Microscopic Basis for the Mesoscopic Extensibility of Dendrimer-Compacted DNA

Mills, Maria; Orr, Brian J.; Holl, Mark M. Banaszak; Andricioaei, Ioan

doi:10.1016/j.bpj.2009.11.020

Cited by 20 publications

(33 citation statements)

References 48 publications

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“…The types of guest molecules considered in this review will include low molecular weight organic molecules [24,29,50,51], and nucleic acids [38,[69][70][71][72][73]. The review of interactions of dendrimers with lipid membrane has been clearly explained in Reference [37].…”

Section: The Physical Properties Of Complex Systems Of Dendrimers Witmentioning

confidence: 99%

“…The free energies of the complex showed that the binding strength increases with higher generation of dendrimer and that the binding energy per protonated primary amine (dendrimer) was maximized for the G4 dendrimer, suggesting that the G4 dendrimer could be the optimum candidate for gene therapy applications. Mills et al performed molecular dynamics simulations with the CHARMM 27 force field to study the binding between a dendrimer and dsDNA [70]. In this work, the local environment effects, such as deformation and the electrostatic interactions, were characterized and related to single molecule pulling experiments.…”

Section: The Physical Properties Of Complex Systems Of Dendrimers Witmentioning

confidence: 99%

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Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Kim

Lamm

2012

Polymers

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Dendrimers have been widely used as nanostructured carriers for guest species in a variety of applications in medicine, catalysis, and environmental remediation. Theory and simulation methods are an important complement to experimental approaches that are designed to develop a fundamental understanding about how dendrimers interact with guest molecules. This review focuses on computational studies aimed at providing a better understanding of the relevant physicochemical parameters at play in the binding and release mechanisms between polyamidoamine (PAMAM) dendrimers and guest species. We highlight recent contributions that model supramolecular dendrimer-guest complexes over the temporal and spatial scales spanned by simulation methods ranging from all-atom molecular dynamics to statistical field theory. The role of solvent effects on dendrimer-guest interactions and the importance of relating model parameters across multiple scales is discussed.

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Section: The Physical Properties Of Complex Systems Of Dendrimers Witmentioning

confidence: 99%

Section: The Physical Properties Of Complex Systems Of Dendrimers Witmentioning

confidence: 99%

Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Kim

Lamm

2012

Polymers

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“…This difference between the two different orientations has been quantified in our previous work. 54 Close to the DNA (see the 20–30 Å range), the two orientations lead to different PMF profiles because the binding geometry is different. However, at distances farther from the DNA (beyond 30 Å), the two orientations lead to essentially the same curves.…”

Section: Discussionmentioning

confidence: 99%

Attractive Hydration Forces in DNA–Dendrimer Interactions on the Nanometer Scale

Mills

Orr²,

Holl

et al. 2013

J. Phys. Chem. B

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The energetic contribution of attractive hydration forces arising from water ordering is an interesting but often neglected aspect of macromolecular interactions. Ordering effects of water can bring about cooperativity in many intermolecular transactions, in both the short and long range. Given its high charge density, this is of particular importance for DNA. For instance, in nanotechnology, highly charged dendrimers are used for DNA compaction and transfection. Hypothesizing that water ordering and hydration forces should be maximal for DNA complexes that show charge complementarity (positive-negative), we present here analysis of water ordering from molecular dynamics simulations and free energy calculations of the interaction between DNA and a nanoparticle with a high positive charge density. Our results indicate not only that complexation of the dendrimer with DNA affects the local water structure, but also that ordered water molecules facilitate long range interactions between the molecules. This contributes significantly to the free energy of binding of dendrimers to DNA and extends the interaction well beyond the electrostatic range of the DNA. Such water effects are of potentially substantial importance in cases when molecules appear to recognize each other across sizable distances, or for which kinetic rates are too fast to be due to pure diffusion. Our results are in good agreement with experiments on the role of solvent in DNA condensation by multivalent cations and exemplify a microscopic realization of mean-field phenomenological theories for hydration forces between mesoscopic surfaces.

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“…[23][24][25] Latest researches have been performed to carry dendrimers and biological macromolecules (DNA or oligonucleotide) complexes into cells without damaging or deactivating DNA fragments. [26][27] Moreover, Shcharbin et al 28 predicted that phosphorus-containing dendrimers would be wonderful gene carrier in the future.…”

Section: Gene Vectormentioning

confidence: 99%

Advances in Applications of Dendritic Compounds

Ma²,

Deng³

et al. 2013

j. nanosci. nanotech.

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Dendritic compounds (so-called dendrimers) with nano-scale represent unique symmetric and spherical structures. They are usually prepared through two fundamental methods based on molecular level which involved the convergent method and divergent method, although the synthetic methods have a tendency towards the diversity and functionalization. The outershell of dendrimers with rich peripheral reactive sites are easily modified by small functional molecules. Moreover, the higher generation dendrimers also possess more exposed functional groups on the surface prior to the previous one and they are much easily customized for much more applications. Consequently, based on previous researches, this review summarized wide applications of dendritic compounds in many fields which were investigated in detail, including gene vector, drug carrier, catalysis, sensor industry, photoelectric material, etc. Dendrimers provide promising tools for the cellular delivery of molecular cargos ranging in size from small molecules and peptides to proteins and DNA. More importantly, it is necessary to explore new synthetic methods and undiscovered applications of new dendrimers.

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Microscopic Basis for the Mesoscopic Extensibility of Dendrimer-Compacted DNA

Cited by 20 publications

References 48 publications

Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Attractive Hydration Forces in DNA–Dendrimer Interactions on the Nanometer Scale

Advances in Applications of Dendritic Compounds

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