Exploring ion induced folding of a single-stranded DNA oligomer from molecular simulation studies

Mutual effects between single-stranded DNA conformation and Na+-Mg2+ ion competition in mixed salt solutions

The ion-dependence of single-stranded DNA (ssDNA) conformational changes has attracted growing attention because of its biological and technological importance. Although single-species ion effects have been extensively explored, it is challenging to study the ssDNA conformational properties under mixed monovalent/divalent ion conditions due to the complications of ssDNA flexibility and ion-ion competition. In this study, we apply Langevin dynamics simulations to investigate mixed Na⁺/Mg²⁺ ion-dependent ssDNA conformations. The ssDNA structure is described using a coarse-grained model, in which the phosphate, base, and sugar of each nucleotide are represented by three different beads. A novel improvement in our simulation model is that mixed-salt-related electrostatic interactions are computed via combining Manning counterion condensation (MCC) theory with the Monte Carlo tightly bound ion (MCTBI) model. Based on this MCC-MCTBI combination, we report new empirical functions to describe the ion-concentration-dependent and ssDNA conformation/structure-dependent electrostatic effects. The calculation results relating to the ion binding properties and the simulation results relating to the ssDNA conformational properties are validated against experimental results. In addition, our simulation results suggest a quantitative relationship between the ssDNA conformation and Na⁺-Mg²⁺ competition; this in turn reveals their mutual impact in the ion atmosphere.

Modulation of DNA conformation in electrolytic nanodroplets

The behavior of deoxyribonucleic acid (DNA) molecules in confinement is of profound importance in various bioengineering and medical applications. In the present study, all-atom molecular dynamics simulation is utilized to investigate the transition of the double-strand DNA (dsDNA) conformation in the electrolytic nanodroplet. Three typical conformations, i.e., C-shaped, folded S-shaped, and double C-shaped, are observed for different droplet sizes and ionic concentrations. To reveal the physics underlying this phenomenon, the characteristics of the dsDNA molecules, such as the overcharging intensity, the end-to-end distance, the radius of gyration, etc. are analyzed in detail based on the numerical results. It is found that the transition can be ascribed to the buckling of the polymer molecules under the compression due to the confinement of the nanodroplet, and it can be modulated by the ionic concentration in the electrolyte. Generally, nanoscale confinement dominates dsDNA behavior over the electrostatic effects in smaller nanodroplets, while the latter becomes more important for larger nanodroplets. This competition results in the persistence length increasing with the nanodroplet radii. Based on these discussions, a non-dimensional elasto-capillary number μ is proposed to classify the dsDNA conformations into three regions.

Effects of Experimental Conditions on the Signaling Fidelity of Impedance-Based Nucleic Acid Sensors

Electrochemical impedance spectroscopy (EIS), an extremely sensitive analytical technique, is a widely used signal transduction method for the electrochemical detection of target analytes in a broad range of applications. The use of nucleic acids (aptamers) for sequence-specific or molecular detection in electrochemical biosensor development has been extensive, and the field continues to grow. Although nucleic acid-based sensors using EIS offer exceptional sensitivity, signal fidelity is often linked to the physical and chemical properties of the electrode-solution interface. Little emphasis has been placed on the stability of nucleic acid self-assembled monolayers (SAMs) over repeated voltammetric and impedimetric analyses. We have studied the stability and performance of electrochemical biosensors with mixed SAMs of varying length thiolated nucleic acids and short mercapto alcohols on gold surfaces under repeated electrochemical interrogation. This systematic study demonstrates that signal fidelity is linked to the stability of the SAM layer and nucleic acid structure and the packing density of the nucleic acid on the surface. A decrease in packing density and structural changes of nucleic acids significantly influence the signal change observed with EIS after routine voltammetric analysis. The goal of this article is to improve our understanding of the effect of multiple factors on EIS signal response and to optimize the experimental conditions for development of sensitive and reproducible sensors. Our data demonstrate a need for rigorous control experiments to ensure that the measured change in impedance is unequivocally a result of a specific interaction between the target analyte and nucleic recognition element.

Computer-Aided aptamer design for sulfadimethoxine antibiotic: step by step mutation based on MD simulation approach

This study introduces a computational method to design a new aptamer with higher binding affinity to a special target in comparison with the experimentally available aptamers. The method is called step by step mutation based on MD simulation, which includes some steps. First, MD simulation is performed for the SELEX-introduced (native) aptamer in the presence of the target. Afterwards, conformational factor (P_i) is calculated for the simulated system, which obtains the affinity of the aptamer residues to the target. A nucleotide exchange is done for the residue with the least P_i parameter to the nucleotide with the highest P_i value that results in a mutant aptamer. MD simulation is performed for the target-mutant complex, and P_i values are calculated again. The nucleotide exchange is performed similarly, and the designing process is proceeded repeatedly that results in a mutant with the improved specificity to the target. The aptamer affinity to the target is also determined in each step through calculating the binding Gibbs energy (ΔG_Bind) as a reliable parameter. The introduced strategy is utilized efficiently to design a mutant aptamer with improved specificity toward sulfadimethoxine (SDM) antibiotic as a case study. The great difference in the ΔG_Bind values about 579.856 kJ mol^-1 highlights that the M5 mutant possesses the improved specificity toward SDM in comparison with the native aptamer. Besides, the selectivity of the M5 aptamer toward SDM is examined among some conventional interfering compounds by using MD simulation that confirms the applicability of the designed aptamer for further experimental studies.

Interaction of Camptothecin with Model Cellular Membranes

Accurate and efficient prediction of drug partitioning in model membranes is of significant interest to the pharmaceutical industry. Herein, we utilize advanced sampling methods, specifically, the adaptive biasing force methodology to calculate the potential of mean force for a model hydrophobic anticancer drug, camptothecin (CPT), across three model interfaces. We consider an octanol bilayer, a thick octanol/water interface, and a model 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/water interface. We characterize the enthalpic and entropic contributions of the drug to the potential of mean force. We show that the rotational entropy of the drug is inversely related to the probability of hydrogen bond formation of the drug with the POPC membrane. In addition, in long-time microsecond simulations of a high concentration of CPT above the POPC membrane, we show that strong drug-drug aromatic interactions shift the spatial orientation of the drug with the membrane. Stacks of hydrophobic drugs form, allowing penetration of the drug just under the POPC head groups. These results imply that inhomogeneous membrane models need to take into account the effect of drug aggregation on the membrane environment.

Biphasic signals during nanopore translocation of DNA and nanoparticles due to strong ion cloud deformation

We report a theory for biphasic ionic current signals during DNA and nanoparticle translocation through a solid-state nanopore that produces scaling results consistent with those of finite element simulations (FEM), molecular dynamics (MD) simulations and experiments. For standard nanopores designed for potential rapid sequencing applications, the electric field is enhanced by orders of magnitude due to field focusing and can severely deform the ion-cloud around the charged DNA. Highly fore-aft asymmetric space charge distribution leads to a universal quasi-steady comet-like structure with a long tail. In contrast to previous biphasic theories, the charge density and length of the tail, which are responsible for the negative resistive pulse, are shown to depend sensitively on the dimensionless applied field, the Peclet number Pe, with a ∓1 scaling, due to a balance between tangential migration and normal diffusion. An optimum Pe is predicted where the negative pulse has the maximum amplitude.

Structural Properties of Small Single-Stranded Circular Nucleic Acids

One strategy to avoid rapid degradation of small nucleic acids in biomedical applications is to covalently link their 3'- and 5'-ends, turning them into circular nucleic acids (circNAs). Here, we examine structural properties of flexible non-base-paired circNAs, containing 6-48 nucleotides, in aqueous solution, using microsecond long molecular dynamics simulations. Analyses of conformational ensembles of circular DNA (circDNA) and RNA (circRNA) molecules of different lengths and sequences reveal how their structures and dynamics are affected by the constraints of their geometries. The circDNAs are more bent and flexible than circRNAs, with distinctly different arrangements of phosphate backbones and bases. Small circNAs can sequester counterions in conformations that resemble crown ethers for the smallest (6-8 nucleotide long) molecules examined, in contrast to their linear counterparts. At millimolar concentrations (7.9 mM), circNA molecules were observed to aggregate, adopting linear chain shapes at physiological ionic strengths.

The investigation of the G-quadruplex aptamer selectivity to Pb2+ ion: a joint molecular dynamics simulation and density functional theory study

The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb²⁺ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb²⁺ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb²⁺. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb²⁺. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb²⁺. The density functional theory (DFT) results show that Pb²⁺ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb²⁺. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb²⁺. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.Communicated by Ramaswamy H. Sarma.

Effects of Metal Ions on Aβ42 Peptide Conformations from Molecular Simulation Studies

In this study, we investigate the conformational characteristics of full-length Aβ₄₂ peptide monomers in the presence of Na⁺ and Zn²⁺ metal ions using atomistic molecular dynamics (MD) simulations with an aim to explore the possible driving forces behind enhanced aggregation rates of the peptides in the presence of salts. The calculations reveal that the presence of metal ions shifts the conformational equilibrium more toward the compact ordered Aβ structures. Such compact ordered structures stabilized by distant nonlocal contacts between two crucial hydrophobic segments, hp1 and hp2, primarily through two important hydrophobic aromatic residues, Phe-19 and Phe-20, are expected to trigger the aggregation process at a faster rate by populating and stabilizing the aggregation prone structures. Formation of a significant number of such distant contacts in the presence of Na⁺ ions has also been found to result in breaking of the N-terminal helix. On the contrary, binding of Zn²⁺ ion to Aβ peptide is highly specific, which stabilizes the N-terminal helix instead of breaking it. This explains why the aggregation rate of Aβ peptides is higher in the presence of divalent Zn²⁺ ions than monovalent Na⁺ ions. Relatively higher overall stability of the most populated Aβ peptide monomers in the presence of Zn²⁺ ions has been found to be associated with specific Zn²⁺-Aβ binding and significant free energy gain.

Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies

DNA is a complex molecule with phenomenal inherent plasticity and the ability to form different hydrogen bonding patterns of varying stabilities. These properties enable DNA to attain a variety of structural and conformational polymorphic forms. Structurally, DNA can exist in single-stranded form or as higher-order structures, which include the canonical double helix as well as the noncanonical duplex, triplex and quadruplex species. Each of these structural forms in turn encompasses an ensemble of dynamically heterogeneous conformers depending on the sequence composition and environmental context. In vivo, the widely populated canonical B-DNA attains these noncanonical polymorphs during important cellular processes. While several investigations have focused on the structure of these noncanonical DNA, studying their dynamics has remained nontrivial. Here, we outline findings from some recent advanced experimental and molecular simulation techniques that have significantly contributed toward understanding the complex dynamics of physiologically relevant noncanonical forms of DNA.

Autoantibody Profiling in Lupus Patients using Synthetic Nucleic Acids

Autoantibodies to nuclear components of cells (antinuclear antibodies, ANA), including DNA (a-DNA), are widely used in the diagnosis and subtyping of certain autoimmune diseases, including systemic lupus erythematosus (SLE). Despite clinical use over decades, precise, reproducible measurement of a-DNA titers remains difficult, likely due to the substantial sequence and length heterogeneity of DNA purified from natural sources. We designed and tested a panel of synthetic nucleic acid molecules composed of native deoxyribonucleotide units to measure a-DNA. ELISA assays using these antigens show specificity and reproducibility. Applying the ELISA tests to serological studies of pediatric and adult SLE, we identified novel clinical correlations. We also observed preferential recognition of a specific synthetic antigen by antibodies in SLE sera. We determined the probable basis for this finding using computational analyses, providing valuable structural information for future development of DNA antigens. Synthetic nucleic acid molecules offer the opportunity to standardize assays and to dissect antibody-antigen interactions.

Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations

Given the ubiquitous nature of protein-DNA interactions, it is important to understand the interaction thermodynamics of individual amino acid side chains for DNA. One way to assess these preferences is to perform molecular dynamics (MD) simulations. Here we report MD simulations of 20 amino acid side chain analogs interacting simultaneously with both a 70-base-pair double-stranded DNA and with a 70-nucleotide single-stranded DNA. The relative preferences of the amino acid side chains for dsDNA and ssDNA match well with values deduced from crystallographic analyses of protein-DNA complexes. The estimated apparent free energies of interaction for ssDNA, on the other hand, correlate well with previous simulation values reported for interactions with isolated nucleobases, and with experimental values reported for interactions with guanosine. Comparisons of the interactions with dsDNA and ssDNA indicate that, with the exception of the positively charged side chains, all types of amino acid side chain interact more favorably with ssDNA, with intercalation of aromatic and aliphatic side chains being especially notable. Analysis of the data on a base-by-base basis indicates that positively charged side chains, as well as sodium ions, preferentially bind to cytosine in ssDNA, and that negatively charged side chains, and chloride ions, preferentially bind to guanine in ssDNA. These latter observations provide a novel explanation for the lower salt dependence of DNA duplex stability in GC-rich sequences relative to AT-rich sequences.