Attractive interactions between rodlike polyelectrolytes:  Polarization, crystallization, and packing

Solis, Francisco J.; Cruz, Mónica Olvera de la

doi:10.1103/physreve.60.4496

Cited by 95 publications

(110 citation statements)

References 17 publications

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“…Collapse of nucleic acids in high valence ions has been observed in several large DNA and RNA systems (17,18,26,36) and is predicted from theory (13,37,38). Nevertheless, the experimental systems used to date are complex or form ill-defined states upon compaction.…”

Section: Resultsmentioning

confidence: 99%

Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution

Bai

Das

Millett

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

127

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Understanding biological and physical processes involving nucleic acids, such as the binding of proteins to DNA and RNA, DNA condensation, and RNA folding, requires an understanding of the ion atmosphere that surrounds nucleic acids. We have used a simple model DNA system to determine how the ion atmosphere modulates interactions between duplexes in the absence of specific metal ion-binding sites and other complicated interactions. In particular, we have tested whether the Coulomb repulsion between nucleic acids can be reversed by counterions to give a net attraction, as has been proposed recently for the rapid collapse observed early in RNA folding. The conformation of two DNA duplexes tethered by a flexible neutral linker was determined in the presence of a series of cations by small angle x-ray scattering. The small angle x-ray scattering profiles of two control molecules with distinct shapes (a continuous duplex and a mimic of the compact DNA) were in good agreement with predictions, establishing the applicability of this approach. Under low-salt conditions (20 mM Na ؉ ), the tethered duplexes are extended because of a Coulombic repulsion estimated to be 2-5 kT͞bp. Addition of high concentrations of Na ؉ (1.2 M), Mg 2؉ (0.6 M), and spermidine 3؉ (75 mM) resulted in electrostatic relaxation to a random state. These results indicate that a counterion-induced attractive force between nucleic acid duplexes is not significant under physiological conditions. An upper limit on the magnitude of the attractive potential under all tested ionic conditions is estimated.correlation ͉ DNA ͉ RNA ͉ folding ͉ electrostatics N ucleic acids play a central role in the storage, transmission, and control of genetic information. DNA and RNA associate with numerous protein and nucleic acid partners to form the complexes that participate in and regulate cellular metabolism and form catalytic components of biological machines such as the ribosome. A comprehensive understanding of these biological processes requires understanding the fundamental physical and chemical principles underlying the behaviors of the participating molecules.Nucleic acids are highly charged biopolymers, with one formal negative charge per monomeric unit. There are many examples of specific interactions of nucleic acids with ions in nucleic acidprotein complexes and in folded RNAs (1, 2). Nevertheless, the vast majority of cations associated with a nucleic acid are nonspecifically bound. These counterions condense onto DNA or RNA and form a thermally fluctuating sheath commonly referred to as the ion atmosphere (3, 4). Indeed, order-of-magnitude calculations estimate enormous repulsive energies for RNA in the absence of counterions (e.g., Ϸ10 3 kT for a folded RNA with Ϸ400 nucleotides, the size of the Tetrahymena group I intron). ʈ This repulsive energy is predominantly overcome by electrostatic interactions with the ion atmosphere (3-5).Despite the clear importance of the ion atmosphere, experimental investigation has been difficult. The dynamic nature of the...

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Section: Resultsmentioning

confidence: 99%

Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution

Bai

Das

Millett

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

127

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“…During the past decades, there have been intensive theoretical investigations to elucidate the mechanism of counterion induced attractive interaction between polyelectrolytes [5,6,7,8,9,10,11,12,13]. Although other types of interactions such as hydration [12,13] and depletion [14] are contributing factors, it has been established that the electrostatic between the polyelectrolytes and their correlated counterions [5,6,7,8,9,10,11,15] is the major cause of like-charge attraction.…”

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Temperature Effects on Threshold Counterion Concentration to Induce Aggregation of fd Virus

Tang

2006

Phys. Rev. Lett.

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We seek to determine the mechanism of like-charge attraction by measuring the temperature dependence of critical divalent counterion concentration (C c ) for the aggregation of fd viruses. We find that an increase in temperature causes C c to decrease, primarily due to a decrease in the dielectric constant (ε) of the solvent. At a constant ε, C c is found to increase as the temperature increases. The effects of T and ε on C c can be combined to that of one parameter: Bjerrum length (l B ). C c decreases exponentially as l B increases, suggesting that entropic effect of counterions plays an important role at the onset of bundle formation.

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“…The counterintuitive nature of the effective attraction implied by bundle formation, in combination with the biological importance of the phenomenon, have made it the topic of numerous studies over the past decades (see Refs. [5,6,7,8,9, 10] and references therein). There is now general agreement that strong electrostatic correlations are a crucial condition [9,11], in accordance with the experimental observation that most condensing agents carry a multivalent charge.…”

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Polyelectrolyte Condensation Induced by Linear Cations

Guáqueta

Luijten

2007

Phys. Rev. Lett.

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We examine the role of the condensing agent in the formation of polyelectrolyte bundles, via grandcanonical Monte Carlo simulations. Following recent experiments we use linear, rigid divalent cations of various lengths to induce condensation. Our results clarify and explain the experimental results for short cations. For longer cations we observe novel condensation behavior owing to alignment of the cations. We also study the role of the polyelectrolyte surface charge density, and find a nonmonotonic variation in bundle stability. This nonmonotonicity captures two trends that have been observed in separate experiments. [1,4] or the fd and M13 virus [2], they aggregate into dense, hexagonally coordinated bundles. The counterintuitive nature of the effective attraction implied by bundle formation, in combination with the biological importance of the phenomenon, have made it the topic of numerous studies over the past decades (see Refs. [5,6,7,8,9, 10] and references therein). There is now general agreement that strong electrostatic correlations are a crucial condition [9,11], in accordance with the experimental observation that most condensing agents carry a multivalent charge. However, other factors that affect the tendency of a system to exhibit condensation are much less well established, mainly because these factors are difficult to disentangle in both experiments and theory.Even for a simple ionic condensing agent, its interaction strength with the polyelectrolyte is affected not only by its valency, but also by its size [12] and by the surface charge density of the polyelectrolyte. In addition, the ionic concentration plays an important role, as it determines the stabilizing osmotic pressure exerted on the bundle by the surrounding solution [2, 4] and also controls the strength of entropic effects such as counterion release and depletion interactions [5]. Thus, even a systematic variation of the ion size can yield results that are difficult to interpret, as it alters both the binding of the ion to the polyelectrolyte and the osmotic pressure of the solution. Likewise, variation of the polyelectrolyte charge not only affects ionic binding, but also the direct electrostatic repulsion between polyelectrolytes. Accordingly, only an integrated approach can resolve the true origin of observed trends in the aggregation behavior.There is a remarkable dearth of such studies. Experimentally, there are technical limitations. For example, examination of the effect of counterion size is hampered by the uncertainty in measuring hydrated ion sizes [13] and variation of counterion valency often entails the simultaneous variation of other ionic properties. Furthermore, it is difficult to measure the ionic concentration within the aggregate and hence to assess the osmotic effects arising from a concentration imbalance with the bulk solution. This osmotic stress is also often ignored in computational and theoretical studies. Inspired by two recent experimental studies [13,14], in this Letter we aim to obtain a more complete u...

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Attractive interactions between rodlike polyelectrolytes: Polarization, crystallization, and packing

Cited by 95 publications

References 17 publications

Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution

Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution

Temperature Effects on Threshold Counterion Concentration to Induce Aggregation of fd Virus

Polyelectrolyte Condensation Induced by Linear Cations

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