Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment
Using molecular dynamics (MD) simulations, we explore the structural and dynamical properties of siRNA within the intercalated environment of a <em>Mg</em>:<em>Al</em> 2:1 Layered Double Hydroxide (LDH) nanoparticle. An <em>ab ini...
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doaj-5d82ed0730724ebba0cfeece084537052020-11-24T21:23:49ZengMDPI AGPharmaceutics1999-49232012-06-014229631310.3390/pharmaceutics4020296Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer EnvironmentSean C. SmithZhiping XuVinuthaa MurthyHong ZhangYunyi WongDefang OuyangUsing molecular dynamics (MD) simulations, we explore the structural and dynamical properties of siRNA within the intercalated environment of a <em>Mg</em>:<em>Al</em> 2:1 Layered Double Hydroxide (LDH) nanoparticle. An <em>ab initio</em> force field (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies: COMPASS) is used for the MD simulations of the hybrid organic-inorganic systems. The structure, arrangement, mobility, close contacts and hydrogen bonds associated with the intercalated RNA are examined and contrasted with those of the isolated RNA. Computed powder X-ray diffraction patterns are also compared with related LDH-DNA experiments. As a method of probing whether the intercalated environment approximates the crystalline or rather the aqueous state, we explore the stability of the principle parameters (e.g., the major groove width) that differentiate both A- and A'- crystalline forms of siRNA and contrast this with recent findings for the same siRNA simulated in water. We find the crystalline forms remain structurally distinct when intercalated, whereas this is not the case in water. Implications for the stability of hybrid LDH-RNA systems are discussed.http://www.mdpi.com/1999-4923/4/2/296layered double hydroxidemolecular dynamics simulationssiRNA deliverygene therapy |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Sean C. Smith Zhiping Xu Vinuthaa Murthy Hong Zhang Yunyi Wong Defang Ouyang |
spellingShingle |
Sean C. Smith Zhiping Xu Vinuthaa Murthy Hong Zhang Yunyi Wong Defang Ouyang Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment Pharmaceutics layered double hydroxide molecular dynamics simulations siRNA delivery gene therapy |
author_facet |
Sean C. Smith Zhiping Xu Vinuthaa Murthy Hong Zhang Yunyi Wong Defang Ouyang |
author_sort |
Sean C. Smith |
title |
Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment |
title_short |
Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment |
title_full |
Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment |
title_fullStr |
Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment |
title_full_unstemmed |
Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment |
title_sort |
hydrotalcite intercalated sirna: computational characterization of the interlayer environment |
publisher |
MDPI AG |
series |
Pharmaceutics |
issn |
1999-4923 |
publishDate |
2012-06-01 |
description |
Using molecular dynamics (MD) simulations, we explore the structural and dynamical properties of siRNA within the intercalated environment of a <em>Mg</em>:<em>Al</em> 2:1 Layered Double Hydroxide (LDH) nanoparticle. An <em>ab initio</em> force field (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies: COMPASS) is used for the MD simulations of the hybrid organic-inorganic systems. The structure, arrangement, mobility, close contacts and hydrogen bonds associated with the intercalated RNA are examined and contrasted with those of the isolated RNA. Computed powder X-ray diffraction patterns are also compared with related LDH-DNA experiments. As a method of probing whether the intercalated environment approximates the crystalline or rather the aqueous state, we explore the stability of the principle parameters (e.g., the major groove width) that differentiate both A- and A'- crystalline forms of siRNA and contrast this with recent findings for the same siRNA simulated in water. We find the crystalline forms remain structurally distinct when intercalated, whereas this is not the case in water. Implications for the stability of hybrid LDH-RNA systems are discussed. |
topic |
layered double hydroxide molecular dynamics simulations siRNA delivery gene therapy |
url |
http://www.mdpi.com/1999-4923/4/2/296 |
work_keys_str_mv |
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1725991135912919040 |