Pharmaceutics 2012, 4(2), 296-313; doi:10.3390/pharmaceutics4020296
Article

Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment

1 Centre for Computational Molecular Science, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Qld 4072, Brisbane, Australia 2 ARC Centre for Functional Nanomaterials, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Qld 4072, Brisbane, Australia 3 School of Life & Health Science, Aston University, Birmingham, B4 7ET, UK 4 School of Environmental and Life Sciences, Charles Darwin University, Darwin NT 0909, Australia 5 School of Chemical & Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651 6 Oak Ridge National Laboratory, Center for Nanophase Materials Sciences, Oak Ridge, TN 37831-6496, USA
* Author to whom correspondence should be addressed.
Received: 17 March 2012; in revised form: 4 June 2012 / Accepted: 4 June 2012 / Published: 7 June 2012
(This article belongs to the Special Issue Gene Therapy)
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Abstract: Using molecular dynamics (MD) simulations, we explore the structural and dynamical properties of siRNA within the intercalated environment of a Mg:Al 2:1 Layered Double Hydroxide (LDH) nanoparticle. An ab initio 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.
Keywords: layered double hydroxide; molecular dynamics simulations; siRNA delivery; gene therapy

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MDPI and ACS Style

Zhang, H.; Ouyang, D.; Murthy, V.; Wong, Y.; Xu, Z.; Smith, S.C. Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment. Pharmaceutics 2012, 4, 296-313.

AMA Style

Zhang H, Ouyang D, Murthy V, Wong Y, Xu Z, Smith SC. Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment. Pharmaceutics. 2012; 4(2):296-313.

Chicago/Turabian Style

Zhang, Hong; Ouyang, Defang; Murthy, Vinuthaa; Wong, Yunyi; Xu, Zhiping; Smith, Sean C. 2012. "Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment." Pharmaceutics 4, no. 2: 296-313.

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