Hexammineruthenium(III) ion interactions with Z-DNA.
Ontology highlight
ABSTRACT:
SUBMITTER: Bharanidharan D
PROVIDER: S-EPMC2344113 | biostudies-literature | 2007 Dec
REPOSITORIES: biostudies-literature
Publications
Hexammineruthenium(III) ion interactions with Z-DNA.
Bharanidharan D D Thiyagarajan S S Gautham N N
Acta crystallographica. Section F, Structural biology and crystallization communications 20071121 Pt 12
The hexamer duplex d(CGCGCA).d(TGCGCG) was crystallized with hexammineruthenium(III) ions in an orthorhombic space group; the crystals diffracted to 1.54 A resolution. Strong ion interactions with the adenine base induce a tautomeric shift from the amino to the imino form. Consequently, the A.T base pairing is disrupted. This structural study may be relevant to metal toxicity. ...[more]
Similar Datasets
Project description:Understanding how DNA carries out its biological roles requires knowledge of its interactions with biological partners. Since DNA is a polyanionic polymer, electrostatic interactions contribute significantly. These interactions are mediated by positively charged protein residues or charge compensating cations. Direct detection of these partners and/or their effect on DNA conformation poses challenges, especially for monitoring conformational dynamics in real time. Small-angle x-ray scattering (SAXS) is uniquely sensitive to both the conformation and local environment (i.e. protein partner and associated ions) of the DNA. The primary challenge of studying multi-component systems with SAXS lies in resolving how each component contributes to the measured scattering. Here, we review two contrast variation (CV) strategies that enable targeted studies of the structures of DNA or its associated partners. First, solution contrast variation enables measurement of DNA conformation within a protein-DNA complex by masking out the protein contribution to the scattering profile. We review a specific example, in which the real-time unwrapping of DNA from a nucleosome core particle is measured during salt-induced disassembly. The second method, heavy atom isomorphous replacement, reports the spatial distribution of the cation cloud around duplex DNA by exploiting changes in the scattering strength of cations with varying atomic numbers. We demonstrate the application of this approach to provide the spatial distribution of monovalent cations (Na+, K+, Rb+, Cs+) around a standard 25-base pair DNA. The CV strategies presented here are valuable tools for understanding DNA interactions with its biological partners.
| S-EPMC4991782 | biostudies-literature
Project description:This article reports the syntheses, characterization, structural description, together with magnetic and spectroscopic properties of two isostructural molecular magnets based on the chiral ligand N,N'-bis((1,2-diphenyl-(pyridine-2-yl)methylene)-(R,R/S,S)-ethane-1,2-diamine), L1, of general formula [Ln2(RR-L1)2(Cl6)]·MeOH·1.5H2O, (Ln = Ce (1) or Nd (2)). Multifrequency electron paramagnetic resonance (EPR), cantilever torque magnetometry (CTM) measurements, and ab initio calculations allowed us to determine single-ion magnetic anisotropy and intramolecular magnetic interactions in both compounds, evidencing a more important role of the anisotropic exchange for the NdIII derivative. The comparison of experimental and theoretical data indicates that, in the case of largely rhombic lanthanide ions, ab initio calculations can fail in determining the orientation of the weakest components, while being reliable in determining their principal values. However, they remain of paramount importance to set the analysis of EPR and CTM on sound basis, thus obtaining a very precise picture of the magnetic interactions in these systems. Finally, the electronic structure of the two complexes, as obtained by this approach, is consistent with the absence of zero-field slow relaxation observed in ac susceptibility.
| S-EPMC8277162 | biostudies-literature
Project description:Ion-mediated interaction between DNAs is essential for DNA condensation, and it is generally believed that monovalent and nonspecifically binding divalent cations cannot induce the aggregation of double-stranded (ds) DNAs. Interestingly, recent experiments found that alkaline earth metal ions such as Mg2+ can induce the aggregation of triple-stranded (ts) DNAs, although there is still a lack of deep understanding of the surprising findings at the microscopic level. In this work, we employed all-atom dynamic simulations to directly calculate the potentials of mean force (PMFs) between tsDNAs, between dsDNAs, and between tsDNA and dsDNA in Mg2+ solutions. Our calculations show that the PMF between tsDNAs is apparently attractive and becomes more strongly attractive at higher [Mg2+], although the PMF between dsDNAs cannot become apparently attractive even at high [Mg2+]. Our analyses show that Mg2+ internally binds into grooves and externally binds to phosphate groups for both tsDNA and dsDNA, whereas the external binding of Mg2+ is much stronger for tsDNA. Such stronger external binding of Mg2+ for tsDNA favors more apparent ion-bridging between helices than for dsDNA. Furthermore, our analyses illustrate that bridging ions, as a special part of external binding ions, are tightly and positively coupled to ion-mediated attraction between DNAs.
| S-EPMC5549645 | biostudies-literature
Project description:Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological nature of helices, while there is still lack of an understanding on the relevant ion-mediated interactions at atomistic level. In this work, we have directly calculated the potentials of mean force (PMF) between two dsRNAs and between two dsDNAs in Co(NH3)6 (3+) (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that at low [Co-Hex], the PMFs between B-DNAs and between A-RNAs are both (strongly) repulsive. However, at high [Co-Hex], the PMF between B-DNAs is strongly attractive, while those between A-RNAs and between A-DNAs are still (weakly) repulsive. The microscopic analyses show that for A-form helices, Co-Hex would become 'internal binding' into the deep major groove and consequently cannot form the evident ion-bridge between adjacent helices, while for B-form helices without deep grooves, Co-Hex would exhibit 'external binding' to strongly bridge adjacent helices. In addition, our further calculations show that, the PMF between A-RNAs could become strongly attractive either at very high [Co-Hex] or when the bottom of deep major groove is fixed with a layer of water.
| S-EPMC4499160 | biostudies-literature
Project description:The ionic atmospheres around nucleic acids play important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle x-ray scattering can provide important insights into the structure and energetics of such atmospheres but are time- and resource intensive. In this article, we use classical density functional theory to explore the balance among ion-DNA, ion-water, and ion-ion interactions in ionic atmospheres of RbCl, SrCl2, and CoHexCl3 (cobalt hexamine chloride) around a B-form DNA molecule. The accuracy of the classical density functional theory calculations was assessed by comparison between simulated and experimental anomalous small-angle x-ray scattering curves, demonstrating that an accurate model should take into account ion-ion correlation and ion hydration forces, DNA topology, and the discrete distribution of charges on the DNA backbone. As expected, these calculations revealed significant differences among monovalent, divalent, and trivalent cation distributions around DNA. Approximately half of the DNA-bound Rb(+) ions penetrate into the minor groove of the DNA and half adsorb on the DNA backbone. The fraction of cations in the minor groove decreases for the larger Sr(2+) ions and becomes zero for CoHex(3+) ions, which all adsorb on the DNA backbone. The distribution of CoHex(3+) ions is mainly determined by Coulomb and steric interactions, while ion-correlation forces play a central role in the monovalent Rb(+) distribution and a combination of ion-correlation and hydration forces affect the Sr(2+) distribution around DNA. This does not imply that correlations in CoHex solutions are weaker or stronger than for other ions. Steric inaccessibility of the grooves to large CoHex ions leads to their binding at the DNA surface. In this binding mode, first-order electrostatic interactions (Coulomb) dominate the overall binding energy as evidenced by low sensitivity of ionic distribution to the presence or absence of second-order electrostatic correlation interactions.
| S-EPMC4724655 | biostudies-literature
Project description:Background: Ependymomas are glial tumors derived from differentiated ependymal cells. In contrast to other types of brain tumors, histological grading is not a good prognostic marker for these tumors. In order to determine genomic changes in an anaplastic ependymoma, we analyzed its mutation patterns by next generation sequencing (NGS). Methods: Tumor DNA was sequenced using an Ion PI v3 chip on Ion Proton instrument and the data were analyzed by Ion Reporter 5.6. Results: NGS analysis identified 19 variants, of which four were previously reported missense variants; c.395G>A in IDH1, c.1173A>G in PIK3CA, c.1416A>T in KDR and c.215C>G in TP53. The frequencies of the three missense mutations ( PIK3CA c.1173A>G, KDR c.1416A>T, TP53, c.215C>G) were high, suggesting that these are germline variants, whereas the IDH1 variant frequency was low (4.81%). However, based on its FATHMM score of 0.94, only the IDH1 variant is pathogenic; other variants TP53, PIK3CA and KDR had FATHMM scores of 0.22, 0.56 and 0.07, respectively. Eight synonymous mutations were found in FGFR3, PDGFRA, EGFR, RET, HRAS, FLT3, APC and SMAD4 genes. The mutation in FLT3 p.(Val592Val) was the only novel variant found. Additionally, two known intronic variants in KDR were found and intronic variants were also found in ERBB4 and PIK3CA. A known splice site mutation at an acceptor site in FLT3, a 3'-UTR variant in the CSF1R gene and a 5'_UTR variant in the SMARCB1 gene were also identified. The p-values were below 0.00001 for all variants and the average coverage for all variants was around 2000x. Conclusions: In this grade III ependymoma, one novel synonymous mutation and one deleterious missense mutation is reported. Many of the variants reported here have not been detected in ependymal tumors by NGS analysis previously and we therefore report these variants in brain tissue for the first time.
| S-EPMC7317822 | biostudies-literature
Project description:Two novel 1D heterobimetallic compounds {[MnIII(SB2+)MIII(CN)6]·4H2O}n (SB2+ = N,N'-ethylenebis(5-trimethylammoniomethylsalicylideneiminate) based on orbitally degenerate cyanidometallates [OsIII(CN)6]3- (1) and [RuIII(CN)6]3- (2) and MnIII Schiff base complex were synthesized and characterized structurally and magnetically. Their crystal structures consist of electrically neutral, well-isolated chains composed of alternating [MIII(CN)6]3- anions and square planar [MnIII(SB2+)]3+ cations bridged by cyanide groups. These -ion magnetic anisotropy of MnIII centers. These results indicate that the presence of compounds exhibit single-chain magnet (SCM) behavior with the energy barriers of Δτ1/kB = 73 K, Δτ2/kB = 41.5 K (1) and Δτ1/kB = 51 K, Δτ2 = 27 K (2). Blocking temperatures of TB = 2.8, 2.1 K and magnetic hysteresis with coercive fields (at 1.8 K) of 8000, 1600 Oe were found for 1 and 2, respectively. Theoretical analysis of the magnetic data reveals that their single-chain magnet behavior is a product of a complicated interplay of extremely anisotropic triaxial exchange interactions in MIII(4d/5d)-CN-MnIII fragments: -JxSMxSMnx-JySMySMny-JzSMzSMnz, with opposite sign of exchange parameters Jx = -22, Jy = +28, Jz = -26 cm-1 and Jx = -18, Jy = +20, Jz = -18 cm-1 in 1 and 2, respectively) and single orbitally degenerate [OsIII(CN)6]3- and [RuIII(CN)6]3- spin units with unquenched orbital angular momentum in the chain compounds 1 and 2 leads to a peculiar regime of slow magnetic relaxation, which is beyond the scope of the conventional Glaubers's 1D Ising model and anisotropic Heisenberg model.
| S-EPMC9921754 | biostudies-literature
Project description:Ion-specific effects in aqueous solution, known as the Hofmeister effect, are prevalent in diverse systems ranging from pure ionic to complex protein solutions. The objective of this paper is to explicitly demonstrate how complex ion-ion and ion-water interactions manifest themselves in the Hofmeister effect based on a series of recent experimental observations. These effects are not considered in the classical descriptions of ion effects, such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, and therefore they fail to describe the origin of the phenomenological Hofmeister effect. However, given that models considering the basic forces of electrostatic and van der Waals interactions can offer rationalization for the core experimental observations, a universal interaction model stands a chance of being developed. In this perspective, we separately derive the contribution from ion-ion electrostatic interactions and ion-water interactions from second harmonic generation (SHG) data at the air-ion solution interface, which yields an estimate of the ion-water interactions in solution. The Hofmeister ion effect observed for biological solutes in solution should be similarly influenced by contributions from ion-ion and ion-water interactions, where the same ion-water interaction parameters derived from SHG data at the air-ion solution interface could be applicable. A key experimental data set available from solution systems to probe ion-water interactions is the modulation of water diffusion dynamics near ions in a bulk ion solution, as well as near biological liposome surfaces. This is obtained from Overhauser dynamic nuclear polarization (ODNP), a nuclear magnetic resonance (NMR) relaxometry technique. The surface water diffusivity is influenced by the contribution from ion-water interactions, both from localized surface charges and adsorbed ions, although the relative contribution of the former is larger on liposome surfaces. In this perspective, ion-water interaction energy values derived from experimental data for various ions are compared with theoretical values in the literature. Ultimately, quantifying ion-induced changes in the surface energy for the purpose of developing valid theoretical models for ion-water interactions will be critical to rationalizing the Hofmeister effect.
| S-EPMC4656249 | biostudies-other
Project description:Human topoisomerase IIalpha utilizes a two-metal-ion mechanism for DNA cleavage. One of the metal ions (M(1)(2+)) is believed to make a critical interaction with the 3'-bridging atom of the scissile phosphate, while the other (M(2)(2+)) is believed to interact with a nonbridging oxygen of the scissile phosphate. Based on structural and mutagenesis studies of prokaryotic nucleic acid enzymes, it has been proposed that the active site divalent metal ions interact with type II topoisomerases through a series of conserved acidic amino acid residues. The homologous residues in human topoisomerase IIalpha are E461, D541, D543, and D545. To address the validity of these assignments and to delineate interactions between individual amino acids and M(1)(2+) and M(2)(2+), we individually mutated each of these acidic amino acid residues in topoisomerase IIalpha to either cysteine or alanine. Mutant enzymes displayed a marked loss of catalytic and DNA cleavage activity as well as a reduced affinity for divalent metal ions. Additional experiments determined the ability of wild-type and mutant topoisomerase IIalpha enzymes to cleave an oligonucleotide substrate that contained a sulfur atom in place of the 3'-bridging oxygen of the scissile phosphate in the presence of Mg2+, Mn2+, or Ca2+. On the basis of the results of these studies, we conclude that the four acidic amino acid residues interact with metal ions in the DNA cleavage/ligation active site of topoisomerase IIalpha. Furthermore, we propose that M(1)(2+) interacts with E461, D543, and D545 and M(2)(2+) interacts with E461 and D541.
| S-EPMC2782489 | biostudies-literature
Project description:Mononuclear lanthanide-based single-ion magnets (SIMs) are known since 2003 with the discovery of SIM properties in a bis-(phthalocyaninato)lanthanide complex. A recent report on [Dy(Cpttt)2][BC6F5] indicating that it exhibits the highest known blocking temperature (60 K) has spurred fresh interest in this area. In this article, we discuss about the various requirements of lanthanide-based SIMs along with representative examples. Specifically, we describe the complexes whose coordination numbers vary from 2 to 8. We also discuss the representative examples of organometallic lanthanide complexes that can function as molecular magnets.
| S-EPMC6644820 | biostudies-literature