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 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.

Publication DOI: https://doi.org/10.3390/pharmaceutics4020296
Divisions: College of Health & Life Sciences > Aston Pharmacy School
College of Health & Life Sciences
College of Health & Life Sciences > Chronic and Communicable Conditions
Additional Information: Creative Commons Attribution License
Uncontrolled Keywords: layered double hydroxide,molecular dynamics simulations,siRNA delivery,gene therapy,Pharmaceutical Science
Publication ISSN: 1999-4923
Last Modified: 27 Jun 2024 08:02
Date Deposited: 03 Jul 2012 11:44
Full Text Link: http://www.mdpi ... 99-4923/4/2/296
Related URLs: http://www.scop ... tnerID=8YFLogxK (Scopus URL)
PURE Output Type: Article
Published Date: 2012-06-07
Authors: Zhang, Hong
Ouyang, Defang
Murthy, Vinuthaa
Wong, Yunyi
Xu, Zhiping
Smith, Sean



Version: Published Version

License: Creative Commons Attribution

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