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In silico design and enzymatic synthesis of functional RNA nanoparticles.

Afonin KA, Kasprzak WK, Bindewald E, Kireeva M, Viard M, Kashlev M, Shapiro BA - Acc. Chem. Res. (2014)

Bottom Line: CONSPECTUS: The use of RNAs as scaffolds for biomedical applications has several advantages compared with other existing nanomaterials.On the other end of the pipeline is an experimental component, which takes the produced sequences and uses them to initialize and characterize their proper assembly and then test the resulting RNA NPs for their function and delivery in cell culture and animal models.We have correlated results from molecular dynamics computations with various experiments to understand the characteristics of such delivery agents.

View Article: PubMed Central - PubMed

Affiliation: Basic Research Laboratory, Center for Cancer Research, National Cancer Institute , Frederick, Maryland 21702, United States.

ABSTRACT
CONSPECTUS: The use of RNAs as scaffolds for biomedical applications has several advantages compared with other existing nanomaterials. These include (i) programmability, (ii) precise control over folding and self-assembly, (iii) natural functionalities as exemplified by ribozymes, riboswitches, RNAi, editing, splicing, and inherent translation and transcription control mechanisms, (iv) biocompatibility, (v) relatively low immune response, and (vi) relatively low cost and ease of production. We have tapped into several of these properties and functionalities to construct RNA-based functional nanoparticles (RNA NPs). In several cases, the structural core and the functional components of the NPs are inherent in the same construct. This permits control over the spatial disposition of the components, intracellular availability, and precise stoichiometry. To enable the generation of RNA NPs, a pipeline is being developed. On one end, it encompasses the rational design and various computational schemes that promote design of the RNA-based nanoconstructs, ultimately producing a set of sequences consisting of RNA or RNA-DNA hybrids, which can assemble into the designed construct. On the other end of the pipeline is an experimental component, which takes the produced sequences and uses them to initialize and characterize their proper assembly and then test the resulting RNA NPs for their function and delivery in cell culture and animal models. An important aspect of this pipeline is the feedback that constantly occurs between the computational and the experimental parts, which synergizes the refinement of both the algorithmic methodologies and the experimental protocols. The utility of this approach is depicted by the several examples described in this Account (nanocubes, nanorings, and RNA-DNA hybrids). Of particular interest, from the computational viewpoint, is that in most cases, first a three-dimensional representation of the assembly is produced, and only then are algorithms applied to generate the sequences that will assemble into the designated three-dimensional construct. This is opposite to the usual practice of predicting RNA structures from a given sequence, that is, the RNA folding problem. To be considered is the generation of sequences that upon assembly have the proper intra- or interstrand interactions (or both). Of particular interest from the experimental point of view is the determination and characterization of the proper thermodynamic, kinetic, functionality, and delivery protocols. Assembly of RNA NPs from individual single-stranded RNAs can be accomplished by one-pot techniques under the proper thermal and buffer conditions or, potentially more interestingly, by the use of various RNA polymerases that can promote the formation of RNA NPs cotransciptionally from specifically designed DNA templates. Also of importance is the delivery of the RNA NPs to the cells of interest in vitro or in vivo. Nonmodified RNAs rapidly degrade in blood serum and have difficulties crossing biological membranes due to their negative charge. These problems can be overcome by using, for example, polycationic lipid-based carriers. Our work involves the use of bolaamphiphiles, which are amphipathic compounds with positively charged hydrophilic head groups at each end connected by a hydrophobic chain. We have correlated results from molecular dynamics computations with various experiments to understand the characteristics of such delivery agents.

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Predicted and measured dimensions of thenanocubes with 1U, 2U,and 3U single-stranded corner linkers. Adapted in part with permissionfrom ref (29). Copyright2013 Elsevier.
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fig5: Predicted and measured dimensions of thenanocubes with 1U, 2U,and 3U single-stranded corner linkers. Adapted in part with permissionfrom ref (29). Copyright2013 Elsevier.

Mentions: Because MD simulations are time-consuming,we evaluated a fasterapproach to generating potential dynamic states of nanostructuresby employing an anisotropic network model (ANM).36 An ANM represents a molecule as a network of nodes connectedby springs providing the potential energy. It can predict directionsand the relative magnitudes of the major collective motions of a structure,indicating, for example, the closure potential in the ring structuresor distortion limits of nanocages, such as our nanocubes. We recentlypresented a full modeling process for three variants of a nanocube,starting with the NanoTiler-built models, through the characterizationof the nanostructures’ flexibility with the aid of ANM simulations.29 The apparent size changes due to the distortionsof the cubes predicted by ANM brought the computational and the experimental(DLS) nanoparticle size measurements into agreement (Figure 5), suggested reasons for the measured melting temperaturedifferences for the cube variants, and offered more insight into theobserved assembly yield differences.


In silico design and enzymatic synthesis of functional RNA nanoparticles.

Afonin KA, Kasprzak WK, Bindewald E, Kireeva M, Viard M, Kashlev M, Shapiro BA - Acc. Chem. Res. (2014)

Predicted and measured dimensions of thenanocubes with 1U, 2U,and 3U single-stranded corner linkers. Adapted in part with permissionfrom ref (29). Copyright2013 Elsevier.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4066900&req=5

fig5: Predicted and measured dimensions of thenanocubes with 1U, 2U,and 3U single-stranded corner linkers. Adapted in part with permissionfrom ref (29). Copyright2013 Elsevier.
Mentions: Because MD simulations are time-consuming,we evaluated a fasterapproach to generating potential dynamic states of nanostructuresby employing an anisotropic network model (ANM).36 An ANM represents a molecule as a network of nodes connectedby springs providing the potential energy. It can predict directionsand the relative magnitudes of the major collective motions of a structure,indicating, for example, the closure potential in the ring structuresor distortion limits of nanocages, such as our nanocubes. We recentlypresented a full modeling process for three variants of a nanocube,starting with the NanoTiler-built models, through the characterizationof the nanostructures’ flexibility with the aid of ANM simulations.29 The apparent size changes due to the distortionsof the cubes predicted by ANM brought the computational and the experimental(DLS) nanoparticle size measurements into agreement (Figure 5), suggested reasons for the measured melting temperaturedifferences for the cube variants, and offered more insight into theobserved assembly yield differences.

Bottom Line: CONSPECTUS: The use of RNAs as scaffolds for biomedical applications has several advantages compared with other existing nanomaterials.On the other end of the pipeline is an experimental component, which takes the produced sequences and uses them to initialize and characterize their proper assembly and then test the resulting RNA NPs for their function and delivery in cell culture and animal models.We have correlated results from molecular dynamics computations with various experiments to understand the characteristics of such delivery agents.

View Article: PubMed Central - PubMed

Affiliation: Basic Research Laboratory, Center for Cancer Research, National Cancer Institute , Frederick, Maryland 21702, United States.

ABSTRACT
CONSPECTUS: The use of RNAs as scaffolds for biomedical applications has several advantages compared with other existing nanomaterials. These include (i) programmability, (ii) precise control over folding and self-assembly, (iii) natural functionalities as exemplified by ribozymes, riboswitches, RNAi, editing, splicing, and inherent translation and transcription control mechanisms, (iv) biocompatibility, (v) relatively low immune response, and (vi) relatively low cost and ease of production. We have tapped into several of these properties and functionalities to construct RNA-based functional nanoparticles (RNA NPs). In several cases, the structural core and the functional components of the NPs are inherent in the same construct. This permits control over the spatial disposition of the components, intracellular availability, and precise stoichiometry. To enable the generation of RNA NPs, a pipeline is being developed. On one end, it encompasses the rational design and various computational schemes that promote design of the RNA-based nanoconstructs, ultimately producing a set of sequences consisting of RNA or RNA-DNA hybrids, which can assemble into the designed construct. On the other end of the pipeline is an experimental component, which takes the produced sequences and uses them to initialize and characterize their proper assembly and then test the resulting RNA NPs for their function and delivery in cell culture and animal models. An important aspect of this pipeline is the feedback that constantly occurs between the computational and the experimental parts, which synergizes the refinement of both the algorithmic methodologies and the experimental protocols. The utility of this approach is depicted by the several examples described in this Account (nanocubes, nanorings, and RNA-DNA hybrids). Of particular interest, from the computational viewpoint, is that in most cases, first a three-dimensional representation of the assembly is produced, and only then are algorithms applied to generate the sequences that will assemble into the designated three-dimensional construct. This is opposite to the usual practice of predicting RNA structures from a given sequence, that is, the RNA folding problem. To be considered is the generation of sequences that upon assembly have the proper intra- or interstrand interactions (or both). Of particular interest from the experimental point of view is the determination and characterization of the proper thermodynamic, kinetic, functionality, and delivery protocols. Assembly of RNA NPs from individual single-stranded RNAs can be accomplished by one-pot techniques under the proper thermal and buffer conditions or, potentially more interestingly, by the use of various RNA polymerases that can promote the formation of RNA NPs cotransciptionally from specifically designed DNA templates. Also of importance is the delivery of the RNA NPs to the cells of interest in vitro or in vivo. Nonmodified RNAs rapidly degrade in blood serum and have difficulties crossing biological membranes due to their negative charge. These problems can be overcome by using, for example, polycationic lipid-based carriers. Our work involves the use of bolaamphiphiles, which are amphipathic compounds with positively charged hydrophilic head groups at each end connected by a hydrophobic chain. We have correlated results from molecular dynamics computations with various experiments to understand the characteristics of such delivery agents.

Show MeSH