Linker Formation in an Overcharged Complex of Two Dendrimers and Linear Polyelectrolyte

Larin, Sergey V.; Darinskii, A. A.; Lyulin, Sergey V.

doi:10.1021/jp908196t

Cited by 26 publications

(47 citation statements)

References 50 publications

(205 reference statements)

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“…The possibility of spontaneous DNA bending has been confirmed experimentally for DNA fragments designed so that the phosphate groups are neutralized on one side of the DNA. 298 Recently, the subject of PE-sphere wrapping and induced overcharging 299 has been investigated in a number of computer simulation [300][301][302][303][304] and theoretical 305 studies. …”

Section: Dna Wrapping In Ncpsmentioning

confidence: 99%

Electrostatic interactions in biological DNA-related systems

Cherstvy

2011

Phys. Chem. Chem. Phys.

160

148

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In this perspective article, we focus on recent developments in the theory of charge effects in biological DNA-related systems. The electrostatic effects on different levels of DNA organization are considered, including the DNA-DNA interactions, DNA complexation with cationic lipid membranes, DNA condensates and DNA-dense cholesteric phases, protein-DNA recognition, DNA wrapping in nucleosomes, and inter-nucleosomal interactions. For these systems, we develop a theoretical framework to describe the physical-chemical mechanisms of structure formation and anticipate some biological consequences. General biophysical principles of DNA compaction in chromatin fibers and DNA spooling inside viral capsids are discussed in the end, with emphasis on electrostatic aspects.

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Section: Dna Wrapping In Ncpsmentioning

confidence: 99%

Electrostatic interactions in biological DNA-related systems

Cherstvy

2011

Phys. Chem. Chem. Phys.

160

148

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“…4.2 Interaction of siRNA with dendrimer 4.2.1 siRNA compaction: Although there exist several computational and theoretical studies on the complexation of dendrimers and oppositely charged model polyelectrolytes (Pavan et al 2009;Lyulin et al 2005Lyulin et al , 2008Larin et al 2009aLarin et al , 2010 and DNA-dendrimer complexation (Maiti and Bagchi 2006;Nandy and Maiti 2011), studies on siRNAdendrimer interaction are really limited. There is a growing interest to study the interaction of siRNA with other nanoscale objects due to their potential application in RNAi therapy.…”

Section: Binding Energymentioning

confidence: 99%

Interaction of nucleic acids with carbon nanotubes and dendrimers

2012

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Nucleic acid interaction with nanoscale objects like carbon nanotubes (CNTs) and dendrimers is of fundamental interest because of their potential application in CNT separation, gene therapy and antisense therapy. Combining nucleic acids with CNTs and dendrimers also opens the door towards controllable self-assembly to generate various supra-molecular and nano-structures with desired morphologies. The interaction between these nanoscale objects also serve as a model system for studying DNA compaction, which is a fundamental process in chromatin organization. By using fully atomistic simulations, here we report various aspects of the interactions and binding modes of DNA and small interfering RNA (siRNA) with CNTs, graphene and dendrimers. Our results give a microscopic picture and mechanism of the adsorption of single-and double-strand DNA (ssDNA and dsDNA) on CNT and graphene. The nucleic acid-CNT interaction is dominated by the dispersive van der Waals (vdW) interaction. In contrast, the complexation of DNA (both ssDNA and dsDNA) and siRNA with various generations of poly-amido-amine (PAMAM) dendrimers is governed by electrostatic interactions. Our results reveal that both the DNA and siRNA form stable complex with the PAMAM dendrimer at a physiological pH when the dendrimer is positively charged due to the protonation of the primary amines. The size and binding energy of the complex increase with increase in dendrimer generation. We also give a summary of the current status in these fields and discuss future prospects.[Nandy B, Santosh M and Maiti PK 2012 Interaction of nucleic acids with carbon nanotubes and dendrimers.

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“…In such complexes, a new LPE conformation is introduced, that of the "linker" between the two dendritic molecules [35]. As in the stoichiometric systems [27,31,33], the dendrimers were also found to be strongly overcharged upon increase of the length of the LPE, with the maximum degree of overcharging observed at a length of the LPE close to that corresponding to the single dendrimer/LPE systems.…”

Section: Introductionmentioning

confidence: 99%

“…A step forward towards elucidating the specifics of the overcharging phenomena in linear LPE/dendrimer complexes was taken recently by considering non-stoichiometric complexes comprised by a linear polyelectrolyte and two oppositely charged dendrimers [35]. In such complexes, a new LPE conformation is introduced, that of the "linker" between the two dendritic molecules [35].…”

Section: Introductionmentioning

confidence: 99%

“…Instead, in the non-stoichiometric complexes increase of the LPE length resulted in the appearance of the "linker" conformation and the gradual separation of the two dendrimers, but this occurrence did not affect the length of the dendrimer-adsorbed LPE parts. An intriguing effect related to the "linker" conformation was the non-monotonic dependence of the "linker" size on the LPE length [35]. Detailed conformational analysis of the LPE chain showed that the "linker" state of the LPE coexisted with a "tail" configuration which could not be accounted for by an approximate theoretical approach developed by the authors [35].…”

Section: Introductionmentioning

confidence: 99%

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Conformational Effects in Non-Stoichiometric Complexes of Two Hyperbranched Molecules with a Linear Polyelectrolyte

et al. 2012

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Abstract:We report results from Brownian dynamics computer simulations of systems comprised by two terminally charged hyperbranched molecules preferentially branched in the periphery, with an oppositely charged linear chain of varying length. Comparison of the findings from the present study to stoichiometric counterparts and to analogous dendrimer-based complexes, reveal that the presence of the second hyperbranched molecule incurs significant changes in the conformational characteristics of both components of the complex. Instead of step-like changes in the average size and shape of the hyperbranched component that were noted in the previously studied stoichiometric systems, a rather smooth change is observed upon increase of the length of the linear component. In addition, a markedly different behavior is also noticed in the conformational characteristics of the linear chain when compared to that in similar dendrimer-based systems. The above findings are consistent with the higher degree of deformability of the peripherally branched molecules which allow appropriate rearrangements in shape in order to accommodate the favorable Coulombic interactions between the two components of the complex. This behavior offers new insight towards the design of more efficient OPEN ACCESSPolymers 2012, 4 241 hyperbranched-based systems which can take advantage of the multifunctionality and the structural properties of the highly branched polymer components.

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Linker Formation in an Overcharged Complex of Two Dendrimers and Linear Polyelectrolyte

Cited by 26 publications

References 50 publications

Electrostatic interactions in biological DNA-related systems

Electrostatic interactions in biological DNA-related systems

Interaction of nucleic acids with carbon nanotubes and dendrimers

Conformational Effects in Non-Stoichiometric Complexes of Two Hyperbranched Molecules with a Linear Polyelectrolyte

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