NUPACK: Analysis and Design of Nucleic Acid Structures, Devices, and Systems

Fornace, Mark E.; Huang, Jining; Newman, Cody T.; Porubsky, Nicholas J.; Pierce, Marshall B.; Pierce, Niles A.

doi:10.26434/chemrxiv-2022-xv98l

Cited by 31 publications

(31 citation statements)

References 28 publications

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“…Our design process includes validation of our sequences by comparing the predicted secondary structures from Vienna RNA 46 and NUPACK 47,48 to our designs. This, coupled with the almost entirely base‐paired nature of our designs, means that prediction of the correct base pairing arrangement (i.e., secondary structure) should be trivial and the real challenge lies in correctly predicting the topological arrangement of helical elements and subtle deviations from ideal A‐form helices.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, the motifs that are incorporated from known structures and can be generated by comparative modeling (e.g., KLs and aptamers) are often different in the context of a larger RNA and in solution than they are in isolation in a crystal structure. 45 Our design process includes validation of our sequences by comparing the predicted secondary structures from Vienna RNA 46 and NUPACK 47,48 to our designs. This, coupled with the almost entirely base-paired nature of our designs, means that prediction of the correct base pairing arrangement (i.e., secondary structure) should be trivial and the real challenge lies in correctly predicting the topological arrangement of helical elements and subtle deviations from ideal A-form helices.…”

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confidence: 99%

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RNA target highlights in CASP15: Evaluation of predicted models by structure providers

et al. 2023

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The first RNA category of the Critical Assessment of Techniques for Structure Prediction competition was only made possible because of the scientists who provided experimental structures to challenge the predictors. In this article, these scientists offer a unique and valuable analysis of both the successes and areas for improvement in the predicted models. All 10 RNA‐only targets yielded predictions topologically similar to experimentally determined structures. For one target, experimentalists were able to phase their x‐ray diffraction data by molecular replacement, showing a potential application of structure predictions for RNA structural biologists. Recommended areas for improvement include: enhancing the accuracy in local interaction predictions and increased consideration of the experimental conditions such as multimerization, structure determination method, and time along folding pathways. The prediction of RNA–protein complexes remains the most significant challenge. Finally, given the intrinsic flexibility of many RNAs, we propose the consideration of ensemble models.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

RNA target highlights in CASP15: Evaluation of predicted models by structure providers

et al. 2023

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“…SE duplex free energy relative to the single-stranded counterparts was calculated using NUPACK, assuming a temperature of 25 °C, 12.5 mM Mg 2+ , and 50 mM Na + ion concentrations. 59 For a convenient comparison between the experimental and theoretical results, we replot the theoretical morphology diagram of Figure 6 with ϵ b − ϵ a on the y-axis, as depicted in Figure 9b. Note that it is not possible to quantitatively compare the experiments to the theory since the models used are a simplified version of the experimental systems.…”

Section: Resultsmentioning

confidence: 99%

“…We summarize these findings in the morphology diagram in Figure a with dsDNA duplex free energies for the SE sequences. SE duplex free energy relative to the single-stranded counterparts was calculated using NUPACK, assuming a temperature of 25 °C, 12.5 mM Mg 2+ , and 50 mM Na + ion concentrations . For a convenient comparison between the experimental and theoretical results, we replot the theoretical morphology diagram of Figure with ϵ b – ϵ a on the y-axis, as depicted in Figure b.…”

Section: Resultsmentioning

confidence: 99%

Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions

Adhikari,

Minevich,

Redeker

et al. 2023

J. Am. Chem. Soc.

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Recent studies have demonstrated novel strategies for the organization of nanomaterials into three-dimensional (3D) ordered arrays with prescribed lattice symmetries using DNA-based self-assembly strategies. In one approach, the nanomaterial is sequestered into DNA origami frames or “material voxels” and then coordinated into ordered arrays based on the voxel geometry and the corresponding directional interactions based on its valency. While the lattice symmetry is defined by the valency of the bonds, a larger-scale morphological development is affected by assembly processes and differences in energies of anisotropic bonds. To facilely model this assembly process, we investigate the self-assembly behavior of hard particles with six interacting vertices via theory and Monte Carlo simulations and exploration of corresponding experimental systems. We demonstrate that assemblies with different 3D crystalline morphologies but the same lattice symmetry can be formed depending on the relative strength of vertex-to-vertex interactions in orthogonal directions. We observed three distinct assembly morphologies for such systems: cube-like, sheet-like, and cylinder-like. A simple analytical theory inspired by well-established ideas in the areas of protein crystallization, based on calculating the second virial coefficient of patchy hard spheres, captures the simulation results and thus represents a straightforward means of modeling this self-assembly process. To complement the theory and simulations, experimental studies were performed to investigate the assembly of octahedral DNA origami frames with varying binding energies at their vertices. X-ray scattering confirms the robustness of the formed nanoscale lattices for different binding energies, while both optical and electron microscopy imaging validated the theoretical predictions on the dependence of the distinct morphologies of assembled state on the interaction strengths in the three orthogonal directions.

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“…Table 1. Sequences were generally designed to contain relatively isoenergetic binding sites and minimal self-structure of each slat as assessed using NUPACK. , For linear growth, growth-slat sequences for v6.1 from Minev et al were used, while for scission growth, growth-slat sequences were optimized as described below. Sequences in the region coupling nuc-x to nuc-y slats were designed to minimize the slat self-structure, have relative isoenergetic binding sites, and keep GC-content within 45–50% and avoid 6-nt repeats.…”

Section: Methodsmentioning

confidence: 99%

Enzyme-Free Exponential Amplification via Growth and Scission of Crisscross Ribbons from Single-Stranded DNA Components

Ershova,

Minev,

Corea-Dilbert

et al. 2023

J. Am. Chem. Soc.

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The self-assembly of DNA-based monomers into higher-order structures has significant potential for realizing various biomimetic behaviors including algorithmic assembly, ultrasensitive detection, and self-replication. For these behaviors, it is desirable to implement high energetic barriers to undesired spurious nucleation, where such barriers can be bypassed via seed-initiated assembly. Jointneighbor capture is a mechanism enabling the construction of such barriers while allowing for algorithmic behaviors, such as bit-copying. Cycles of polymerization with division could accordingly be used for implementing exponential growth in self-replicating materials. Previously, we demonstrated crisscross polymerization, a strategy that attains robust seed-dependent self-assembly of single-stranded DNA and DNA-origami monomers via joint-neighbor capture. Here, we expand the crisscross assembly to achieve autonomous, isothermal exponential amplification of ribbons through their concurrent growth and scission via toehold-mediated strand displacement. We demonstrate how this crisscross chain reaction, or 3CR, can be used as a detection strategy through coupling to single-and double-stranded nucleic acid targets and introduce a rule-based stochastic modeling approach for simulating molecular self-assembly behaviors such as crisscross-ribbon scission.

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NUPACK: Analysis and Design of Nucleic Acid Structures, Devices, and Systems

Cited by 31 publications

References 28 publications

RNA target highlights in CASP15: Evaluation of predicted models by structure providers

RNA target highlights in CASP15: Evaluation of predicted models by structure providers

Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions

Enzyme-Free Exponential Amplification via Growth and Scission of Crisscross Ribbons from Single-Stranded DNA Components

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