Compaction of single-chain DNA by histone-inspired nanoparticles

ct-DNA compaction by nanoparticles formed by silica and gemini surfactants having hydroxyl group substituted spacers: In vitro, in vivo, and ex vivo gene uptake to cancer cells

Hybrid nanoparticles formed by Silica (SiO2) coated with cationic gemini surfactants with variable hydroxyl group substituted spacers, 12-4(OH)-12,2Br- and 12-4(OH)2-12,2Br- have shown a great extent of compaction of calf thymus DNA (ct-DNA) compared to conventional counterpart cationic surfactant, dodecyl trimethylammonium bromide (DTAB). Study shows not only the hydrophobicity of the spacer but also the hydrogen bonding interactions between the hydroxyl group substituted spacer and DNA have a great role in DNA compaction. 12-4(OH)2-12,2Br- is more efficient in compacting ct-DNA compared to 12-4(OH)-12,2Br- due to the stronger binding of the former with ct-DNA than the latter. While 12-4(OH)-12,2Br- makes 50 % ct-DNA compaction at its 0.63 μM concentration in the presence of SiO2 nanoparticles, the same % of compaction can be achieved at a concentration as low as 0.25 μM of 12-4(OH)2-12,2Br-. However, DTAB makes 50 % ct-DNA compaction at a concentration as high as 7.00 μM under the same condition. Therefore, the present systems address the very common challenge, i.e., cytotoxicity due to cationic surfactants. The system of 12-4(OH)2-12,2Br- coated SiO2 nanoparticles displays the maximum cell viability (≥90 %), causing the least cell death in the mouse fibroblast cells (NIH3T3) cell lines compared to the cell viability of ≤80 % for DTAB. 12-4(OH)2-12,2Br- coated SiO2 nanoparticles system has presented excellent in vitro cellular uptake of genes on mouse mammary gland adenocarcinoma (4T1) cells after incubating for 3 h and 6 h. In vivo study shows that 12-4(OH)2-12,2Br- coated SiO2 nanoparticles system takes the highest amount of ct-DNA in cells and tumors in a time-dependent manner. The ex vivo studies using different organs of the mice demonstrate that the tumor sites in the breast of the mice are most affected by these formulations. Cytotoxicity assays and cellular uptake studies suggest that the present systems can be used for potential applications for gene delivery and oncological therapies.

Compaction of Calf Thymus DNA by a Potential One-Head-Two-Tail Surfactant: Properties of Nanomaterials and Biological Testing for Gene Delivery

A one-head-two-tail cationic surfactant, Dilauryldimethylammonium bromide (DDAB) has shown a great extent of calf thymus DNA (ct-DNA) compaction being adsorbed on the surfaces of negatively charged SiO2 nanoparticles (NPs). DDAB molecules show high adsorption efficiency and induce many positive surface charges per-unit surface area of the SiO2 NPs compared to cationic Gemini (12-6-12) and conventional (DTAB) surfactants in an aqueous medium at pH 7.4, as evident from zeta potential and EDAX data. Transmission electron microscopy and field emission scanning electron microscopy images, along with ethidium bromide exclusion assay and DLS data support the compaction of ct-DNA. Fluorescence microscopic images show that in the presence of SiO2 NPs, DDAB can perform 50% compaction of ct-DNA at a concentration ∼58% and ∼99% lower than that of 12-6-12 and DTAB, respectively. Better ct-DNA compaction by DDAB is evident compared to other Gemini surfactants (12-4-12 and 12-8-12) as well reported before. Time-correlated single photon counting fluorescence intensity decay measurements of a probe DAPI in ct-DNA have revealed the average lifetime value that is decreased by ∼61% at 2.5 μM of DDAB in the presence of SiO2 NPs as compared to a decrease by only ∼29% in its absence, supporting NPs-induced stronger surfactant binding with ct-DNA. Fluorescence lifetime data have also demonstrated the crowding effect of NPs. At 2.5 μM of DDAB, both fast and slow rotational relaxation components of DAPI contribute almost equally to depolarization with the absence of NPs; however, with the presence of NPs, ∼96% weightage of the anisotropy decay is for the fast component. The present DDAB-SiO2 NPs combination has proved to be an excellent gene delivery system based on the cell viability in the mouse mammary gland adenocarcinoma cells (4T1) and human embryonic kidney (HEK) 293 cell lines, and in vitro and in vivo studies.

Potential of Mean Force for DNA Wrapping Around a Cationic Nanoparticle

Sharp bending and wrapping of DNA around proteins and nanoparticles (NPs) has been of extensive research interest. Here, we present the potential of mean force (PMF) for wrapping a DNA double helix around a cationic NP using coarse-grained models of a double-stranded DNA and a cationic NP. Starting from a NP wrapped around by DNA, the PMF was calculated along the distance between the center of the NP and one end of the DNA molecule. A relationship between the distance and the extent of DNA wrapping is used to calculate the PMF as a function of DNA wrapping around a NP. In particular, the PMF was compared for two DNA sequences of (AT)₂₅/(AT)₂₅ and (AC)₂₅/(GT)₂₅, for which the persistence lengths are different by ∼10 nm. The simulation results provide solid evidence of the thermodynamic preference for complex formation of a cationic NP with more flexible DNA over the less flexible DNA. Furthermore, we estimated the elastic energy of DNA bending, which was in good order-of-magnitude agreement with the theoretical prediction of elastic rods. This work suggests that the variation of sequence-dependent DNA flexibility can be utilized in DNA nanotechnologies, in which the position and dynamics of NPs are regulated on large-scale DNA structures, or the structural transformation of DNA is triggered by the sequence-dependent binding of NPs.

DNA-assisted assembly of cationic gold nanoparticles: Monte Carlo simulation

DNA-assisted assembly of ligand-stabilized gold nanoparticles is studied using Monte Carlo simulations with coarse-grained models for DNA and AuNP. Their interaction in a periodic simulation box is described by a combination of electrostatic and pairwise hard core potentials. We first probe the self-assembly of AuNPs resulting in an ordered distribution on a single fixed DNA strand. Subsequently, the effective force calculated between a pair of parallel DNA in the presence of AuNPs shows the attraction between them at short distance associated to a stable equilibrium position. Finally, the osmotic pressure calculated in a compact DNA-AuNP lattice with various amounts of monovalent salt ions shows that an increasing amount of salt prevents aggregate formation.

Effect of DNA Flexibility on Complex Formation of a Cationic Nanoparticle with Double-Stranded DNA

We present extensive molecular dynamics simulations of a cationic nanoparticle and a double-stranded DNA molecule to discuss the effect of DNA flexibility on the complex formation of a cationic nanoparticle with double-stranded DNA. Martini coarse-grained models were employed to describe double-stranded DNA molecules with two different flexibilities and cationic nanoparticles with three different electric charges. As the electric charge of a cationic nanoparticle increases, the degree of DNA bending increases, eventually leading to the wrapping of DNA around the nanoparticle at high electric charges. However, a small increase in the persistence length of DNA by 10 nm requires a cationic nanoparticle with a markedly increased electric charge to bend and wrap DNA around. Thus, a more flexible DNA molecule bends and wraps around a cationic nanoparticle with an intermediate electric charge, whereas a less flexible DNA molecule binds to a nanoparticle with the same electric charge without notable bending. This work provides solid evidence that a small difference in DNA flexibility (as small as 10 nm in persistence length) has a substantial influence on the complex formation of DNA with proteins from a biological perspective and suggests that the variation of sequence-dependent DNA flexibility can be utilized in DNA nanotechnology as a new tool to manipulate the structure of DNA molecules mediated by nanoparticle binding.

DNA Compaction and Charge Neutralization Regulated by Divalent Ions in very Low pH Solution

DNA conformation is strongly dependent on the valence of counterions in solution, and a valence of at least three is needed for DNA compaction. Recently, we directly demonstrated DNA compaction and its regulation, mediated by divalent cations, by lowering the pH of a solution. In the present study, we found that the critical electrophoretic mobility of DNA is promoted to around -1.0 × 10-4 cm² V-1 s-1 to incur DNA compaction or condensation in a tri- and tetravalent counterions solution, corresponding to an about 89% neutralized charge fraction of DNA. This is also valid for DNA compaction by divalent counterions in a low pH solution. It is notable that the critical charge neutralization of DNA for compaction is only about 1% higher than the saturated charge fraction of DNA in a mild divalent ion solution. We also found that DNA compaction by divalent cations at low pH is weakened and even decondensed with an increasing concentration of counterions.

Investigation of compacted DNA structures induced by Na+ and K+ monovalent cations using biological nanopores

In aqueous solutions, an elongated, negatively charged DNA chain can quickly change its conformation into a compacted globule in the presence of positively charged molecules, or cations. This well-known process, called DNA compaction, is a method with great potential for gene therapy and delivery. Experimental conditions to induce these compacted DNA structures are often limited to the use of common compacting agents, such as cationic surfactants, polymers, and multivalent cations. In this study, we show that in highly concentrated buffers of 1 M monovalent cation solutions at pH 7.2 and 10, biological nanopores allow real-time sensing of individual compacted structures induced by K⁺ and Na⁺, the most abundant monovalent cations in human bodies. Herein, we studied the ratio between compacted and linear structures for 15-mer single-stranded DNA molecules containing only cytosine nucleotides, optimizing the probability of linear DNA chains being compacted. Since the binding affinity of each nucleotide to cation is different, the ability of the DNA strand to fold into a compacted structure greatly depends on the type of cations and nucleotides present. Our experimental results compare favorably with findings from previous molecular dynamics simulations for the DNA compacting potential of K⁺ and Na⁺ monovalent cations. We estimate that the majority of single-stranded DNA molecules in our experiment are compacted. From the current traces of nanopores, the ratio of compacted DNA to linear DNA molecules is approximately 30 : 1 and 15 : 1, at a pH of 7.2 and 10, respectively. Our comparative studies reveal that Na⁺ monovalent cations have a greater potential of compacting the 15C-ssDNA than K⁺ cations.

From Tunable DNA/Polymer Self-Assembly to Tailorable and Morphologically Pure Core-Shell Nanofibers

In reported experimental studies, DNA/polymer self-assemblies are usually kinetically trapped, leading to the encapsulation and irregular collapse of DNA chains within the resultant assemblies. In striking contrast, eukaryotic cells use tetrasome-to-nucleosome pathways to escape possible kinetic trapping for the formation of well-defined 10 nm chromatin fibers. Here, we report a novel pathway for DNA and amphiphilic diblock copolymer self-assembly inspired by the tetrasome pathway with highly controllable kinetics. The polymer is an A- b-B diblock copolymer with a hydrophilic and noninteractive block A and a hydrophobic and interactive block B. Below the critical water content for the micellization, B blocks wrap the backbone of a DNA chain by weak electrostatic interactions to form a linear DNA/polymer complex. With a gradual increase in the water content, the diblock copolymer unimers in the bulk solution tend to aggregate on the linear DNA/polymer complex, which induces the originally wrapped DNA chain, to change its conformation to wrap around the polymer aggregate, guiding and tailoring the self-assembly. Highly controllable kinetics is achieved via the reduced DNA/polymer electrostatic interactions and the high dynamics of the polymer chains in the system. DNA/polymer self-assembly leads to tailorable and morphologically pure core-shell nanofibers. Compared to the DNA/micelle self-assembly pathway described in our previous study, the present self-assembly pathway exhibits advantages for the fabrication of flexible nanofibers with lengths in micrometers and the potential for unique applications in preparing not only 2D networks at extremely low percolation thresholds but also chemiresistors with large on/off current ratios.

Progress in ligand design for monolayer-protected nanoparticles for nanobio interfaces

Ligand-functionalized inorganic nanoparticles, also known as monolayer-protected nanoparticles, offer great potential as vehicles for in vivo delivery of drugs, genes, and other therapeutics. These nanoparticles offer highly customizable chemistries independent of the size, shape, and functionality imparted by the inorganic core. Their success as drug delivery agents depends on their interaction with three major classes of biomolecules: nucleic acids, proteins, and membranes. Here, the authors discuss recent advances and open questions in the field of nanoparticle ligand design for nanomedicine, with a focus on atomic-scale interactions with biomolecules. While the importance of charge and hydrophobicity of ligands for biocompatibility and cell internalization has been demonstrated, ligand length, flexibility, branchedness, and other properties also influence the properties of nanoparticles. However, a comprehensive understanding of ligand design principles lies in the cost associated with synthesizing and characterizing diverse ligand chemistries and the ability to carefully assess the structural integrity of biomolecules upon interactions with nanoparticles.

Understanding and improving aggregated gold nanoparticle/dsDNA interactions by molecular spectroscopy and deconvolution methods

It is well known that single-stranded DNA (ssDNA) is easily able to adsorb on citrate-capped, non-functionalized gold nanoparticles (AuNPs). However, the affinity of double-stranded DNA (dsDNA) for them is much more limited. The present work demonstrates that long dsDNA suffers from a bending conformational change when anionic nanoparticles are present in solution. A striking decrease in the persistence length of the double helix in the absence of salt is observed through dynamic light scattering (DLS), viscometric, and atomic force microscopy (AFM) methods. Long dsDNA is therefore shown to be able to interact with anionic gold nanoparticles. To date, only ssDNA detection has been described by making use of interparticle cross-linking aggregation mechanisms; however, the data shown in this work allow for the development of new methods for detecting dsDNA in solution by using aggregated AuNPs as a starting point. The aggregation state is induced by the controlled addition of an inert electrolyte. A deconvolution procedure of the experimental plasmon shows how individual bands corresponding to aggregated nanoclusters diminish as the DNA concentration increases in the presence of 0.075 M NaCl.

Directional rolling of positively charged nanoparticles along a flexibility gradient on long DNA molecules

Directing the motion of molecules/colloids in any specific direction is of great interest in many applications of chemistry, physics, and biological sciences, where regulated positioning or transportation of materials is highly desired. Using Brownian dynamics simulations of coarse-grained models of a long, double-stranded DNA molecule and positively charged nanoparticles, we observed that the motion of a single nanoparticle bound to and wrapped by the DNA molecule can be directed along a gradient of DNA local flexibility. The flexibility gradient is constructed along a 0.8 kilobase-pair DNA molecule such that local persistence length decreases gradually from 50 nm to 40 nm, mimicking a gradual change in sequence-dependent flexibility. Nanoparticles roll over a long DNA molecule from less flexible regions towards more flexible ones as a result of the decreasing energetic cost of DNA bending and wrapping. In addition, the rolling becomes slightly accelerated as the positive charge of nanoparticles decreases due to a lower free energy barrier of DNA detachment from charged nanoparticle for processive rolling. This study suggests that the variation in DNA local flexibility can be utilized in constructing and manipulating supramolecular assemblies of DNA molecules and nanoparticles in structural DNA nanotechnology.

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.

Role of the ratio of biopolyelectrolyte persistence length to nanoparticle size in the structural tuning of electrostatic complexes

Aggregation of nanoparticles of given size R induced by addition of a polymer strongly depends on its degree of rigidity. This is shown here on a large variety of silica nanoparticle self-assemblies obtained by electrostatic complexation with carefully selected oppositely charged biopolyelectrolytes of different rigidity. The effective rigidity is quantified by the total persistence length L_{T} representing the sum of the intrinsic (L_{p}) and electrostatic (L_{e}) polyelectrolyte persistence length, which depends on the screening, i.e., on ionic strength due to counterions and external salt concentrations. We experimentally show that the ratio L_{T}/R is the main tuning parameter that controls the fractal dimension D_{f} of the nanoparticles' self-assemblies, which is determined using small-angle neutron scattering: (i) For L_{T}/R<0.3 (obtained with flexible poly-l-lysine in the presence of an excess of salt), chain flexibility promotes easy wrapping around nanoparticles in excess, hence ramified structures with D_{f}∼2. (ii) For 0.3<L_{T}/R≤1 (semiflexible chitosan or hyaluronan complexes), chain stiffness promotes the formation of one-dimensional nanorods (in excess of nanoparticles), in good agreement with computer simulations. (iii) For L_{T}/R>1,L_{e} is strongly increased due to the absence of salt and repulsions between nanoparticles cannot be compensated for by the polyelectrolyte wrapping, which allows a spacing between nanoparticles and the formation of one-dimensional pearl necklace complexes. (iv) Finally, electrostatic screening, i.e., ionic strength, turned out to be a reliable way of controlling D_{f} and the phase diagram behavior. It finely tunes the short-range interparticle potential, resulting in larger fractal dimensions at higher ionic strength.

Photochromic switching of the DNA helicity induced by azobenzene derivatives

The photochromic properties of azobenzene, involving conformational changes occurring upon interaction with light, provide an excellent tool to establish new ways of selective regulation applied to biosystems. We report here on the binding of two water-soluble 4-(phenylazo)benzoic acid derivatives (Azo-2N and Azo-3N) with double stranded DNA and demonstrate that the photoisomerization of Azo-3N leads to changes in DNA structure. In particular, we show that stabilization and destabilization of the B-DNA secondary structure can be photochemically induced in situ by light. This photo-triggered process is fully reversible and could be an alternative pathway to control a broad range of biological processes. Moreover, we found that the bicationic Azo-3N exhibited a higher DNA-binding constant than the monocationic Azo-2N pointing out that the number of positive charges along the photosensitive polyamines chain plays a pivotal role in stabilizing the photochrome-DNA complex.

DNA conformational behavior and compaction in biomimetic systems: Toward better understanding of DNA packaging in cell

In a living cell, long genomic DNA is strongly compacted and exists in the environment characterized by a dense macromolecular crowding, high concentrations of mono- and divalent cations, and confinement of ca. 10μm size surrounded by a phospholipid membrane. Experimental modelling of such complex biological system is challenging but important to understand spatiotemporal dynamics and functions of the DNA in cell. The accumulated knowledge about DNA condensation/compaction in conditions resembling those in the real cell can be eventually used to design and construct partly functional "artificial cells" having potential applications in drug delivery systems, gene therapy, and production of synthetic cells. In this review, I would like to overview the past progress in our understanding of the DNA conformational behavior and, in particular, DNA condensation/compaction phenomenon and its relation to the DNA biological activity. This understanding was gained by designing relevant experimental models mimicking DNA behavior in the environment of living cell. Starting with a brief summary of classic experimental systems to study DNA condensation/compaction, in later parts, I highlight recent experimental methodologies to address the effects of macromolecular crowding and nanoscale and microscale confinements on DNA conformation dynamics. All the studies are discussed in the light of their relevance to DNA behavior in living cells, and future prospects of the field are outlined.

Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics

The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.

Phase diagrams of DNA-photosensitive surfactant complexes: effect of ionic strength and surfactant structure

Realization of all-optically controlled and efficient DNA compaction is the major motivation in the study of interactions between DNA and photosensitive surfactants. In this article, using recently published approach of phase diagram construction [Y. Zakrevskyy, P. Cywinski, M. Cywinska, J. Paasche, N. Lomadze, O. Reich, H.-G. Löhmannsroben, and S. Santer, J. Chem. Phys. 140, 044907 (2014)], a strategy for substantial reduction of compaction agent concentration and simultaneous maintaining the light-induced decompaction efficiency is proposed. The role of ionic strength (NaCl concentration), as a very important environmental parameter, and surfactant structure (spacer length) on the changes of positions of phase transitions is investigated. Increase of ionic strength leads to increase of the surfactant concentration needed to compact DNA molecule. However, elongation of the spacer results to substantial reduction of this concentration. DNA compaction by surfactants with longer tails starts to take place in diluted solutions at charge ratios Z < 1 and is driven by azobenzene-aggregation compaction mechanism, which is responsible for efficient decompaction. Comparison of phase diagrams for different DNA-photosensitive surfactant systems allowed explanation and proposal of a strategy to overcome previously reported limitations of the light-induced decompaction for complexes with increasing surfactant hydrophobicity.

Inverted critical adsorption of polyelectrolytes in confinement

What are the fundamental laws for the adsorption of charged polymers onto oppositely charged surfaces, for convex, planar, and concave geometries? This question is at the heart of surface coating applications, various complex formation phenomena, as well as in the context of cellular and viral biophysics. It has been a long-standing challenge in theoretical polymer physics; for realistic systems the quantitative understanding is however often achievable only by computer simulations. In this study, we present the findings of such extensive Monte-Carlo in silico experiments for polymer-surface adsorption in confined domains. We study the inverted critical adsorption of finite-length polyelectrolytes in three fundamental geometries: planar slit, cylindrical pore, and spherical cavity. The scaling relations extracted from simulations for the critical surface charge density σc-defining the adsorption-desorption transition-are in excellent agreement with our analytical calculations based on the ground-state analysis of the Edwards equation. In particular, we confirm the magnitude and scaling of σc for the concave interfaces versus the Debye screening length 1/κ and the extent of confinement a for these three interfaces for small κa values. For large κa the critical adsorption condition approaches the known planar limit. The transition between the two regimes takes place when the radius of surface curvature or half of the slit thickness a is of the order of 1/κ. We also rationalize how σc(κ) dependence gets modified for semi-flexible versus flexible chains under external confinement. We examine the implications of the chain length for critical adsorption-the effect often hard to tackle theoretically-putting an emphasis on polymers inside attractive spherical cavities. The applications of our findings to some biological systems are discussed, for instance the adsorption of nucleic acids onto the inner surfaces of cylindrical and spherical viral capsids.

Shape-tailored colloidal molecules obtained by self-assembly of model gold nanoparticles with flexible polyelectrolyte

We study for the first time the structure of stable finite size clusters (i.e., colloidal molecules) obtained by self-assembly of cationic gold nanoparticles (i.e., atoms) mediated by a flexible polyanion. We reveal with nondenaturizing techniques a striking structural transition from 1D small chains of 12 gold nanoparticles (AuNPs) with a self-avoiding conformation to 3D fractal clusters of 130 AuNPs with short-range ordering around the charge inversion threshold. Interestingly, these well-defined structures are obtained by simple mixing in water without anisotropic functionalization or external forces. As a preliminary step, we introduce a new synthesis pathway leading to well-defined cationic AuNPs of controllable size that can be dispersed in H2O or D2O without aggregation and ligands' self-assemblies. On this occasion, we point for the first time that usual procedures do not enable to eliminate cationic ligands' self-assemblies that could play an undesired role in AuNPs' self-assembly through electrostatic interactions.

A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction

We present computer simulations of the phase behaviour of an ensemble of proteins interacting with a polymer, mimicking non-specific binding to a piece of bacterial DNA or eukaryotic chromatin. The proteins can simultaneously bind to the polymer in two or more places to create protein bridges. Despite the lack of any explicit interaction between the proteins or between DNA segments, our simulations confirm previous results showing that when the protein-polymer interaction is sufficiently strong, the proteins come together to form clusters. Furthermore, a sufficiently large concentration of bridging proteins leads to the compaction of the swollen polymer into a globular phase. Here we characterise both the formation of protein clusters and the polymer collapse as a function of protein concentration, protein-polymer affinity and fibre flexibility.

Topological constraints strongly affect chromatin reconstitution in silico

The fundamental building block of chromatin, and of chromosomes, is the nucleosome, a composite material made up from DNA wrapped around a histone octamer. In this study we provide the first computer simulations of chromatin self-assembly, starting from DNA and histone proteins, and use these to understand the constraints which are imposed by the topology of DNA molecules on the creation of a polynucleosome chain. We take inspiration from the in vitro chromatin reconstitution protocols which are used in many experimental studies. Our simulations indicate that during self-assembly, nucleosomes can fall into a number of topological traps (or local folding defects), and this may eventually lead to the formation of disordered structures, characterised by nucleosome clustering. Remarkably though, by introducing the action of topological enzymes such as type I and II topoisomerase, most of these defects can be avoided and the result is an ordered 10-nm chromatin fibre. These findings provide new insight into the biophysics of chromatin formation, both in the context of reconstitution in vitro and in terms of the topological constraints which must be overcome during de novo nucleosome formation in vivo, e.g. following DNA replication or repair.

Tunable nanoparticle arrays at charged interfaces

Structurally tunable two-dimensional (2D) arrays of nanoscale objects are important for modulating functional responses of thin films. We demonstrate that such tunable and ordered nanoparticles (NP) arrays can be assembled at charged air-water interfaces from nanoparticles coated with polyelectrolyte chains, DNA. The electrostatic attraction between the negatively charged nonhybridizing DNA-coated gold NPs and a positively charged lipid layer at the interface facilitates the formation of a 2D hexagonally closed packed (HCP) nanoparticle lattice. We observed about 4-fold change of the monolayer nanoparticle density by varying the ionic strength of the subphase. The tunable NP arrays retain their structure reasonably well when transferred to a solid support. The influence of particle's DNA corona and lipid layer composition on the salt-induced in-plane and normal structural evolution of NP arrays was studied in detail using a combination of synchrotron-based in situ surface scattering methods, grazing incidence X-ray scattering (GISAXS), and X-ray reflectivity (XRR). Comparative analysis of the interparticle distances as a function of ionic strength reveals the difference between the studied 2D nanoparticle arrays and analogous bulk polyelectrolyte star polymers systems, typically described by Daoud-Cotton model and power law scaling. The observed behavior of the 2D nanoparticle array manifests a nonuniform deformation of the nanoparticle DNA corona due to its electrostatically induced confinement at the lipid interface. The present study provides insight on the interfacial properties of the NPs coated with charged soft shells.

Chiral symmetry breaking of a double-stranded helical chain through bend-writhe coupling

This paper explores asymmetric elasticity of a double-stranded helical chain, which serves as a minimal model of biopolymers. The model consists of two elastic chains that mutually intertwine in a right-handed manner, forming a double-stranded helix. A simple numerical experiment for structural relaxation, which reduces the total elastic energy of the model monotonically without thermal fluctuations, reveals possible asymmetric elasticity inherent in the helical chain. It is first shown that a short segment of the double-stranded helical chain has a tendency to unwind when it is bent. It is also shown that a short segment of the helical chain has a tendency to writhe in the left direction upon bending. This tendency gives rise to a propensity for a longer segment of the chain to form a left-handed superhelix spontaneously upon bending. Finally, this propensity of the helical chain to form a left-handed superhelix is proposed to be a possible origin of the uniform left-handed wrapping of DNA around nucleosome core particles in nature. The results presented here could provide deeper insights into the roles and significance of helical chirality of biopolymers.

Noncovalent interactions of tiopronin-protected gold nanoparticles with DNA: two methods to quantify free energy of binding

The binding of gold nanoparticles capped with N-(2-mercaptopropionyl)glycine (Au@tiopronin) with double-stranded DNA has been investigated and quantified in terms of free energies by using two different approaches. The first approach follows the DNA conformational changes induced by gold nanoparticles using the CD technique. The second methodology consists in the use of pyrene-1-carboxaldehyde as a fluorescent probe. This second procedure implies the determination of the "true" free energy of binding of the probe with DNA, after corrections through solubility measurements. Working at different salt concentrations, the nonelectrostatic and electrostatic components of the binding free energy have been separated. The results obtained revealed that the binding is of nonelectrostatic character, fundamentally. The procedure used in this work could be extended to quantify the binding affinity of other AuNPs/DNA systems.

Critical adsorption of polyelectrolytes onto charged Janus nanospheres

The conditions of critical polyelectrolyte adsorption onto spherical charged Janus nano-particles are exploited by Monte-Carlo computer simulations and theoretically.

Progressive macromolecular self-assembly: from biomimetic chemistry to bio-inspired materials

Macromolecular self-assembly (MSA) has been an active and fruitful research field since the 1980s, especially in this new century, which is promoted by the remarkable developments in controlled radical polymerization in polymer chemistry, etc. and driven by the demands in bio-related investigations and applications. In this review, we try to summarize the trends and recent progress in MSA in relation to biomimetic chemistry and bio-inspired materials. Our paper covers representative achievements in the fabrication of artificial building blocks for life, cell-inspired biomimetic materials, and macromolecular assemblies mimicking the functions of natural materials and their applications. It is true that the current status of the deliberately designed and obtained nano-objects based on MSA including a variety of micelles, multicompartment vesicles, and some hybrid and complex nano-objects is at their very first stage to mimic nature, but significant and encouraging progress has been made in achieving a certain similarity in morphologies or properties to that of natural ones. Such achievements also demonstrate that MSA has played an important and irreplaceable role in the grand and long-standing research of biomimetic and bio-inspired materials, the future success of which depends on mutual and persistent efforts in polymer science, material science, supramolecular chemistry, and biology.

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

Molecular dynamics simulations are used to model proteins that diffuse to DNA, bind, and dissociate; in the absence of any explicit interaction between proteins, or between templates, binding spontaneously induces local DNA compaction and protein aggregation. Small bivalent proteins form into rows [as on binding of the bacterial histone-like nucleoid-structuring protein (H-NS)], large proteins into quasi-spherical aggregates (as on nanoparticle binding), and cylinders with eight binding sites (representing octameric nucleosomal cores) into irregularly folded clusters (like those seen in nucleosomal strings). Binding of RNA polymerase II and a transcription factor (NFκB) to the appropriate sites on four human chromosomes generates protein clusters analogous to transcription factories, multiscale loops, and intrachromosomal contacts that mimic those found in vivo. We suggest that this emergent behavior of clustering is driven by an entropic bridging-induced attraction that minimizes bending and looping penalties in the template.

Generic pathways to stability in concentrated protein mixtures

We present a series of experimental results that disclose the crucial role of ionic strength and partial volume fractions in the control of the phase behaviour of binary protein mixtures. Our findings can be understood as that the ionic strength determines the relative contribution of the entropy of the protein counter-ions to the overall thermodynamics of the system. Associative phase separation and crystallization observed at, respectively, low and high ionic strength are suppressed at intermediate salt concentrations, where the entropy gain upon releasing the counter-ions from the double layer of the proteins is negligible and the entropy loss upon confining the counter-ions within the protein crystal phase significant. Moreover, we find that the partial volume fraction of the protein prone to crystallize determines the crystallization boundary and that the presence of other proteins strongly delays crystallization, leading to temporarily stable mixtures. These findings suggest that stability in more complex protein mixtures, such as the cytosol, relates to the ionic strength and protein composition rather than to protein specific properties.

Enhancement of DNA compaction by negatively charged nanoparticles: effect of nanoparticle size and surfactant chain length

We study the compaction of genomic DNA by a series of alkyltrimethylammonium bromide surfactants having different hydrocarbon chain lengths n: dodecyl-(DTAB, n=12), tetradecyl-(TTAB, n=14) and hexadecyl-(CTAB, n=16), in the absence and in the presence of negatively charged silica nanoparticles (NPs) with a diameter in the range 15-100 nm. We show that NPs greatly enhance the ability of all cationic surfactants to induce DNA compaction and that this enhancement increases with an increase in NP diameter. In the absence of NP, the ability of cationic surfactants to induce DNA compaction increases with an increase in n. Conversely, in the presence of NPs, the enhancement of DNA compaction increases with a decrease in n. Therefore, although CTAB is the most efficient surfactant to compact DNA, maximal enhancement by NPs is obtained for the largest NP diameter (here, 100 nm) and the smallest surfactant chain length (here, DTAB). We suggest a mechanism where the preaggregation of surfactants on NP surface mediated by electrostatic interactions promotes cooperative binding to DNA and thus enhances the ability of surfactants to compact DNA. We show that the amplitude of enhancement is correlated with the difference between the surfactant concentration corresponding to aggregation on DNA alone and that corresponding to the onset of adsorption on nanoparticles.