<i>Colloquium</i>: The physics of charge inversion in chemical and biological systems

Grosberg, Alexander Y.; Nguyen, Toan T.; Shklovskiǐ, B. I.

doi:10.1103/revmodphys.74.329

Cited by 1,048 publications

(1,215 citation statements)

References 84 publications

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“…TAT can have strong electrostatic interactions with different components of the cell besides the cell membrane, in ways that contributes to its activity. Useful reviews of electrostatic interactions in biological physics include [85][86][87][88][89][90].…”

Section: Discussionmentioning

confidence: 99%

Arginine‐rich cell‐penetrating peptides

et al. 2009

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a b s t r a c tArginine-rich cell-penetrating peptides are short cationic peptides capable of traversing the plasma membranes of eukaryotic cells. While successful intracellular delivery of many biologically active macromolecules has been accomplished using these peptides, their mechanisms of cell entry are still under investigation. Recent dialogue has centered on a debate over the roles that direct translocation and endocytotic pathways play in internalization of cell-penetrating peptides. In this paper, we review the evidence for the broad range of proposed mechanisms, and show that each distinct process requires negative Gaussian membrane curvature as a necessary condition. Generation of negative Gaussian curvature by cell-penetrating peptides is directly related to their arginine content. We illustrate these concepts using HIV TAT as an example.

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Section: Discussionmentioning

confidence: 99%

Arginine‐rich cell‐penetrating peptides

et al. 2009

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“…While simulation experiments and the aggregation of DNA and RNA in ethanol during standard precipitation procedures and other conditions demonstrate the existence of such attractive forces under some conditions, their exact magnitude and significance for folding in vitro was unknown [61,62]. The magnitude of these attractive forces was tested with a simple model: two DNA helices tethered together by a neutral polyethylene glycol tether.…”

Section: Simple Forces Underlying the Complex Behavior Of Rnamentioning

confidence: 99%

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Chu

Herschlag

2008

Current Opinion in Structural Biology

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SummaryThe rapid development of our understanding of the diverse biological roles fulfilled by non-coding RNA has motivated interest in the basic macromolecular behavior, structure, and function of RNA. We focus on two areas in the behavior of complex RNAs. First, we present advances in the understanding of how RNA folding is accomplished in vivo by presenting a mechanism for the action of DEAD-box proteins. Members of this family are intimately associated with almost all cellular processes involving RNA, mediating RNA structural rearrangements and chaperoning their folding. Next, we focus on advances in understanding and characterizing the basic biophysical forces that govern the folding of complex RNAs. Ultimately we expect that a confluence and synergy between these approaches will lead to profound understanding of RNA and its biology.The explosion in our knowledge about noncoding RNA (ncRNA) -RNA that is not translated into protein -has expanded interest in RNA beyond the traditional RNA community. Diverse ncRNAs include the recently-discovered riboswitches, whose novel gene-regulation function is induced by the binding of small metabolites [1]; most of the so-called "Human Accelerated Regions" (HAR) of the human genome, whose recent evolution may be linked to the emergence of the human brain [2]; and many ncRNAs of unknown function [3]. These discoveries underscore the need to understand the fundamental macromolecular behavior of RNA, its structure and dynamics, and how these RNAs are handled and exploited in biology.Study of catalytic RNAs, which allow detection of correct folding via activity measurements, has established basic thermodynamic and kinetic properties of RNA folding. Large catalytic RNAs such as the group I intron from Tetrahymena thermophila and the RNase P RNA from Bacillus subtilis fold at vastly different rates under different conditions upon addition of Mg 2+ and have been shown to fold via multiple parallel pathways, in which different molecules follow different routes with different rates and intermediates, to a common final folded structure [4,5]. These observations support the common view that RNAs traverse rugged energy landscapes as they fold [6,7]. However, little is known about the true shape of these

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“…Excluded volume interactions between condensed counterions, however, result in spatial correlations that position any two metal ions at distances greater than the sum of their ionic radii. 15 As both Z and the volume (V) of the ions contribute to the distribution of ions around the RNA, they also both determine the nature of the counterion-induced compact states of RNA. Thus, the natural variable that controls RNA stability is the charge density ζ = Ze/V where Ze is the charge and V is the volume of the cation.…”

Section: Introductionmentioning

confidence: 99%

Charge Density of Divalent Metal Cations Determines RNA Stability

et al. 2007

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RNA molecules are exquisitely sensitive to the properties of counterions. The folding equilibrium of the Tetrahymena ribozyme is measured by non-denaturing gel electrophoresis in the presence of divalent group IIA metal cations. The stability of the folded ribozyme increases with the charge density (ζ) of the cation. Similar scaling is found when the free energy of the RNA folded in small and large metal cations is measured by urea denaturation. Brownian dynamics simulations of a polyelectrolyte show that the experimental observations can be explained by non-specific ion-RNA interactions in the absence of site-specific metal chelation. The experimental and simulation results establish that RNA stability is largely determined by a combination of counterion charge and the packing efficiency of condensed cations that depends on the excluded volume of the cations.

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Colloquium: The physics of charge inversion in chemical and biological systems

Cited by 1,048 publications

References 84 publications

Arginine‐rich cell‐penetrating peptides

Arginine‐rich cell‐penetrating peptides

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Charge Density of Divalent Metal Cations Determines RNA Stability

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