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Hydrotalcite intercalated siRNA: computational characterization of the interlayer environment

Zhang, Hong, Ouyang, Defang, Murthy, Vinuthaa, Wong, Yunyi, Xu, Zhiping and Smith, Sean C. (2012). Hydrotalcite intercalated siRNA: computational characterization of the interlayer environment. Pharmaceutics,4(2):296-313.

Document type: Journal Article
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IRMA ID 82057923xPUB419
Title Hydrotalcite intercalated siRNA: computational characterization of the interlayer environment
Author Zhang, Hong
Ouyang, Defang
Murthy, Vinuthaa
Wong, Yunyi
Xu, Zhiping
Smith, Sean C.
Journal Name Pharmaceutics
Publication Date 2012
Volume Number 4
Issue Number 2
ISSN 19994923   (check CDU catalogue open catalogue search in new window)
Scopus ID 2-s2.0-84863204312
Start Page 296
End Page 313
Total Pages 18
Place of Publication Switzerland
Publisher M D P I AG
HERDC Category C1 - Journal Article (DIISR)
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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