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

Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending

Histones are essential for genome compaction and transcription regulation in eukaryotes, where they assemble into octamers to form the nucleosome core. In contrast, archaeal histones assemble into dimers that form hypernucleosomes upon DNA binding. Although histone homologs have been identified in bacteria recently, their DNA-binding characteristics remain largely unexplored. Our study reveals that the bacterial histone HBb (Bd0055) is indispensable for the survival of Bdellovibrio bacteriovorus, suggesting critical roles in DNA organization and gene regulation. By determining crystal structures of free and DNA-bound HBb, we unveil its distinctive dimeric assembly, diverging from those of eukaryotic and archaeal histones, while also elucidating how it binds and bends DNA through interaction interfaces reminiscent of eukaryotic and archaeal histones. Building on this, by employing various biophysical and biochemical approaches, we further substantiated the ability of HBb to bind and compact DNA by bending in a sequence-independent manner. Finally, using DNA affinity purification and sequencing, we reveal that HBb binds along the entire genomic DNA of B. bacteriovorus without sequence specificity. These distinct DNA-binding properties of bacterial histones, showcasing remarkable similarities yet significant differences from their archaeal and eukaryotic counterparts, highlight the diverse roles histones play in DNA organization across all domains of life.

Visualizing the 4D Impact of Gold Nanoparticles on DNA

The genotoxicity of AuNPs has sparked a scientific debate, with one perspective attributing it to direct DNA damage and another to oxidative damage through reactive oxygen species (ROS) activation. This controversy poses challenges for the widespread use of AuNPs in biomedical applications. To address this debate, we employed four-dimensional atomic force microscopy (4DAFM) to examine the ability of AuNPs to damage DNA in vitro in the absence of ROS. To further examine whether the size and chemical coupling of these AuNPs are properties that control their toxicity, we exposed individual DNA molecules to three different types of AuNPs: small (average diameter = 10 nm), large (average diameter = 22 nm), and large conjugated (average diameter = 39 nm) AuNPs. We found that all types of AuNPs caused rapid (within minutes) and direct damage to the DNA molecules without the involvement of ROS. This research holds significant promise for advancing nanomedicines in diverse areas like viral therapy (including COVID-19), cancer treatment, and biosensor development for detecting DNA damage or mutations by resolving the ongoing debate regarding the genotoxicity mechanism. Moreover, it actively contributes to the continuous endeavors aimed at fully harnessing the capabilities of AuNPs across diverse biomedical fields, promising transformative healthcare solutions.

Gold nanoparticle design for RNA compaction

RNA-based therapeutics hold a great promise in treating a variety of diseases. However, double-stranded RNAs (dsRNAs) are inherently unstable, highly charged, and stiff macromolecules that require a delivery vehicle. Cationic ligand functionalized gold nanoparticles (AuNPs) are able to compact nucleic acids and assist in RNA delivery. Here, we use large-scale all-atom molecular dynamics simulations to show that correlations between ligand length, metal core size, and ligand excess free volume control the ability of nanoparticles to bend dsRNA far below its persistence length. The analysis of ammonium binding sites showed that longer ligands that bind deep within the major groove did not cause bending. By limiting ligand length and, thus, excess free volume, we have designed nanoparticles with controlled internal binding to RNA's major groove. NPs that are able to induce RNA bending cause a periodic variation in RNA's major groove width. Density functional theory studies on smaller models support large-scale simulations. Our results are expected to have significant implications in packaging of nucleic acids for their applications in nanotechnology and gene delivery.

All-Atom Simulation Method for Zeeman Alignment and Dipolar Assembly of Magnetic Nanoparticles

Magnetic nanoparticles (MNPs) can organize into novel structures in solutions with excellent order and unique geometries. However, studies of the self-assembly of smaller MNPs are challenging due to a complicated interplay between external magnetic fields and van der Waals, electrostatic, dipolar, steric, and hydrodynamic interactions. Here, we present a novel all-atom molecular dynamics simulation method to enable detailed studies of the dynamics, self-assembly, structure, and properties of MNPs as a function of core sizes and shapes, ligand chemistry, solvent properties, and external field. We demonstrate the use and effectiveness of the model by simulating the self-assembly of oleic acid ligand-functionalized magnetite (Fe₃O₄) nanoparticles, with spherical and cubic shapes, into rings, lines, chains, and clusters under a uniform external magnetic field. We found that the long-range electrostatic interactions can favor the formation of a chain over a ring, the ligands promote MNP cluster growth, and the solvent can reduce the rotational diffusion of the MNPs. The algorithm has been parallelized to take advantage of multiple processors of a modern computer and can be used as a plugin for the popular simulation software LAMMPS to study the behavior of small MNPs and gain insights into the physics and chemistry of different magnetic assembly processes with atomistic details.

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.

Molecular dynamics simulation study of gold nanosheet as drug delivery vehicles for anti-HIV-1 aptamers

The adsorption process of three aptamers with gold nanosheet (GNS) as a drug carrier has been investigated with the help of molecular dynamics simulations. The sequencing of the considered aptamers are as (CUUCAUUGUAACUUCUCAUAAUUUCCCGAGGCUUUUACUUUCGGGGUCCU) and (CCGGGUCGUCCCCUACGGGGACUAAAGACUGUGUCCAACCGCCCUCGCCU) for AP1 and AP2, respectively. AP3 is a muted version of AP1 in which nucleotide positions 4, 6, 18, 28 and 39 have C4A, U6G, A18G, G28A, and U39C mutations. At positions 24, and 40, a deletion mutation is seen to eliminate U24 and U40 bases. These aptamers are inhibitors for HIV-1 protease and can be candidates as potential pharmaceutics for treatment of AIDS in the future. The interactions between considered aptamers and GNS have been analyzed in detail with help of structural and energetic properties. These analyses showed that all three aptamers could well adsorb on GNS. Overall, the final results show that the adsorption of AP2 on the GNS is more favorable than other considered ones and consequently GNS can be considered as a device in order to immobilize these aptamers.

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.

The Interplay of Ligand Properties and Core Size Dictates the Hydrophobicity of Monolayer-Protected Gold Nanoparticles

The hydrophobicity of monolayer-protected gold nanoparticles is a crucial design parameter that influences self-assembly, preferential binding to proteins and membranes, and other nano-bio interactions. Predicting the effects of monolayer components on nanoparticle hydrophobicity is challenging due to the nonadditive, cooperative perturbations to interfacial water structure that dictate hydrophobicity at the nanoscale. In this work, we quantify nanoparticle hydrophobicity by using atomistic molecular dynamics simulations to calculate local hydration free energies at the nanoparticle-water interface. The simulations reveal that the hydrophobicity of large gold nanoparticles is determined primarily by ligand end group chemistry, as expected. However, for small gold nanoparticles, long alkanethiol ligands interact to form anisotropic bundles that lead to substantial spatial variations in hydrophobicity even for homogeneous monolayer compositions. We further show that nanoparticle hydrophobicity is modulated by changing the ligand structure, ligand chemistry, and gold core size, emphasizing that single-ligand properties alone are insufficient to characterize hydrophobicity. Finally, we illustrate that hydration free energy measurements correlate with the preferential binding of propane as a representative hydrophobic probe molecule. Together, these results show that both physical and chemical properties influence the hydrophobicity of small nanoparticles and must be considered together when predicting gold nanoparticle interactions with biomolecules.

Uncertainty Quantification and Sensitivity Analysis of Partial Charges on Macroscopic Solvent Properties in Molecular Dynamics Simulations with a Machine Learning Model

The molecular dynamics (MD) simulation technique is among the most broadly used computational methods to investigate atomistic phenomena in a variety of chemical and biological systems. One of the most common (and most uncertain) parametrization steps in MD simulations of soft materials is the assignment of partial charges to atoms. Here, we apply uncertainty quantification and sensitivity analysis calculations to assess the uncertainty associated with partial charge assignment in the context of MD simulations of an organic solvent. Our results indicate that the effect of partial charge variance on bulk properties, such as solubility parameters, diffusivity, dipole moment, and density, measured from MD simulations is significant; however, measured properties are observed to be less sensitive to partial charges of less accessible (or buried) atoms. Diffusivity, for example, exhibits a global sensitivity of up to 22 × 10^-5 cm²/s per electron charge on some acetonitrile atoms. We then demonstrate that machine learning techniques, such as Gaussian process regression (GPR), can be effective and rapid tools for uncertainty quantification of MD simulations. We show that the formulation and application of an efficient GPR surrogate model for the prediction of responses effectively reduces the computational time of additional sample points from hours to milliseconds. This study provides a much-needed context for the effect that partial charge uncertainty has on MD-derived material properties to illustrate the benefit of considering partial charges as distributions rather than point-values. To aid in this treatment, this work then demonstrates methods for rapid characterization of resulting sensitivity in MD simulations.

Strategy for Finely Aligned Gold Nanorod Arrays Using Polymer Brushes as a Template

The development of a strategy for the assembly of nanoscale building blocks, in particular, anisotropic nanoparticles, into desired structures is important for the construction of functional materials and devices. However, control over the orientation of rod-shaped nanoparticles on a substrate for integration into solid-state devices remains challenging. Here, we report a strategy for the fabrication of finely aligned gold nanorod (GNR) arrays using polymer (DNA) brushes as a nanoscale template. The gold nanorods modified with cationic surface ligands were electrostatically adsorbed onto the DNA brush substrates under various conditions. The orientational behavior of the GNRs was examined by spectral analyses and transmission electron microtomography (TEMT). As a result, we found several important factors, such as moderate interaction between GNRs and polymers and polymer densities on the substrate, related to the vertical alignment of GNRs on the substrates. We also developed a purification method to remove the undesired adsorption of GNRs onto the arrays. Finally, we have succeeded in the fabrication of extensive vertical GNR arrays of high quality via the easy bottom-up process.

Molecular Bases of DNA Packaging in Bacteria Revealed by All-Atom Molecular Dynamics Simulations: The Case of Histone-Like Proteins in Borrelia burgdorferi

DNA compaction is essential to ensure the packaging of the genetic material in living cells and also plays a key role in the epigenetic regulation of gene expression. In both humans and bacteria, DNA packaging is achieved by specific well-conserved proteins. Here, by means of all-atom molecular dynamics simulations, including the determination of relevant free-energy profiles, we rationalize the molecular bases for this remarkable process in bacteria, illustrating the crucial role played by positively charged amino acids of a small histone-like protein. We also present compelling evidence that this histone-like protein alone can induce strong bending of a DNA duplex around its core domain, a process that requires overcoming a major free-energy barrier.

Epigenetic Aspects of Engineered Nanomaterials: Is the Collateral Damage Inevitable?

The extensive application of engineered nanomaterial (ENM) in various fields increases the possibilities of human exposure, thus imposing a huge risk of nanotoxicity. Hence, there is an urgent need for a detailed risk assessment of these ENMs in response to their toxicological profiling, predominantly in biomedical and biosensor settings. Numerous "toxico-omics" studies have been conducted on ENMs, however, a specific "risk assessment paradigm" dealing with the epigenetic modulations in humans owing to the exposure of these modern-day toxicants has not been defined yet. This review aims to address the critical aspects that are currently preventing the formation of a suitable risk assessment approach for/against ENM exposure and pointing out those researches, which may help to develop and implement effective guidance for nano-risk assessment. Literature relating to physicochemical characterization and toxicological behavior of ENMs were analyzed, and exposure assessment strategies were explored in order to extrapolate opportunities, challenges, and criticisms in the establishment of a baseline for the risk assessment paradigm of ENMs exposure. Various challenges, such as uncertainty in the relation of the physicochemical properties and ENM toxicity, the complexity of the dose-response relationships resulting in difficulty in its extrapolation and measurement of ENM exposure levels emerged as issues in the establishment of a traditional risk assessment. Such an appropriate risk assessment approach will provide adequate estimates of ENM exposure risks and will serve as a guideline for appropriate risk communication and management strategies aiming for the protection and the safety of humans.

Molecular Mechanism of Spontaneous Nucleosome Unraveling

Meters of DNA wrap around histone proteins to form nucleosomes and fit inside the micron-diameter nucleus. For the genetic information encoded in the DNA to become available for transcription, replication, and repair, the DNA-histone assembly must be disrupted. Experiment has indicated that the outer stretches of nucleosomal DNA "breathe" by spontaneously detaching from and reattaching to the histone core. Here, we report direct observation of spontaneous DNA breathing in atomistic molecular dynamics simulations, detailing a microscopic mechanism of the DNA breathing process. According to our simulations, the outer stretches of nucleosomal DNA detach in discrete steps involving 5 or 10 base pairs, with the detachment process being orchestrated by the motion of several conserved histone residues. The inner stretches of nucleosomal DNA are found to be more stably associated with the histone core by more abundant nonspecific DNA-protein contacts, providing a microscopic interpretation of nucleosome unraveling experiments. The CG content of nucleosomal DNA is found to anticorrelate with the extent of unwrapping, supporting the possibility that AT-rich segments may signal the start of transcription by forming less stable nucleosomes.

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.

Efficient Binding, Protection, and Self-Release of dsRNA in Soil by Linear and Star Cationic Polymers

Double stranded RNA (dsRNA) exhibits severe degradation within 3 days in live soil, limiting its potential application in crop protection. Herein we report the efficient binding, protection, and self-release of dsRNA in live soil through the usage of a cationic polymer. Soil stability assays show that linear poly(2-(dimethylamino)ethyl acrylate) can delay the degradation of dsRNA by up to 1 week while the star shaped analogue showed an increased stabilization of dsRNA by up to 3 weeks. Thus, the architecture of the polymer can significantly affect the lifetime of dsRNA in soil. In addition, the hydrolysis and dsRNA binding and release profiles of these polymers were carefully evaluated and discussed. Importantly, hydrolysis could occur independently of environmental conditions (e.g., different pH, different temperature) showing the potential for many opportunities in agrochemicals where protection and subsequent self-release of dsRNA in live soil is required.

Complexation of short ds RNA/DNA oligonucleotides with Gemini micelles: a time resolved SAXS and computational study

Gene therapy is based on nucleic acid delivery to pathogenic cells in order to modulate their gene expression. The most used non viral vectors are lipid-based nanoaggregates, which are safer than viral carriers and have been shown to assemble easily with both DNA and RNA. However, the transfection efficiency of non viral carriers still needs to be improved before intensive practise in clinical trials can be implemented. For this purpose, the in depth characterization of the complexes formed by nucleic acids and their transporters is of great relevance. In particular, information on the structure and assembly mechanism can be useful to improve our general knowledge of these artificial transfection agents. In this paper, the complexation mechanism of short interfering RNA and DNA molecules (siRNA and siDNA, respectively) with cationic micelles is investigated by combining small angle X-ray scattering experiments and molecular dynamics simulations. Micelles were obtained by Gemini surfactants with different spacer lengths (12-3-12, 12-6-12). The siRNA and siDNA used were double strand molecules characterized by the same length and homologous sequence, in order to perform a close comparison. We showed that complexes appear in solution immediately after mixing and, therefore, the investigation of complex formation requires fast experimental techniques, such as time resolved synchrotron SAXS (Tr-SAXS). The obtained systems had internal arrangement constituted by layers of squeezed micelles alternating the nucleic acids. Both SAXS and MD analyses allowed us to evaluate the mean size of complexes in the range of a few nanometers, with looser and less ordered stacking for the DNA containing aggregates.

Decorating a single giant DNA with gold nanoparticles

We decorated a single giant DNA (1.66 × 10⁵ base pairs) with gold nanoparticles through the simple procedure of mild warming, without denaturation of the DNA molecule. Single-molecule observation with fluorescence microscopy revealed that individual decorated DNA molecules stay in the bulk solution by avoiding aggregation and precipitation, and exhibit translational and conformational fluctuation, i.e., Brownian motion. An analysis of the intra-chain fluctuation of single DNA molecules revealed that the apparent spring constant and damping coefficient of a DNA chain increased by ca. 13- and 5-fold, respectively, upon decoration with gold nanoparticles. Observation by transmission electron microscopy revealed that gold nanoparticles were stably attached to the DNA skeleton. UV-visible measurements revealed the absence of any detectable change in surface plasmon resonance, suggesting that the gold nanoparticles assemble without the formation of a densely packed aggregate. CD measurements showed that the secondary structure of decorated DNA is still essentially the B-form.

We decorated a single giant DNA (1.66 × 10⁵ base pairs) with gold nanoparticles through the simple procedure of mild warming, without denaturation of the DNA molecule.

DNA Brush-Directed Vertical Alignment of Extensive Gold Nanorod Arrays with Controlled Density

Control over the orientation of metal nanorods is important for both fundamental and applied research. We show that gold nanorods (GNRs) can be aligned in a single direction by adsorbing positively charged GNRs onto a double-strand DNA-grafted substrate through electrostatic interaction. The ordered structure can be optimized by controlling the density of the positive charges on the surface of the GNRs. We found, in agreement with the results of theoretical simulation, that the resultant structure exhibits plasmonic properties that are dependent on the GNR orientation relative to the direction of an oscillating electric field. Our approach provides new insights into the polymer-assisted self-assembly of rod-shaped nanoparticles utilizing electrostatic interactions.

Interfacial Mechanical Properties of Graphene on Self-Assembled Monolayers: Experiments and Simulations

Self-assembled monolayers (SAMs) have been widely used to engineer the electronic properties of substrate-supported graphene devices. However, little is known about how the surface chemistry of SAMs affects the interfacial mechanical properties of graphene supported on SAMs. Fluctuations and changes in these properties affect the stress transfer between substrate and the supported graphene and thus the performance of graphene-based devices. The changes in interfacial mechanical properties can be characterized by measuring the out-of-plane elastic properties. Combining contact resonance atomic force microcopy experiments with molecular dynamics simulations, we show that the head group chemistry of a SAM, which affects the interfacial interactions, can have a significant effect on the out-of-plane elastic modulus of the graphene-SAM heterostructure. Graphene supported on hydrophobic SAMs leads to heterostructures stiffer than those of graphene supported on hydrophilic SAMs, which is largely due to fewer water molecules present at the graphene-SAM interface. Our results provide an important, and often overlooked, insight into the mechanical properties of substrate-supported graphene electronics.

Binding of single stranded nucleic acids to cationic ligand functionalized gold nanoparticles

The interactions of nanoparticles (NPs) with single stranded nucleic acids (NAs) have important implications in gene delivery, and nanotechnological and biomedical applications. Here, the complexation of cationic ligand functionalized gold nanoparticles with single stranded deoxyribose nucleic acid (DNA) and ribonucleic acid (RNA) are examined using all atom molecular dynamics simulations. The results indicated that complexation depends mostly on charge of nanoparticle, and, to lesser extent, sequence and type of nucleic acid. For cationic nanoparticles, electrostatic interactions between charged ligands and the nucleic acid backbone dominate binding regardless of nanoparticle charge. Highly charged nanoparticles bind more tightly and cause compaction of the single-stranded NAs through disruption of intrastrand π-π stacking and hydrogen bonding. However, poly-purine strands (polyA-DNA, polyA-RNA) show less change in structure than poly-pyrimidine strands (polyT-DNA, polyU-RNA). Overall, the results show that control over ssNA structure may be achieved with cationic NPs with a charge of more than 30, but the extent of the structural changes depends on sequence.