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Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment.

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.

SUBMITTER: Zhang H

PROVIDER: S-EPMC3834912 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature

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Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment.

Zhang Hong H Ouyang Defang D Murthy Vinuthaa V Wong Yunyi Y Xu Zhiping Z Smith Sean C SC

Pharmaceutics 20120607 2

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 ...[more]

PMID: 24300233

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Project description:BackgroundSmall interfering RNAs (siRNAs) have become an important tool in cell and molecular biology. Reliable design of siRNA molecules is essential for the needs of large functional genomics projects.ResultsTo improve the design of efficient siRNA molecules, we performed a comparative, thermodynamic and correlation analysis on a heterogeneous set of 653 siRNAs collected from the literature. We used this training set to select siRNA features and optimize computational models. We identified 18 parameters that correlate significantly with silencing efficiency. Some of these parameters characterize only the siRNA sequence, while others involve the whole mRNA. Most importantly, we derived an siRNA position-dependent consensus, and optimized the free-energy difference of the 5' and 3' terminal dinucleotides of the siRNA antisense strand. The position-dependent consensus is based on correlation and t-test analyses of the training set, and accounts for both significantly preferred and avoided nucleotides in all sequence positions. On the training set, the two parameters' correlation with silencing efficiency was 0.5 and 0.36, respectively. Among other features, a dinucleotide content index and the frequency of potential targets for siRNA in the mRNA added predictive power to our model (R = 0.55). We showed that our model is effective for predicting the efficiency of siRNAs at different concentrations. We optimized a neural network model on our training set using three parameters characterizing the siRNA sequence, and predicted efficiencies for the test siRNA dataset recently published by Novartis. On this validation set, the correlation coefficient between predicted and observed efficiency was 0.75. Using the same model, we performed a transcriptome-wide analysis of optimal siRNA targets for 22,600 human mRNAs.ConclusionWe demonstrated that the properties of the siRNAs themselves are essential for efficient RNA interference. The 5' ends of antisense strands of efficient siRNAs are U-rich and possess a content similarity to the pyrimidine-rich oligonucleotides interacting with the polypurine RNA tracks that are recognized by RNase H. The advantage of our method over similar methods is the small number of parameters. As a result, our method requires a much smaller training set to produce consistent results. Other mRNA features, though expensive to compute, can slightly improve our model.

Project description:A Na-smectite clay (Na-SWy-2) was exchanged with various amounts of dimethyldioctadecylammonium bromide (DODA-Br) up to twice the cation exchange capacity (CEC). The organoclay (DODA-SWy-2) with DODA-Br added at 2 × CEC exhibited a maximum 4.2 nm d-spacing and a 31.4% carbon content, which demonstrates DODA(+) intercalation. DODA-SWy-2 was evaluated as an archetype of commercial products used to sequester hydrophobic contaminants, and the nature of the primarily C18 alkylhydrocarbon-chain interlayer environment was emhasized. Shifts in ?(CH) and CH(2) rocking band positions in DODA-SWy-2-complex FTIR-spectra indicate that DODA C18 chains were more ordered as DODA surface coverage was increased. Differential scanning calorimetry analysis indicated a DODA-SWy-2 gel-to-liquid transition temperature much lower than the melting point of crystalline DODA-Br and similar to that of aqueous DODA-Br vesicles. This suggests that the transition was governed by C18 alkyl tail-tail interactions in the clay interlamellar region. Dibenzo-p-dioxin (DD) sorption from water by DODA-SWy-2 was compared to DD sorption by the geosorbents granular activated carbon (GAC), K-exchanged saponite, and a muck soil. The linear K(l) sorption coefficients (log K(l)) from a linear fit of the sorption isotherms were 4.37 for DODA-SWy-2, 5.55 for GAC, 3.19 for muck soil, and 2.46 for K-saponite. The DD-organic-matter-normalized sorption coefficient (K(om)) was ?2.4 times the octanol-water partition coefficient (K(ow)). This indicates that DD has a higher affinity for the nonpolar interlayer DODA organic phase than for octanol. In contrast, the K(om) for muck soil DD sorption was ~10 times less than K(ow), which reflects the higher polarity of amorphous soil organic matter relative to octanol. Enhanced DD uptake by the DODA-derived lipophilic phase in the organoclay is attributed to the low polarity, "open" C18 alkyl structure due to the physical dimensions of "v-shaped" DODA(+) molecular, and low density of the interlamellar phase (~0.50 g/cm3) density of intercalated DODA(+).

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Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment.

Publications

Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment.

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