Complexes of Nucleic Acids with Group I and II Cations

Hsiao, Chiaolong; Tannenbaum, Emmanuel; VanDeusen, Halena R.; Hershkovitz, Eli; Perng, Ginger; Tannenbaum, Allen; Williams, Loren Dean

doi:10.1039/9781847558763-00001

Cited by 34 publications

(59 citation statements)

References 158 publications

(281 reference statements)

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“…Magnesium plays a special role in folding of large globular RNAs (Draper 2008;Hsiao et al 2008). These RNAs are closely associated with magnesium ions, many of which can be visualized by X-ray diffraction.…”

Section: Introductionmentioning

confidence: 99%

“…Tight packing and crowding is a hallmark of first-shell magnesium ligands, leading to highly restrained geometry and strong ligandligand interactions. Bidentate chelation of magnesium by RNA is associated with noncanonical conformation states of the backbone (Klein et al 2004;Hsiao et al 2008;Hsiao and Williams 2009).…”

Section: Introductionmentioning

confidence: 99%

“…1B; Hsiao et al 2008;Hsiao and Williams 2009). An example of such a bidentate RNA-magnesium complex, extracted from the LSU of H. marismortui is shown in Figure 2A.…”

Section: Introductionmentioning

confidence: 99%

“…These bidentate clamps appear to be elemental units of RNA folding and assembly. Tri-and tetradentate RNA-magnesium complexes nearly always contain at least one of these bidentate clamps (Hsiao et al 2008). A magnesium ion is clamped twice, by both the mRNA and the rRNA, in the assembled Thermus thermophilus ribosome (PDB entry 2J01, described in Selmer et al 2006).…”

Section: Introductionmentioning

confidence: 99%

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Bidentate RNA–magnesium clamps: On the origin of the special role of magnesium in RNA folding

Petrov

Bowman²,

Harvey³

et al. 2010

RNA

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Magnesium plays a special role in RNA function and folding. Although water is magnesium's most common first-shell ligand, the oxyanions of RNA have significant affinity for magnesium. Here we provide a quantum mechanical description of first-shell RNA-magnesium and DNA-magnesium interactions, demonstrating the unique features that characterize the energetics and geometry of magnesium complexes within large folded RNAs. Our work focuses on bidentate chelation of magnesium by RNA or DNA, where multiple phosphate oxyanions enter the first coordination shell of magnesium. These bidentate RNA clamps of magnesium occur frequently in large RNAs. The results here suggest that magnesium, compared to calcium and sodium, has an enhanced ability to form bidentate clamps with RNA. Bidentate RNA-sodium clamps, in particular, are unstable and spontaneously open. Due to magnesium's size and charge density it binds more intimately than other cations to the oxyanions of RNA, so that magnesium clamps are stabilized not only by electrostatic interactions, but also by charge transfer, polarization, and exchange interactions. These nonelectrostatic components of the binding are quite substantial with the high charge and small interatomic distances within the magnesium complexes, but are less pronounced for calcium due to its larger size, and for sodium due to its smaller charge. Additionally, bidentate RNA clamps of magnesium are more stable than those with DNA. The source of the additional stability of RNA complexes is twofold: there is a slightly attenuated energetic penalty for ring closure in the formation of RNA bidentate chelation complexes and dipole interactions between the 29-hydroxyl group and cations.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…1B; Hsiao et al 2008;Hsiao and Williams 2009). An example of such a bidentate RNA-magnesium complex, extracted from the LSU of H. marismortui is shown in Figure 2A.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Bidentate RNA–magnesium clamps: On the origin of the special role of magnesium in RNA folding

Petrov

Bowman²,

Harvey³

et al. 2010

RNA

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“…(i) If the counterions are adsorbed in the grooves [21] they will form an additional helical pattern of positive charges, which follows the helices of negative charges on the phosphates. The electric field of such charge distribution is screened by the electrolyte and decays with a characteristic length of is the DNA helical pitch (≈34 Å) and D λ is the Debye screening length (≈7-10 Å in physiological ionic conditions).…”

Section: Introductionmentioning

confidence: 99%

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

Cortini

Cheng

Smith

2017

J. Phys.: Condens. Matter

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Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of k T 1 B . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.

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Counterion condensation and shape within Poisson–Boltzmann theory

Lamm

Pack

2010

Biopolymers

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An analytical approximation to the nonlinear Poisson-Boltzmann (PB) equation is applied to charged macromolecules that possess one-dimensional symmetry and can be modeled by a plane, infinite cylinder, or sphere. A functional substitution allows the nonlinear PB equation subject to linear boundary conditions to be transformed into an approximate linear (Debye-Hückel-type) equation subject to nonlinear boundary conditions. A simple analytical result for the surface potential of such polyelectrolytes follows, leading to expressions for the amount of condensed (or renormalized) charge and the electrostatic Helmholtz energy for polyelectrolytes. Analytical high-charge/low-salt and low-charge/high-salt limits are shown to be similar to results obtained by others based on PB or counterion condensation theory. Several important general observations concerning polyelectrolytes treated within the context of PB theory can be made including: (1) all charged surfaces display some counterion condensation for finite electrolyte concentration, (2) the effect of surface geometry is described primarily by the sum of the Debye constant and the mean curvature of the surface, (3) two surfaces with the same surface charge density and mean curvature condense approximately identical fractions of counterions, (4) the amount of condensation is not determined by a predefined "condensation distance" although such a distance can be determined uniquely from it, and (5) substantial condensation occurs if the Debye constant of the electrolyte is much less than the mean curvature of a highly charged polyelectrolyte.

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Complexes of Nucleic Acids with Group I and II Cations

Cited by 34 publications

References 158 publications

Bidentate RNA–magnesium clamps: On the origin of the special role of magnesium in RNA folding

Bidentate RNA–magnesium clamps: On the origin of the special role of magnesium in RNA folding

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

Counterion condensation and shape within Poisson–Boltzmann theory

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