Interpolyelectrolyte Complexes Formed by DNA and Astramol Poly(propylene imine) Dendrimers

Kabanov, V.A.; Sergeyev, Vladimir G.; Pyshkina, O. A.; Zinchenko, Anatoly; Зезин, А. Б.; Joosten, J. G. H.; Brackman, J.; Yoshikawa, Kenichi

doi:10.1021/ma000674u

Cited by 166 publications

(148 citation statements)

References 32 publications

(63 reference statements)

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“…Another system involves polymer-stabilized colloidal dispersions (36) or dispersions in liquid crystals (37); in the latter case, minimizing elastic distortions in the host medium induces a flocculation analogous to our cluster formation. Polycations can also induce DNA condensation through a process known as disproportionation (38); partially neutralized DNA segments aggregate into droplets (driven by short-range and Coulombic forces), surrounded by a halo of negatively charged segments (39)(40)(41). Although we do not consider Coulombic interactions, the principles are related: interstrand attraction is mediated by bridging polycations (which compacts DNA) as configurational entropy of unbound regions is maximized.…”

Section: Discussionmentioning

confidence: 99%

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

Brackley

Taylor²,

Papantonis

et al. 2013

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

246

344

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Molecular dynamics simulations are used to model proteins that diffuse to DNA, bind, and dissociate; in the absence of any explicit interaction between proteins, or between templates, binding spontaneously induces local DNA compaction and protein aggregation. Small bivalent proteins form into rows [as on binding of the bacterial histone-like nucleoid-structuring protein (H-NS)], large proteins into quasi-spherical aggregates (as on nanoparticle binding), and cylinders with eight binding sites (representing octameric nucleosomal cores) into irregularly folded clusters (like those seen in nucleosomal strings). Binding of RNA polymerase II and a transcription factor (NFκB) to the appropriate sites on four human chromosomes generates protein clusters analogous to transcription factories, multiscale loops, and intrachromosomal contacts that mimic those found in vivo. We suggest that this emergent behavior of clustering is driven by an entropic bridging-induced attraction that minimizes bending and looping penalties in the template.polymer physics | Brownian dynamics | chromatin looping | nucleosome D NA in living cells associates with proteins that continuously bind and dissociate. Some proteins affect local structure (such as histones and histone-like proteins), whereas others act globally to compact whole chromosomal segments [such as CCCTC-binding factor (CTCF)] (1-3). Bound proteins also cluster into supramolecular structures; for example, different transcription factors often bind to the same hot spots in the fly genome (4), and active molecules of RNA polymerase II coassociate in transcription factories (5, 6). In the latter case, clustering generates high local concentrations that facilitate production of the appropriate transcripts, as well as organizing the genome in 3D space.Against this background, biophysicists have begun to model DNA folding driven by DNA-binding proteins (3,(7)(8)(9)(10)(11)(12). Usually, the effects of DNA binding are incorporated into an effective potential that influences DNA dynamics; for instance, by stipulating that selected protein-binding regions in the polymer attract each other (11,12). Here, we use molecular dynamics (MD) to model proteins that diffuse to DNA, bind, and dissociate. In the absence of any explicit mutual attraction between proteins or between monomers in the polymer, we uncover an emergent property of the system: binding spontaneously induces protein clustering and genome compaction. For example, simulations yield structures seen experimentally when proteins representing bacterial histone-like nucleoid-structuring protein (H-NS) (1, 2, 13), gold nanoparticles (14, 15), and nucleosome cores bind to DNA. Using data derived from ChIP coupled to high-throughput sequencing (ChIP-seq) (16), we also model binding of RNA polymerase II and its transcription factor, NFκB, to the appropriate (cognate) sites on four human chromosomes; the two proteins spontaneously cluster into factories that are surrounded by loops that reflect those detected in cells using chromatin inte...

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Section: Discussionmentioning

confidence: 99%

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

Brackley

Taylor²,

Papantonis

et al. 2013

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

246

344

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“…This intriguing phenomenology has been observed in a variety of polyelectrolyte-colloid systems dispersed in aqueous solutions such as polyelectrolyte-micelle complexes, [20] latex particles [21,22], dendrimers [23], ferric oxide particles [24], phospholipid vesicles (liposomes) [25][26][27], 'hybrid niosome' vesicles [28].…”

Section: Introductionmentioning

confidence: 89%

Interaction between like-charged polyelectrolyte-colloid complexes in electrolyte solutions: A Monte Carlo simulation study in the Debye–Hückel approximation

Truzzolillo

Bordi

Sciortino

et al. 2010

The Journal of Chemical Physics

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We study the effective interaction between differently charged polyelectrolyte-colloid complexes in electrolyte solutions via Monte Carlo simulations. These complexes are formed when short and flexible polyelectrolyte chains adsorb onto oppositely charged colloidal spheres, dispersed in an electrolyte solution. In our simulations the bending energy between adjacent monomers is small compared to the electrostatic energy, and the chains, once adsorbed, do not exchange with the solution, although they rearrange on the particles surface to accomodate further adsorbing chains or due to the electrostatic interaction with neighbor complexes. Rather unexpectedly, when two interacting particles approach each others, the rearrangement of the surface charge distribution invariably produces anti-parallel dipolar doublets, that invert their orientation at the isoelectric point. These findings clearly rule out a contribution of dipole-dipole interactions to the observed attractive interaction between the complexes, pointing out that such suspensions can not be considered dipolar fluids. On varying the ionic strength of the electrolyte, we find that a screening length κ −1 , short compared with the size of the colloidal particles, is required in order to observe the attraction between like charged complexes due to the non-uniform distribution of the electric charge on their surface ('patch attraction'). On the other hand, by changing the polyelectrolyte/particle charge ratio, ξ s , the interaction between like-charged polyelectrolyte-decorated (pd) particles, at short separations, evolves from purely repulsive to strongly attractive. Hence, the effective interaction between the complexes is characterized by a potential barrier, whose height depends on the net charge and on the non-uniformity of their surface charge distribution.2

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“…Several experimental studies [5,6,7] clarify general structure of dendrimerlinear polyelectrolyte (PE) complexes. In particular, atomic-force-microscopy data [8] and titration combined with spectroscopy [9] indicate that DNA macromolecules wrap around charged dendrimer-like polymers. Recently these experimental results were confirmed by the fully-atomistic molecular-dynamics (MD) simulations of Maiti and Bagchi [10].…”

Section: Introductionmentioning

confidence: 99%

Dynamics of Complexation of a Charged Dendrimer by Linear Polyelectrolyte: Computer Modelling

Lyulin

Darinskii

2007

E-Polymers

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Brownian-dynamics simulations have been performed for complexes formed by a charged dendrimer and a long oppositely charged linear polyelectrolyte when overcharging phenomenon is always observed. After complex formation the orientational mobility of the individual dendrimer bonds, the fluctuations of the dendrimer size, and the dendrimer rotational diffusion have been simulated. Corresponding relaxation times do not depend on the linear-chain length in a complex and are close to those for a single neutral dendrimer. At the same time fluctuations of the size of a complex are completely defined by the corresponding fluctuations of a linear polyelectrolyte size. Adsorbed polyelectrolyte practically does not feel the rotation of a dendrimer; simulated complexes may be considered as nuts with light core (dendrimer) and heavy shell (adsorbed linear polymer); the electrostatic contacts between dendrimer and oppositely charged linear polymer are easily broken due to the very fast dendrimer-size fluctuations.

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Interpolyelectrolyte Complexes Formed by DNA and Astramol Poly(propylene imine) Dendrimers

Cited by 166 publications

References 32 publications

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

Interaction between like-charged polyelectrolyte-colloid complexes in electrolyte solutions: A Monte Carlo simulation study in the Debye–Hückel approximation

Dynamics of Complexation of a Charged Dendrimer by Linear Polyelectrolyte: Computer Modelling

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