrations of these cations.

The non-dominance of counterions in charge-asymmetric electrolytes: non-monotonic precedence of electrostatic screening and local inversion of the electric field by multivalent coions

The asymptotic convergence of the thermodynamic and structural properties of unequally-sized charge-symmetric ions in strong electric fields was postulated more than thirty years ago by Valleau and Torrie as the dominance of counterions via the non-linear Poisson-Boltzmann theory [Valleau and Torrie, J. Chem. Phys., 1982, 76, 4623]. According to this mean field prescription, the properties of the electrical double layer near a highly charged electrode immersed in a size-asymmetric binary electrolyte converge to those of a size-symmetric electrolyte if the properties of counterions are the same in both instances. On the other hand, some of the present authors have shown that, in fact, counterions do not dominate the electrical properties of a spherical macroion in the presence of unequally-sized ions, symmetric in valence, if ion correlations and ionic excluded volume effects are taken into account consistently. These ingredients are neglected in the classical Poisson-Boltzmann picture. In the present work, we show the occurrence of the non-dominance of counterions in the opposite scenario, that is, when ions are equally-sized but asymmetric in valence. This is performed in the presence of highly charged colloidal surfaces of spherical and planar geometries for different ionic volume fractions. In addition to the phenomenon of non-dominance of counterions, our simulations and theoretical data also exhibit a non-monotonic order or precedence in the mean electrostatic potential, or electrostatic screening, at the Helmholtz plane of a charged colloid. This interesting behaviour is analyzed as a function of the coion's valence, the ionic volume fraction, and the charge and size of the colloidal particle. All these phenomena are explained in terms of the decay of the electric field near the colloidal surface, and by the appearance of a local inversion of both the electric field and the integrated surface charge density of the colloidal particle in the presence of monovalent counterions and multivalent coions.

The structure and intermolecular forces of DNA condensates

Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. Reproducing the setup of the DNA condensation experiments, we measured the internal pressure of DNA arrays as a function of the DNA–DNA distance, showing a quantitative agreement between the results of our simulations and the experimental data. Analysis of the MD trajectories determined the DNA–DNA force in a DNA condensate to be pairwise, the DNA condensation to be driven by electrostatics of polycations and not hydration, and the concentration of bridging cations, not adsorbed cations, to determine the magnitude and the sign of the DNA–DNA force. Finally, our simulations quantitatively characterized the orientational correlations of DNA in DNA arrays as well as diffusive motion of DNA and cations.

Ion-mediated interactions between net-neutral slabs: Weak and strong disorder effects

We investigate the effective interaction between two randomly charged but otherwise net-neutral, planar dielectric slabs immersed in an asymmetric Coulomb fluid containing a mixture of mobile monovalent and multivalent ions. The presence of charge disorder on the apposed bounding surfaces of the slabs leads to substantial qualitative changes in the way they interact, as compared with the standard picture provided by the van der Waals and image-induced, ion-depletion interactions. While, the latter predict purely attractive interactions between strictly neutral slabs, we show that the combined effects from surface charge disorder, image depletion, Debye (or salt) screening, and also, in particular, their coupling with multivalent ions, give rise to a more diverse behavior for the effective interaction between net-neutral slabs at nano-scale separations. Disorder effects show large variation depending on the properly quantified strength of disorder, leading either to non-monotonic effective interaction with both repulsive and attractive branches when the surface charges are weakly disordered (small disorder variance) or to a dominating attractive interaction that is larger both in its range and magnitude than what is predicted from the van der Waals and image-induced, ion-depletion interactions, when the surfaces are strongly disordered (large disorder variance).

Strong coupling electrostatics for randomly charged surfaces: antifragility and effective interactions

We study the effective interaction mediated by strongly coupled Coulomb fluids between dielectric surfaces carrying quenched, random monopolar charges with equal mean and variance, both when the Coulomb fluid consists only of mobile multivalent counterions and when it consists of an asymmetric ionic mixture containing multivalent and monovalent (salt) ions in equilibrium with an aqueous bulk reservoir. We analyze the consequences that follow from the interplay between surface charge disorder, dielectric and salt image effects, and the strong electrostatic coupling that results from multivalent counterions on the distribution of these ions and the effective interaction pressure they mediate between the surfaces. In a dielectrically homogeneous system, we show that the multivalent counterions are attracted towards the surfaces with a singular, disorder-induced potential that diverges logarithmically on approach to the surfaces, creating a singular but integrable counterion density profile that exhibits an algebraic divergence at the surfaces with an exponent that depends on the surface charge (disorder) variance. This effect drives the system towards a state of lower thermal 'disorder', one that can be described by a renormalized temperature, exhibiting thus a remarkable antifragility. In the presence of an interfacial dielectric discontinuity, the singular behavior of counterion density at the surfaces is removed but multivalent counterions are still accumulated much more strongly close to randomly charged surfaces as compared with uniformly charged ones. The interaction pressure acting on the surfaces displays in general a highly non-monotonic behavior as a function of the inter-surface separation with a prominent regime of attraction at small to intermediate separations. This attraction is caused directly by the combined effects from charge disorder and strong coupling electrostatics of multivalent counterions, which dominate the surface-surface repulsion due to the (equal) mean charges on the two surfaces and the osmotic pressure of monovalent ions residing between them. These effects can be quite significant even with a small degree of surface charge disorder relative to the mean surface charge. The strong coupling, disorder-induced attraction is typically much stronger than the van der Waals interaction between the surfaces, especially within a range of several nanometers for the inter-surface separation, where such effects are predicted to be most pronounced.

Multivalent ion effects on electrostatic stability of virus-like nano-shells

Electrostatic properties and stability of charged virus-like nano-shells are examined in ionic solutions with monovalent and multivalent ions. A theoretical model based on a thin charged spherical shell and multivalent ions within the "dressed multivalent ion" approximation, yielding their distribution across the shell and the corresponding electrostatic (osmotic) pressure acting on the shell, is compared with extensive implicit Monte-Carlo simulations. It is found to be accurate for positive or low negative surface charge densities of the shell and for sufficiently high (low) monovalent (multivalent) salt concentrations. Phase diagrams involving electrostatic pressure exhibit positive and negative values, corresponding to an outward and an inward facing force on the shell, respectively. This provides an explanation for the high sensitivity of viral shell stability and self-assembly of viral capsid shells on the ionic environment.

Nuclear aggregates of polyamines in a radiation-induced DNA damage model

Polyamines (PA) are believed to protect DNA minimizing the effect of radiation damage either by inducing DNA compaction and aggregation or acting as scavengers of free radicals. Using an in vitro pDNA double strand breakage assay based on gel electrophoretic mobility, we compared the protective capability of PA against γ-radiation with that of compounds generated by the supramolecular self-assembly of nuclear polyamines and phosphates, named Nuclear Aggregates of Polyamines (NAPs). Both unassembled PA and in vitro produced NAPs (ivNAPs) were ineffective in conferring pDNA protection at the sub-mM concentration. Single PA showed an appreciable protective effect only at high (mM) concentrations. However, concentrations of spermine (4+) within a critical range (0.481 mM) induced pDNA precipitation, an event that was not observed with NAPs-pDNA interaction. We conclude that the interaction of individual PA is ineffective to assure DNA protection, simultaneously preserving the flexibility and charge density of the double strand. Furthermore, data obtained by testing polyamine and ivNAPS with the current radiation-induced DNA damage model support the concept that PA-phosphate aggregates are the only forms through which PA interact with DNA.

Effect of magnesium ions on dielectric relaxation in semidilute DNA aqueous solutions

The effect of magnesium ion Mg(2+) on the dielectric relaxation of semidilute DNA aqueous solutions has been studied by means of dielectric spectroscopy in the 100 Hz-100 MHz frequency range. de Gennes-Pfeuty-Dobrynin semidilute solution correlation length is the pertinent fundamental length scale for sufficiently low concentration of added salt, describing the collective properties of Mg-DNA solutions. No relaxation fingerprint of the DNA denaturation bubbles, leading to exposed hydrophobic core scaling, was detected at low DNA concentrations, thus indicating an increased stability of the double-stranded conformation in Mg-DNA solutions as compared to the case of Na-DNA solutions. Some changes are detected in the behavior of the fundamental length scale pertaining to the single molecule DNA properties, reflecting modified electrostatic screening effects of the Odijk-Skolnick-Fixman type. All results consistently demonstrate that Mg(2+) ions interact with DNA in a similar way as Na(1+) ions do, their effect being mostly describable through an enhanced screening.

An advanced coarse-grained nucleosome core particle model for computer simulations of nucleosome-nucleosome interactions under varying ionic conditions

In the eukaryotic cell nucleus, DNA exists as chromatin, a compact but dynamic complex with histone proteins. The first level of DNA organization is the linear array of nucleosome core particles (NCPs). The NCP is a well-defined complex of 147 bp DNA with an octamer of histones. Interactions between NCPs are of paramount importance for higher levels of chromatin compaction. The polyelectrolyte nature of the NCP implies that nucleosome-nucleosome interactions must exhibit a great influence from both the ionic environment as well as the positively charged and highly flexible N-terminal histone tails, protruding out from the NCP. The large size of the system precludes a modelling analysis of chromatin at an all-atom level and calls for coarse-grained approximations. Here, a model of the NCP that include the globular histone core and the flexible histone tails described by one particle per each amino acid and taking into account their net charge is proposed. DNA wrapped around the histone core was approximated at the level of two base pairs represented by one bead (bases and sugar) plus four beads of charged phosphate groups. Computer simulations, using a Langevin thermostat, in a dielectric continuum with explicit monovalent (K(+)), divalent (Mg(2+)) or trivalent (Co(NH(3))(6) (3+)) cations were performed for systems with one or ten NCPs. Increase of the counterion charge results in a switch from repulsive NCP-NCP interaction in the presence of K(+), to partial aggregation with Mg(2+) and to strong mutual attraction of all 10 NCPs in the presence of CoHex(3+). The new model reproduced experimental results and the structure of the NCP-NCP contacts is in agreement with available data. Cation screening, ion-ion correlations and tail bridging contribute to the NCP-NCP attraction and the new NCP model accounts for these interactions.

A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation

We report a systematic study of the condensation of plasmid DNA by oligocations with variation of the charge, Z, from +3 to +31. The oligocations include a series of synthetic linear ε-oligo(L-lysines), (denoted εKn, n = 3–10, 31; n is the number of lysines with the ligand charge Z = n+1) and branched α-substituted homologues of εK10: εYK10, εLK10 (Z = +11); εRK10, εYRK10 and εLYRK10 (Z = +21). Data were obtained by light scattering, UV absorption monitored precipitation assay and isothermal titration calorimetry in a wide range concentrations of DNA and monovalent salt (KCl, CKCl). The dependence of EC50 (ligand concentration at the midpoint of DNA condensation) on C(KCl) shows the existence of a salt-independent regime at low C(KCl) and a salt-dependent regime with a steep rise of EC50 with increase of C(KCl). Increase of the ligand charge shifts the transition from the salt-independent to salt-dependent regime to higher C(KCl). A novel and simple relationship describing the EC50 dependence on DNA concentration, charge of the ligand and the salt-dependent dissociation constant of the ligand–DNA complex is derived. For the ε-oligolysines εK6–εK10, the experimental dependencies of EC50 on C(KCl) and Z are well-described by an equation with a common set of parameters. Implications from our findings for understanding DNA condensation in chromatin are discussed.