Salt effects on nucleic acids

Multiplexed miRNA and Protein Analysis Using Digital Quantitative PCR in Microwell Arrays

Proteins and microRNAs (miRNAs) act in tandem within biological pathways to regulate cellular functions, and their misregulation has been correlated to numerous diseases. Because of their interconnectedness, both miRNAs and proteins must be evaluated together to obtain accurate insights into the molecular pathways of pathogenesis. However, few analytical techniques can measure both classes of biomolecules in parallel from a single biological sample. Here, microfluidic digital quantitative PCR (dqPCR) was developed to simultaneously quantify miRNA and protein targets in a multiplexed assay using a single detection chemistry. This streamlined analysis was achieved by integrating base-stacking PCR and immuno-PCR in a microfluidic array platform. Analyses of let-7a (miRNA) and IL-6 (protein) were first optimized separately to identify thermocycling and capture conditions amenable to both biomolecules. Singleplex dqPCR studies exhibited the expected digital signals and quantification cycles for both analytes over a range of concentrations. Multiplexed analyses were then conducted to quantify both let-7a and IL-6 with high sensitivity (LODs ∼ 3 fM) over a broad dynamic range (5-5000 fM) using only standard PCR reagents. This multiplexed dqPCR was then translated to the analysis of HEK293 cell lysate, where endogenous let-7a and IL-6 were measured simultaneously without sample purification or pretreatment. Collectively, these studies demonstrate that the integration of BS-PCR and immuno-PCR achieves a sensitive and streamlined approach for multiplexed analyses of miRNAs and proteins, which will enable researchers to gain better insights into disease pathogenesis in future applications.

Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations

Biological processes require DNA and RNA helices to pack together in specific interhelical orientations. While electrostatic repulsion between backbone charges is expected to be maximized when helices are in parallel alignment, such orientations are commonplace in nature. To better understand how the repulsion is overcome, we used experimental and computational approaches to investigate how the orientational preferences of DNA helices depend on the concentration and valence of mobile cations. We used Förster resonance energy transfer (FRET) to probe the relative orientations of two 24-bp helices held together via a freely rotating PEG linker. At low cation concentrations, the helices preferred more "cross"-like orientations over those closer to parallel, and this preference was reduced with increasing salt concentrations. The results were in good quantitative agreement with Poisson-Boltzmann (PB) calculations for monovalent salt (Na+). However, PB underestimated the ability of mixtures of monovalent and divalent ions (Mg2+) to reduce the conformational preference. As a complementary approach, we performed all-atom molecular dynamics (MD) simulations and found better agreement with the experimental results. While MD and PB predict similar electrostatic forces, MD predicts a greater accumulation of Mg2+ in the ion atmosphere surrounding the DNA. Mg2+ occupancy is predicted to be greater in conformations close to the parallel orientation than in conformations close to the crossed orientation, enabling a greater release of Na+ ions and providing an entropic gain (one bound ion for two released). MD predicts an entropy gain larger than that of PB because of the increased Mg2+ occupancy. The entropy changes have a negligible effect at low Mg2+ concentrations because the free energies are dominated by electrostatic repulsion. However, as the Mg2+ concentration increases, charge screening is more effective and the mixing entropy produces readily detectable changes in packing preferences. Our results underline the importance of mixing entropy of counterions in nucleic acid interactions and provide a new understanding on the impact of a mixed ion atmosphere on the packing of DNA helices.

Why Na+ has higher propensity than K+ to condense DNA in a crowded environment

Experimentally, in the presence of the crowding agent polyethylene glycol (PEG), sodium ions compact double-stranded DNA more readily than potassium ions. Here, we have used molecular dynamics simulations and the "ion binding shells model" of DNA condensation to provide an explanation for the observed variations in condensation of short DNA duplexes in solutions containing different monovalent cations and PEG; several predictions are made. According to the model we use, externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, the number of externally bound Na+ ions is larger than the number of K+ ions over a wide range of chloride concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation that is at least 0.2kBT per base pair more favorable in solution with NaCl than with KCl at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+ depends noticeably on the DNA sequence; we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. Counter-intuitively, the addition of a small amount of a crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA-DNA attraction, shifting the equilibrium away from the DNA condensed phase.

Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes

RNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is a highly negatively charged polyelectrolyte, which leads to intimate interactions with an ion atmosphere. Although RNA molecules are formally single-stranded, canonical (Watson-Crick) duplexes are key components of folded RNAs. A double-stranded (ds) RNA is also important for the design of RNA-based nanostructures and assemblies. Despite the fact that the description of canonical dsRNA is considered the least problematic part of RNA modeling, the imperfect shape and flexibility of dsRNA can lead to imbalances in the simulations of larger RNAs and RNA-containing assemblies. We present a comprehensive set of molecular dynamics (MD) simulations of four canonical A-RNA duplexes. Our focus was directed toward the characterization of the influence of varying ion concentrations and of the size of the solvation box. We compared several water models and four RNA force fields. The simulations showed that the A-RNA shape was most sensitive to the RNA force field, with some force fields leading to a reduced inclination of the A-RNA duplexes. The ions and water models played a minor role. The effect of the box size was negligible, and even boxes with a small fraction of the bulk solvent outside the RNA hydration sphere were sufficient for the simulation of the dsRNA.

Three-Way DNA Junction as an End Label for DNA in Atomic Force Microscopy Studies

Atomic Force Microscopy (AFM) is widely used for topographic imaging of DNA and protein-DNA complexes in ambient conditions with nanometer resolution. In AFM studies of protein-DNA complexes, identifying the protein’s location on the DNA substrate is one of the major goals. Such studies require distinguishing between the DNA ends, which can be accomplished by end-specific labeling of the DNA substrate. We selected as labels three-way DNA junctions (3WJ) assembled from synthetic DNA oligonucleotides with two arms of 39–40 bp each. The third arm has a three-nucleotide overhang, GCT, which is paired with the sticky end of the DNA substrate generated by the SapI enzyme. Ligation of the 3WJ results in the formation of a Y-type structure at the end of the linear DNA mole cule, which is routinely identified in the AFM images. The yield of labeling is 69%. The relative orientation of arms in the Y-end varies, such dynamics were directly visualized with time-lapse AFM studies using high-speed AFM (HS-AFM). This labeling approach was applied to the characterization of the nucleosome arrays assembled on different DNA templates. HS-AFM experiments revealed a high dynamic of nucleosomes resulting in a spontaneous unraveling followed by disassembly of nucleosomes.

Computational methods for calculation of protein-ligand binding affinities in structure-based drug design

Drug design is an expensive and time-consuming process. Any method that allows reducing the time the costs of the drug development project can have great practical value for the pharmaceutical industry. In structure-based drug design, affinity prediction methods are of great importance. The majority of methods used to predict binding free energy in protein-ligand complexes use molecular mechanics methods. However, many limitations of these methods in describing interactions exist. An attempt to go beyond these limits is the application of quantum-mechanical description for all or only part of the analyzed system. However, the extensive use of quantum mechanical (QM) approaches in drug discovery is still a demanding challenge. This chapter briefly reviews selected methods used to calculate protein-ligand binding affinity applied in virtual screening (VS), rescoring of docked poses, and lead optimization stage, including QM methods based on molecular simulations.

Chloride Enhances DNA Reactivity with Chlorine under Conditions Relevant to Water Treatment

Free available chlorine (FAC) is widely used to inactivate viruses by oxidizing viral components, including genomes. It is commonly assumed that hypochlorous acid (HOCl) is the chlorinating agent responsible for virus inactivation; however, recent studies have underscored that minor constituents of FAC existing in equilibrium with HOCl, such as molecular chlorine (Cl₂), can influence FAC reactivity toward select organic compounds. This study measures the FAC reaction kinetics with dsDNA and ssDNA extracted from representative bacteriophages (T3 and ϕX174) in samples augmented with chloride. Herein, chloride enhances FAC reactivity toward dsDNA and, to a lesser extent, toward ssDNA, especially at pH < 7.5. The enhanced reactivity can be attributed to the formation of Cl₂. Second-order rate constants were determined for reactions of ssDNA and dsDNA with HOCl and Cl₂. DNA chlorination kinetics followed the reactivity-selectivity principle, where the more-reactive nucleophilic species (ssDNA, ∼100× more reactive than dsDNA) reacted less selectively with electrophilic FAC species. The addition of chloride was also shown to enhance the inactivation of bacteriophage T3 (dsDNA genome) by FAC but did not enhance the inactivation of bacteriophage ϕX174 (ssDNA genome). Overall, the results suggest that Cl₂ is an important chlorinating agent of nucleic acids and viruses.

Modified Poisson–Boltzmann theory for polyelectrolytes in monovalent salt solutions with finite-size ions

We present a soft-potential-enhanced Poisson–Boltzmann (SPB) theory to efficiently capture ion distributions and electrostatic potential around rodlike charged macromolecules. The SPB model is calibrated with a coarse-grained particle-based model for polyelectrolytes (PEs) in monovalent salt solutions as well as compared to a full atomistic molecular dynamics simulation with the explicit solvent. We demonstrate that our modification enables the SPB theory to accurately predict monovalent ion distributions around a rodlike PE in a wide range of ion and charge distribution conditions in the weak-coupling regime. These include excess salt concentrations up to 1M and ion sizes ranging from small ions, such as Na+ or Cl−, to softer and larger ions with a size comparable to the PE diameter. The work provides a simple way to implement an enhancement that effectively captures the influence of ion size and species into the PB theory in the context of PEs in aqueous salt solutions.

Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking

To better understand the forces that mediate nucleic acid compaction in biology, we developed the disulfide cross-linking approach xHEED (X-linking of Helices to measure Electrostatic Effects at Distance) to measure the distance-dependent encounter frequency of two DNA helices in solution. Using xHEED, we determined the distance that the electrostatic potential extends from DNA helices, the dependence of this distance on ionic conditions, and the magnitude of repulsion when two helices approach one another. Across all conditions tested, the potential falls to that of the bulk solution within 15 Å of the major groove surface. For separations of ∼30 Å, we measured a repulsion of 1.8 kcal/mol in low monovalent ion concentration (30 mM Na+), with higher Na+ concentrations ameliorating this repulsion, and 2 M Na+ or 100 mM Mg2+ eliminating it. Strikingly, we found full screening at very low Co3+ concentrations and net attraction at higher concentrations, without the higher-order DNA condensation that typically complicates studies of helical attraction. Our measurements define the relevant distances for electrostatic interactions of nucleic-acid helices in biology and introduce a new method to propel further understanding of how these forces impact biological processes.

Dynamics of Cations around DNA and Protein as Revealed by 23Na Diffusion NMR Spectroscopy

Counterions are vital for the structure and function of biomolecules. However, the behavior of counterions remains elusive due to the difficulty in characterizing mobile ions. Here, we demonstrate that the dynamics of cations around biological macromolecules can be revealed by ²³Na diffusion nuclear magnetic resonance (NMR) spectroscopy. NMR probe hardware capable of generating strong magnetic field gradients enables ²³Na NMR-based diffusion measurements for Na⁺ ions in solutions of biological macromolecules and their complexes. The dynamic properties of Na⁺ ions interacting with the macromolecules can be investigated using apparent ²³Na diffusion coefficients measured under various conditions. Our diffusion data clearly show that Na⁺ ions retain high mobility within the ion atmosphere around DNA. The ²³Na diffusion NMR method also permits direct observation of the release of Na⁺ ions from nucleic acids upon protein-nucleic acid association. The entropy change due to the ion release can be estimated from the diffusion data.

Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models

We have compared distributions of sodium and potassium ions around double-stranded DNA, simulated using fixed charge SPC/E, TIP3P, and OPC water models and the Joung/Cheatham (J/C) ion parameter set, as well as the Li/Merz HFE 6-12 (L/M HFE) ion parameters for OPC water. In all the simulations, the ion distributions are in qualitative agreement with Manning's condensation theory and the Debye-Hückel theory, where expected. In agreement with experiment, binding affinity of monovalent ions to DNA does not depend on ion type in every solvent model. However, behavior of deeply bound ions, including ions bound to specific sites, depends strongly on the solvent model. In particular, the number of potassium ions in the minor groove of AT-tracts differs at least 3-fold between the solvent models tested. The number of sodium ions associated with the DNA agrees quantitatively with the experiment for the OPC water model, followed closely by TIP3P+J/C; the largest deviation from the experiment, ∼10%, is seen for SPC/E+J/C. On the other hand, SPC/E+J/C model is most consistent (67%) with the experimental potassium binding sites, followed by OPC+J/C (60%), TIP3P+J/C (53%), and OPC+L/M HFE (27%). The use of NBFIX correction with TIP3P+J/C improves its consistency with the experiment. In summary, the choice of the solvent model matters little for simulating the diffuse atmosphere of sodium and potassium ions around DNA, but ion distributions become increasingly sensitive to the solvent model near the helical axis. We offer an explanation for these trends. There is no single gold standard solvent model, although OPC water with J/C ions or TIP3P with J/C + NBFIX may offer an imperfect compromise for practical simulations of ionic atmospheres around DNA.

Cation enrichment in the ion atmosphere is promoted by local hydration of DNA

Electrostatic interactions are central to the structure and function of nucleic acids, including their folding, condensation, and interaction with proteins and other charged molecules. These interactions are profoundly affected by ions surrounding nucleic acids, the constituents of the so-called ion atmosphere. Here, we report precise Fourier Transform-Terahertz/Far-Infrared (FT-THz/FIR) measurements in the frequency range 30-500 cm^-1 for a 24-bp DNA solvated in a series of alkali halide (NaCl, NaF, KCl, CsCl, and CsF) electrolyte solutions which are sensitive to changes in the ion atmosphere. Cation excess in the ion atmosphere is detected experimentally by observation of cation modes of Na⁺, K⁺, and Cs⁺ in the frequency range between 70-90 cm^-1. Based on MD simulations, we propose that the magnitude of cation excess (which is salt specific) depends on the ability of the electrolyte to perturb the water network at the DNA interface: In the NaF atmosphere, the ions reduce the strength of interactions between water and the DNA more than in case of a NaCl electrolyte. Here, we explicitly take into account the solvent contribution to the chemical potential in the ion atmosphere: A decrease in the number of bound water molecules in the hydration layer of DNA is correlated with enhanced density fluctuations, which decrease the free energy cost of ion-hydration, thus promoting further ion accumulation within the DNA atmosphere. We propose that taking into account the local solvation is crucial for understanding the ion atmosphere.

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers

Pre-miRNA-377 is a hairpin-shaped regulatory RNA associated with heart failure. Here, we use single-molecule optical tweezers to unzip pre-miRNA-377 and study its stability and dynamics. We show that magnesium ions have a strong stabilizing effect, and that sodium ions stabilize the hairpin more than potassium ions. The hairpin unfolds in a single step, regardless of buffer composition. Interestingly, hairpin folding occurs either in a single step (type 1) or through the formation of intermediates, in multiple steps (type 2) or gradually (type 3). Type 3 occurs only in the presence of both sodium and magnesium, while type 1 and 2 take place in all buffers, with type 1 being the most prevalent. By reducing the size of the native hairpin loop from fourteen to four nucleotides, we demonstrate that the folding heterogeneity originates from the large size of the hairpin loop. Further, while efficient pre-miRNA-377 binders are lacking, we demonstrate that the recently developed C2 ligand displays bimodal activity: it enhances the mechanical stability of the pre-miRNA-377 hairpin and perturbs its folding. The knowledge regarding pre-miRNA stability and dynamics that we provide is important in understanding its regulatory function and how it can be modulated to achieve a therapeutic effect, e.g., in heart failure treatment.

Origin of heat capacity increment in DNA folding: The hydration effect

BACKGROUND

Understanding DNA folding thermodynamics is crucial for prediction of DNA thermal stability. It is now well established that DNA folding is accompanied by a decrease of the heat capacity ∆c_{p, F}, however its molecular origin is not understood. In analogy to protein folding it has been assumed that this is due to dehydration of DNA constituents, however no evidence exists to support this conclusion.

METHODS

Here we analyze partial molar heat capacity of nucleic bases and nucleosides in aqueous solutions obtained from calorimetric experiments and calculate the hydration heat capacity contribution ∆c_p^hyd.

RESULTS

We present hydration heat capacity contributions of DNA constituents and show that they correlate with the solvent accessible surface area. The average contribution for nucleic base dehydration is +0.56 J mol^-1 K^-1 Å^-2 and can be used to estimate the ∆c_{p, F} contribution for DNA folding.

CONCLUSIONS

We show that dehydration is one of the major sources contributing to the observed ∆c_{p, F} increment in DNA folding. Other possible sources contributing to the overall ∆c_{p, F} should be significant but appear to compensate each other to high degree. The calculated ∆c_p^hyd for duplexes and noncanonical DNA structures agree excellently with the overall experimental ∆c_{p, F} values. By contrast, empirical parametrizations developed for proteins result in poor ∆c_p^hyd predictions and should not be applied to DNA folding.

GENERAL SIGNIFICANCE

Heat capacity is one of the main thermodynamic quantities that strongly affects thermal stability of macromolecules. At the molecular level the heat capacity in DNA folding stems from removal of water from nucleobases.

Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces

Molecular association of proteins with nucleic acids is required for many biological processes essential to life. Electrostatic interactions via ion pairs (salt bridges) of nucleic acid phosphates and protein side chains are crucial for proteins to bind to DNA or RNA. Counterions around the macromolecules are also key constituents for the thermodynamics of protein–nucleic acid association. Until recently, there had been only a limited amount of experiment-based information about how ions and ionic moieties behave in biological macromolecular processes. In the past decade, there has been significant progress in quantitative experimental research on ionic interactions with nucleic acids and their complexes with proteins. The highly negatively charged surfaces of DNA and RNA electrostatically attract and condense cations, creating a zone called the ion atmosphere. Recent experimental studies were able to examine and validate theoretical models on ions and their mobility and interactions with macromolecules. The ionic interactions are highly dynamic. The counterions rapidly diffuse within the ion atmosphere. Some of the ions are released from the ion atmosphere when proteins bind to nucleic acids, balancing the charge via intermolecular ion pairs of positively charged side chains and negatively charged backbone phosphates. Previously, the release of counterions had been implicated indirectly by the salt-concentration dependence of the association constant.

Recently, direct detection of counterion release by NMR spectroscopy has become possible and enabled more accurate and quantitative analysis of the counterion release and its entropic impact on the thermodynamics of protein–nucleic acid association. Recent studies also revealed the dynamic nature of ion pairs of protein side chains and nucleic acid phosphates. These ion pairs undergo transitions between two major states. In one of the major states, the cation and the anion are in direct contact and form hydrogen bonds. In the other major state, the cation and the anion are separated by water. Transitions between these states rapidly occur on a picosecond to nanosecond time scale. When proteins interact with nucleic acids, interfacial arginine (Arg) and lysine (Lys) side chains exhibit considerably different behaviors. Arg side chains show a higher propensity to form rigid contacts with nucleotide bases, whereas Lys side chains tend to be more mobile at the molecular interfaces. The dynamic ionic interactions may facilitate adaptive molecular recognition and play both thermodynamic and kinetic roles in protein–nucleic acid interactions.

Growth, Cell Division, and Gene Expression of Escherichia coli at Elevated Concentrations of Magnesium Sulfate: Implications for Habitability of Europa and Mars

We perform quantitative studies of the growth, death, and gene expression of Escherichia coli in a wide range of magnesium sulfate (MgSO 4 ) concentrations (0-2.5 M). Elevated concentration of MgSO 4 causes the inhibition of cell growth, leading to an increase in the population doubling time. We find that cells exhibit three distinct morphological phenotypes-(i) normal, (ii) filamentous, and (iii) small cells at 1 . 25 M MgSO 4 . Filamentous cells arise due to the lack of cell division, while the small cells arise due to the partial plasmolysis of the cells. We further find that cell death starts for salt concentrations >1.25 M and increases with an increasing concentration of MgSO 4 . For salt concentrations ≥1.66 M, the growth of cells stops and all the cells become smaller than the control cells, suggesting the plasmolysis of the population. Cells grown at salt concentration up to 2 . 07 M are reversible in both the growth rate and morphology upon the removal of the salt stress. The time scale of reversibility increases with increasing salt concentration. Finally, we investigate the expression of an osmotically inducible gene (osmC), genes involved in magnesium transport (corA), sulfate transport (cysP), and osmotically driven transport of water (aqpZ). We find that a high concentration of magnesium sulfate leads to the upregulation of cysP and osmC.

Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting

RNAs are one of the most charged polyelectrolytes in nature, and understanding their electrostatics is fundamental to their structure and biological functions. An effective way to characterize the electrostatic field generated by nucleic acids is to quantify interactions between nucleic acids and ions that surround the molecules. These ions form a loosely associated cloud referred to as an ion atmosphere. Although theoretical and computational studies can describe the ion atmosphere around RNAs, benchmarks are needed to guide the development of these approaches, and experiments to date that read out RNA-ion interactions are limited. Here, we present ion counting studies to quantify the number of ions surrounding well-defined model systems of RNA and DNA duplexes. We observe that the RNA duplex attracts more cations and expels fewer anions compared to the DNA duplex, and the RNA duplex interacts significantly stronger with the divalent cation Mg²⁺, despite their identical total charge. These experimental results suggest that the RNA duplex generates a stronger electrostatic field than DNA, as is predicted based on the structural differences between their helices. Theoretical calculations using a nonlinear Poisson-Boltzmann equation give excellent agreement with experiments for monovalent ions but underestimate Mg²⁺-DNA and Mg²⁺-RNA interactions by 20%. These studies provide needed stringent benchmarks to use against other all-atom theoretical models of RNA-ion interactions, interactions that likely must be accurately accounted for in structural, dynamic, and energetic terms to confidently model RNA structure, interactions, and function.

Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0]

Nucleic acids are highly charged macromolecules sensitive to their surroundings of water, salt, and other biomolecules. Molecular dynamics simulations with accurate biomolecular force fields provide a detailed atomistic view into DNA and RNA that has been useful to study the structure and dynamics of these molecules and their biological relevance. In this work we study the Drew-Dickerson dodecamer duplex with the sequence d(GCGCAATTGCGC)₂ in three different salt concentrations and using different monvalent salt types to detect possible structural influence. Overall, the DNA shows no major structural changes regardless of amount or type of monovalent ions used. Our results show that only at very high salt conditions (5M) is a small structural effect observed in the DNA duplex, which mainly consist of narrowing of the grooves due to increased residence of ions. We also present the importance of sampling time to achieve a converged ensemble, which is of major relevance in any simulation to avoid biased or non-meaningful results.

Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding

How ions affect RNA folding thermodynamics and kinetics is an important but a vexing problem that remains unsolved. Experiments have shown that the free-energy change, Δ G( c), of RNA upon folding varies with the salt concentration ( c) as, Δ G( c) = k _c ln  c + const, where the coefficient k _c is proportional to the difference in the ion preferential coefficient, ΔΓ. We performed simulations of a coarse-grained model, by modeling electrostatic interactions implicitly and with explicit representation of ions, to elucidate the molecular underpinnings of the relationship between Δ G and ΔΓ. The simulations quantitatively reproduce the heat capacity for a pseudoknot, thus validating the model. We show that Δ G( c), calculated directly from ΔΓ, varies linearly with ln  c ( c < 0.2 M), for a hairpin and the pseudoknot, demonstrating a molecular link between the two quantities. Explicit ion simulations also show the linear dependence of Δ G( c) on ln  c at all c with k _c = 2 k_B T, except that Δ G( c) values are shifted by ∼2 kcal/mol higher than experiments. The discrepancy is due to an underestimation of Γ for both the folded and unfolded states while giving accurate values for ΔΓ. The predictions for the salt dependence of ΔΓ are amenable to test using single-molecule pulling experiments. The framework provided here can be used to obtain accurate thermodynamics for other RNA molecules as well.

The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell

Protein-DNA interactions are highly dependent on salt concentration. To gain insight into how such interactions are maintained in the highly saline cytoplasm of halophilic archaea, we determined the 3-D structure of VNG0258H/RosR, the first haloarchaeal DNA-binding protein from the extreme halophilic archaeon Halobactrium salinarum. It is a dimeric winged-helix-turn-helix (wHTH) protein with unique features due to adaptation to the halophilic environment. As ions are major players in DNA binding processes, particularly in halophilic environments, we investigated the solution structure of the ionic envelope and located anions in the first shell around the protein in the crystal using anomalous scattering. Anions that were found to be tightly bound to residues in the positively charged DNA-binding site would probably be released upon DNA binding and will thus make significant contribution to the driving force of the binding process. Unexpectedly, ions were also found in a buried internal cavity connected to the external medium by a tunnel. Our structure lays a solid groundwork for future structural, computational and biochemical studies on complexes of the protein with cognate DNA sequences, with implications to protein-DNA interactions in hyper-saline environments.

Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

The ion atmosphere is a critical structural, dynamic, and energetic component of nucleic acids that profoundly affects their interactions with proteins and ligands. Experimental methods that "count" the number of ions thermodynamically associated with the ion atmosphere allow dissection of energetic properties of the ion atmosphere, and thus provide direct comparison to theoretical results. Previous experiments have focused primarily on the cations that are attracted to nucleic acid polyanions, but have also showed that anions are excluded from the ion atmosphere. Herein, we have systematically explored the properties of anion exclusion, testing the zeroth-order model that anions of different identity are equally excluded due to electrostatic repulsion. Using a series of monovalent salts, we find, surprisingly, that the extent of anion exclusion and cation inclusion significantly depends on salt identity. The differences are prominent at higher concentrations and mirror trends in mean activity coefficients of the electrolyte solutions. Salts with lower activity coefficients exhibit greater accumulation of both cations and anions within the ion atmosphere, strongly suggesting that cation-anion correlation effects are present in the ion atmosphere and need to be accounted for to understand electrostatic interactions of nucleic acids. To test whether the effects of cation-anion correlations extend to nucleic acid kinetics and thermodynamics, we followed the folding of P4-P6, a domain of the Tetrahymena group I ribozyme, via single-molecule fluorescence resonance energy transfer in solutions with different salts. Solutions of identical concentration but lower activity gave slower and less favorable folding. Our results reveal hitherto unknown properties of the ion atmosphere and suggest possible roles of oriented ion pairs or anion-bridged cations in the ion atmosphere for electrolyte solutions of salts with reduced activity. Consideration of these new results leads to a reevaluation of the strengths and limitations of Poisson-Boltzmann theory and highlights the need for next-generation atomic-level models of the ion atmosphere.

Competitive interaction of monovalent cations with DNA from 3D-RISM

The composition of the ion atmosphere surrounding nucleic acids affects their folding, condensation and binding to other molecules. It is thus of fundamental importance to gain predictive insight into the formation of the ion atmosphere and thermodynamic consequences when varying ionic conditions. An early step toward this goal is to benchmark computational models against quantitative experimental measurements. Herein, we test the ability of the three dimensional reference interaction site model (3D-RISM) to reproduce preferential interaction parameters determined from ion counting (IC) experiments for mixed alkali chlorides and dsDNA. Calculations agree well with experiment with slight deviations for salt concentrations >200 mM and capture the observed trend where the extent of cation accumulation around the DNA varies inversely with its ionic size. Ion distributions indicate that the smaller, more competitive cations accumulate to a greater extent near the phosphoryl groups, penetrating deeper into the grooves. In accord with experiment, calculated IC profiles do not vary with sequence, although the predicted ion distributions in the grooves are sequence and ion size dependent. Calculations on other nucleic acid conformations predict that the variation in linear charge density has a minor effect on the extent of cation competition.

Understanding nucleic acid-ion interactions

Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the folding and dynamics of RNA and DNA and their complexes with proteins and with each other cannot be understood without a reasonably sophisticated appreciation of these ions' electrostatic interactions. However, the underlying behavior of the ion atmosphere follows physical rules that are distinct from the rules of site binding that biochemists are most familiar and comfortable with. The main goal of this review is to familiarize nucleic acid experimentalists with the physical concepts that underlie nucleic acid-ion interactions. Throughout, we provide practical strategies for interpreting and analyzing nucleic acid experiments that avoid pitfalls from oversimplified or incorrect models. We briefly review the status of theories that predict or simulate nucleic acid-ion interactions and experiments that test these theories. Finally, we describe opportunities for going beyond phenomenological fits to a next-generation, truly predictive understanding of nucleic acid-ion interactions.

DNA conformational flexibility study using phosphate backbone neutralization model

Due to the critical role of DNA in the processes of the cell cycle, the structural and physicochemical properties of DNA have long been of concern. In the present work, the effect of interplay between the DNA duplex and metal ions in solution on the DNA structure and conformational flexibility is studied by comparing the structure and dynamic conformational behavior of a duplex in a normal form and its “null isomer” using molecular dynamics methods. It was found that the phosphate neutralization changes the cation atmosphere around the DNA duplex greatly, increases the major groove width, decreases the minor groove width, and reduces the global bending direction preference. We also noted that the probability of BI phosphate linkages increases significantly because of the charge reduction in the backbone phosphate groups. More importantly, we found that the electrostatic effect on the DNA conformational flexibility is dependent on the sequence; that is, the phosphate backbone neutralization induces the global dynamic bending to be less flexible for GC-rich sequences but more flexible for AT-rich sequences.

Analysis of diffuse K+ and Mg2+ ion binding to a two-base-pair kissing complex by single-molecule mechanical unfolding

The folding and stability of RNA tertiary interactions depend critically on cationic conditions. It is usually difficult, however, to isolate such effects on tertiary interactions from those on the entire RNA. By manipulating conformations of single RNA molecules using optical tweezers, we distinguished individual steps of breaking and forming of a two-base-pair kissing interaction from those of secondary folding. The binding of metal ions to the small tertiary structure appeared to be saturable with an apparent Kd of 160 mM for K(+) and 1.5 mM for Mg(2+). The kissing formation was estimated to be associated with binding of ~2-3 diffuse K(+) or Mg(2+) ions. At their saturated binding, Mg(2+) provided ~3 kcal/mol more stabilizing energy to the structure than K(+). Furthermore, the cations change the unkissing forces significantly more than the kissing ones. For example, the presence of Mg(2+) ions increased the average unkissing force from 21 pN to 44 pN, surprisingly high for breaking merely two base pairs; in contrast, the mean kissing force was changed by only 4.5 pN. Interestingly, the differential salt effects on the transition forces were not caused by different changes in the height of the kinetic barriers but were instead attributed to how different molecular structures respond to the applied force. Our results showed the importance of diffuse cation binding to the stability of tertiary interaction and demonstrated the utility of mechanical unfolding in studying tertiary interactions.

Asymptotic analysis of the Poisson-Boltzmann equation in biological membrane channels

The Poisson-Boltzmann equation has been increasingly used for the description of biomolecular systems in order to derive their electrostatic properties. We here consider a domain consisting of two living cells which communicate through a system of proteins which assemble at specific membrane areas building microchannels called gap junctions. We describe the asymptotic behavior of the solution of the Poisson-Boltzmann equation posed in this domain. Using Γ-convergence tools, we derive some electrostatic properties of the biological membrane with respect to a vanishing parameter which is simultaneously associated to the membrane thinness, to the diameter of the gap junction microchannels and to the Debye length parameter which characterizes the spatial scale electrostatic interactions between particles within the gap junctions.

Electrostatics of nucleic acid folding under conformational constraint

RNA folding is enabled by interactions between the nucleic acid and its ion atmosphere, the mobile sheath of aqueous ions that surrounds and stabilizes it. Understanding the ion atmosphere requires the interplay of experiment and theory. However, even an apparently simple experiment to probe the ion atmosphere, measuring the dependence of DNA duplex stability upon ion concentration and identity, suffers from substantial complexity, because the unfolded ensemble contains many conformational states that are difficult to treat accurately with theory. To minimize this limitation, we measured the unfolding equilibrium of a DNA hairpin using a single-molecule optical trapping assay, in which the unfolded state is constrained to a limited set of elongated conformations. The unfolding free energy increased linearly with the logarithm of monovalent cation concentration for several cations, such that smaller cations tended to favor the folded state. Mg(2+) stabilized the hairpin much more effectively at low concentrations than did any of the monovalent cations. Poisson-Boltzmann theory captured trends in hairpin stability measured for the monovalent cation titrations with reasonable accuracy, but failed to do so for the Mg(2+) titrations. This finding is consistent with previous work, suggesting that Poisson-Boltzmann and other mean-field theories fail for higher valency cations where ion-ion correlation effects may become significant. The high-resolution data herein, because of the straightforward nature of both the folded and the unfolded states, should serve as benchmarks for the development of more accurate electrostatic theories that will be needed for a more quantitative and predictive understanding of nucleic acid folding.

RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations

RNA molecules play critical roles in many cellular processes. Traditionally viewed as genetic messengers, RNA molecules were recently discovered to have diverse functions related to gene regulation and expression. RNA also has great potential as a therapeutic and a tool for further investigation of gene regulation. Metal ions are an integral part of RNA structure and should be considered in any experimental or theoretical study of RNA. Here, we report a multidisciplinary approach that combines anomalous small-angle x-ray scattering and molecular-dynamics (MD) simulations with explicit solvent and ions around RNA. From experiment and simulation results, we find excellent agreement in the number and distribution of excess monovalent and divalent ions around a short RNA duplex. Although similar agreement can be obtained from a continuum description of the solvent and mobile ions (by solving the Poisson-Boltzmann equation and accounting for finite ion size), the use of MD is easily extended to flexible RNA systems with thermal fluctuations. Therefore, we also model a short RNA pseudoknot and find good agreement between the MD results and the experimentally derived solution structures. Surprisingly, both deviate from crystal structure predictions. These favorable comparisons of experiment and simulations encourage work on RNA in all-atom dynamic models.

The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations

The distributions of different cations around A-RNA are computed by Poisson-Boltzmann (PB) equation and replica exchange molecular dynamics (MD). Both the nonlinear PB and size-modified PB theories are considered. The number of ions bound to A-RNA, which can be measured experimentally, is well reproduced in all methods. On the other hand, the radial ion distribution profiles show differences between MD and PB. We showed that PB results are sensitive to ion size and functional form of the solvent dielectric region but not the solvent dielectric boundary definition. Size-modified PB agrees with replica exchange molecular dynamics much better than nonlinear PB when the ion sizes are chosen from atomistic simulations. The distribution of ions 14 Å away from the RNA central axis are reasonably well reproduced by size-modified PB for all ion types with a uniform solvent dielectric model and a sharp dielectric boundary between solvent and RNA. However, this model does not agree with MD for shorter distances from the A-RNA. A distance-dependent solvent dielectric function proposed by another research group improves the agreement for sodium and strontium ions, even for shorter distances from the A-RNA. However, Mg(2+) distributions are still at significant variances for shorter distances.

Counting ions around DNA with anomalous small-angle X-ray scattering

The majority of charge-compensating ions around nucleic acids form a diffuse counterion "cloud" that is not amenable to investigation by traditional methods that rely on rigid structural interactions. Although various techniques have been employed to characterize the ion atmosphere around nucleic acids, only anomalous small-angle X-ray scattering (ASAXS) provides information about the spatial distribution of ions. Here we present an experimentally straightforward extension of ASAXS that can be used to count the number of ions around nucleic acids.

Undulations enhance the effect of helical structure on DNA interactions

During the past decade, theory and experiments have provided clear evidence that specific helical patterns of charged groups and adsorbed (condensed) counterions on the DNA surface are responsible for many important features of DNA-DNA interactions in hydrated aggregates. The effects of helical structure on DNA-DNA interactions result from a preferential juxtaposition of the negatively charged sugar phosphate backbone with counterions bound within the grooves of the opposing molecule. Analysis of X-ray diffraction experiments confirmed the mutual alignment of parallel molecules in hydrated aggregates required for such juxtaposition. However, it remained unclear how this alignment and molecular interactions might be affected by intrinsic and thermal fluctuations, which cause structural deviations away from an ideal double helical conformation. We previously argued that the torsional flexibility of DNA allows the molecules to adapt their structure to accommodate a more electrostatically favorable alignment between molecules, partially compensating disruptive fluctuation effects. In the present work, we develop a more comprehensive theory, incorporating also stretching and bending fluctuations of DNA. We found the effects of stretching to be qualitatively and quantitatively similar to those of twisting fluctuations. However, this theory predicts more dramatic and surprising effects of bending. Undulations of DNA in hydrated aggregates strongly amplify rather than weaken the helical structure effects. They enhance the structural adaptation, leading to better alignment of neighboring molecules and pushing the geometry of the DNA backbone closer to that of an ideal helix. These predictions are supported by a quantitative comparison of the calculated and measured osmotic pressures in DNA.

A quantitative Raman spectroscopic signal for metal-phosphodiester interactions in solution

Accurate identification and quantification of metal ion-phosphodiester interactions are essential for understanding the role of metal ions as determinants of three-dimensional folding of large RNAs and as cofactors in the active sites of both RNA and protein phosphodiesterases. Accomplishing this goal is difficult due to the dynamic and complex mixture of direct and indirect interactions formed with nucleic acids and other phosphodiesters in solution. To address this issue, Raman spectroscopy has been used to measure changes in bond vibrational energies due to metal interactions. However, the contributions of inner-sphere, H-bonding, and electrostatic interactions to the Raman spectrum of phosphoryl oxygens have not been analyzed quantitatively. Here, we report that all three forms of metal ion interaction result in attenuation of the Raman signal for the symmetric vibration of the nonbridging phosphate oxygens (nu(s)PO(2)(-)), while only inner-sphere coordination gives rise to an apparent shift of nu(s)PO(2)(-) to higher wavenumbers (nu(s)PO(2)(-)M) in solution. Formation of nu(s)PO(2)(-)M is shown to be both dependent on metal ion identity and an accurate measure of site-specific metal ion binding. In addition, the spectroscopic parameter reflecting the energetic difference between nu(s)PO(2)(-) and nu(s)PO(2)(-)M (DeltanuM) is largely insensitive to changes in phosphodiester structure but strongly dependent on the absolute electronegativity and hardness of the interacting metal ion. Together, these studies provide strong experimental support for the use of nu(s)PO(2)(-)M and DeltanuM as general spectroscopic features for the quantitative analysis of metal binding affinity and the identification of metal ions associated with phosphodiesters in solution.

Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains

A major obstacle towards elucidating the molecular basis of transcriptional regulation is the lack of a detailed understanding of the interplay between non-specific and specific protein–DNA interactions. Based on molecular dynamics simulations of C₂H₂ zinc fingers (ZFs) and engrailed homeodomain transcription factors (TFs), we show that each of the studied DNA-binding domains has a set of highly constrained side chains in preset configurations ready to form hydrogen bonds with the DNA backbone. Interestingly, those domains that bury their recognition helix into the major groove are found to have an electrostatic hot spot for Cl⁻ ions located on the same binding cavity as the most buried DNA phosphate. The spot is characterized by three protein hydrogen bond donors, often including two basic side chains. If bound, Cl⁻ ions, likely mimicking phosphates, steer side chains that end up forming specific contacts with bases into bound-like conformations. These findings are consistent with a multi-step DNA-binding mechanism in which a pre-organized set of TF side chains assist in the desolvation of phosphates into well defined sites, prompting the re-organization of specificity determining side chains into conformations suitable for the recognition of their cognate sequence.

Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA

The recent discovery of the RNA interference mechanism emphasizes the biological importance of short, isolated, double-stranded (ds) RNA helices and calls for a complete understanding of the biophysical properties of dsRNA. However, most previous studies of the electrostatics of nucleic acid duplexes have focused on DNA. Here, we present a comparative investigation of electrostatic effects in RNA and DNA. Using resonant (anomalous) and non-resonant small-angle X-ray scattering, we characterized the charge screening efficiency and counterion distribution around short (25 bp) dsDNA and RNA molecules of comparable sequence. Consistent with theoretical predictions, we find counterion mediated screening to be more efficient for dsRNA than dsDNA. Furthermore, the topology of the RNA A-form helix alters the spatial distribution of counterions relative to B-form DNA. The experimental results reported here agree well with ion-size-corrected non-linear Poisson-Boltzmann calculations. We propose that differences in electrostatic properties aid in selective recognition of different types of short nucleic acid helices by target binding partners.

Probing nucleic acid-ion interactions with buffer exchange-atomic emission spectroscopy

The ion atmosphere of nucleic acids directly affects measured biochemical and biophysical properties. However, study of the ion atmosphere is difficult due to its diffuse and dynamic nature. Standard techniques available have significant limitations in sensitivity, specificity, and directness of the assays. Buffer exchange-atomic emission spectroscopy (BE-AES) was developed to overcome many of the limitations of previously available techniques. This technique can provide a complete accounting of all ions constituting the ionic atmosphere of a nucleic acid at thermodynamic equilibrium. Although initially developed for the study of the ion atmosphere of nucleic acids, BE-AES has also been applied to study site-bound ions in RNA and protein.

How RNA unfolds and refolds

Understanding how RNA folds and what causes it to unfold has become more important as knowledge of the diverse functions of RNA has increased. Here we review the contributions of single-molecule experiments to providing answers to questions such as: How much energy is required to unfold a secondary or tertiary structure? How fast is the process? How do helicases unwind double helices? Are the unwinding activities of RNA-dependent RNA polymerases and of ribosomes different from other helicases? We discuss the use of optical tweezers to monitor the unfolding activities of helicases, polymerases, and ribosomes, and to apply force to unfold RNAs directly. We also review the applications of fluorescence and fluorescence resonance energy transfer to measure RNA dynamics.

Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble

Electrostatic forces, acting between helices and modulated by the presence of the ion atmosphere, are key determinants in the energetic balance that governs RNA folding. Previous studies have employed Poisson-Boltzmann (PB) theory to compute the energetic contribution of these forces in RNA folding. However, the complex interaction of these electrostatic forces with RNA features such as tertiary contact formation, specific ion-binding, and complex interhelical junctions present in prior studies precluded a rigorous evaluation of PB theory, especially in physiologically important Mg(2+) solutions. To critically assess PB theory, we developed a model system that isolates these electrostatic forces. The model system, composed of two DNA duplexes tethered by a polyethylene glycol junction, is an analog for the unfolded state of canonical helix-junction-helix motifs found in virtually all structured RNAs. This model system lacks the complicating features that have precluded a critical assessment of PB in prior studies, ensuring that interhelical electrostatic forces dominate the behavior of the system. The system's simplicity allows PB predictions to be directly compared with small-angle X-ray scattering experiments over a range of monovalent and divalent ion concentrations. These comparisons indicate that PB is a reasonable description of the underlying electrostatic energies for monovalent ions, but large deviations are observed for divalent ions. The validation of PB for monovalent solutions allows analysis of the change in the conformational ensemble of this simple motif as salt concentration is changed. Addition of ions allows the motif to sample more compact microstates, increasing its conformational entropy. The increase of conformational entropy presents an additional barrier to folding by stabilizing the unfolded state. Neglecting this effect will adversely impact the accuracy of folding analyses and models.

An electrostatic network and long-range regulation of Src kinases

The regulatory mechanism of Src tyrosine kinases includes conformational activation by a change in the catalytic domain tertiary structure and in domain-domain contacts between the catalytic domain and the SH2/SH3 regulatory domains. The kinase is activated when tyrosine phosphorylation occurs on the activation loop, but without phosphorylation of the C-terminal tail. Activation also occurs by allostery when contacts between the catalytic domain (CD) and the regulatory SH3 and SH2 domains are released as a result of exogenous protein binding. The aim of this work is to examine the proposed role of an electrostatic network in the conformational transition and to elucidate the molecular mechanism for long-range, allosteric conformational activation by using a combination of experimental enzyme kinetics and nonequilibrium molecular dynamics simulations. Salt dependence of the induction phase is observed in kinetic assays and supports the role of an electrostatic network in the transition. In addition, simulations provide evidence that allosteric activation involves a concerted motion coupling highly conserved residues, and spanning several nanometers from the catalytic site to the regulatory domain interface to communicate between the CD and the regulatory domains.

Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors

Binding free energies were calculated for the inhibitors lopinavir, ritonavir, saquinavir, indinavir, amprenavir, and nelfinavir bound to HIV-1 protease. An MMPB/SA-type analysis was applied to conformational samples from 3 ns explicit solvent molecular dynamics simulations of the enzyme-inhibitor complexes. Binding affinities and the sampled conformations of the inhibitor and enzyme were compared between different HIV-1 protease protonation states to find the most likely protonation state of the enzyme in the complex with each of the inhibitors. The resulting set of protonation states leads to good agreement between calculated and experimental binding affinities. Results from the MMPB/SA analysis are compared with an explicit/implicit hybrid scheme and with MMGB/SA methods. It is found that the inclusion of explicit water molecules may offer a slight advantage in reproducing absolute binding free energies while the use of the Generalized Born approximation significantly affects the accuracy of the calculated binding affinities.

Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids

The ion atmosphere around nucleic acids critically affects biological and physical processes such as chromosome packing, RNA folding, and molecular recognition. However, the dynamic nature of the ion atmosphere renders it difficult to characterize. The basic thermodynamic description of this atmosphere, a full accounting of the type and number of associated ions, has remained elusive. Here we provide the first complete accounting of the ion atmosphere, using buffer equilibration and atomic emission spectroscopy (BE-AES) to accurately quantitate the cation association and anion depletion. We have examined the influence of ion size and charge on ion occupancy around simple, well-defined DNA molecules. The relative affinity of monovalent and divalent cations correlates inversely with their size. Divalent cations associate preferentially over monovalent cations; e.g., with Na+ in 4-fold excess of Mg2+ (20 vs 5 mM), the ion atmosphere nevertheless has 3-fold more Mg2+ than Na+. Further, the dicationic polyamine putrescine2+ does not compete effectively for association relative to divalent metal ions, presumably because of its lower charge density. These and other BE-AES results can be used to evaluate and guide the improvement of electrostatic treatments. As a first step, we compare the BE-AES results to predictions from the widely used nonlinear Poisson Boltzmann (NLPB) theory and assess the applicability and precision of this theory. In the future, BE-AES in conjunction with improved theoretical models, can be applied to complex binding and folding equilibria of nucleic acids and their complexes, to parse the electrostatic contribution from the overall thermodynamics of important biological processes.

Computer Simulation of the Ionic Atmosphere around Z-DNA

We describe a coarse-grained model for Z-DNA that mimics the DNA shape with a relatively small number of repulsive interaction sites. In addition, negative charges are placed at the phosphate positions. The ionic atmosphere around this grooved Z-DNA model is then investigated with Monte Carlo simulation. Cylindrically averaged concentration profiles as well as the spatial distribution of ions have been calculated. The results are compared to those for other DNA models differing in the repulsive core. This allows the examination of the effect of the DNA shape in the ionic distribution. It is seen that the penetrability of the ions to the DNA groove plays an important role in the ionic distribution. The results are also compared with those reported for B-DNA. In both conformers the ions are structured in alternating layers of positive and negative charge. In Z-DNA the layers are more or less concentric to the molecular axis. Besides, no coions enter into the single groove of this conformer. On the contrary, the alternating layers of B-DNA are also structured along the axial coordinate with some coions penetrating into the major groove. In both cases we have found five preferred locations of the counterions and two for the coions. The concentration of counterions reaches its absolute maximum at the narrow Z-DNA groove and at the minor groove of B-DNA, the value of the maximum being higher in the Z conformer.