Influence of the single-strand linker composition on the structural/dynamical properties of a truncated octahedral DNA nano-cage family

Simulation-Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging

DNA-based nanodevices equipped with localized modules have been promising probes for biomarker detection. Such devices heavily rely on the intramolecular hybridization reaction. However, there is a lack of mechanistic insights into this reaction that limits the sensing speed and sensitivity. A coarse-grained model is utilized to simulate the intramolecular hybridization of localized DNA circuits (LDCs) not only optimizing the performance, but also providing mechanistic insights into the hybridization reaction. The simulation guided-LDCs enable the detection of multiple biomarkers with high sensitivity and rapid speed showing good consistency with the simulation. Fluorescence assays demonstrate that the simulation-guided LDC shows an enhanced sensitivity up to 9.3 times higher than that of the same probes without localization. The detection limits of ATP, miRNA, and APE1 reach 0.14 mM, 0.68 pM, and 0.0074 U mL^-1 , respectively. The selected LDC is operated in live cells with good success in simultaneously detecting the biomarkers and discriminating between cancer cells and normal cells. LDC is successfully applied to detect the biomarkers in cancer tissues from patients, allowing the discrimination of cancer/adjacent/normal tissues. This work herein presents a design workflow for DNA nanodevices holding great potential for expanding the applications of DNA nanotechnology in diagnostics and therapeutics.

Simulative Analysis of a Family of DNA Tetrahedrons Produced by Changing the Twisting Number of Each Double Helix

In this paper, three tetrahedral nanocages, composed of six DNA double helix edges with all having the twist number 1, 2 or 3, have been characterized using classical molecular dynamics simulation to measure the specific structural and conformational features produced by only changing the twisting number of each double helix. The simulation result indicates that three tetrahedral cages are relatively stable and are maintained along the entire trajectory. Each double helix is more inclined to behave as a whole in the 2TD and 3TD cages than in the 1TD cage according to the cross-correlation maps for three nanocages, and also their local motions are more easily induced by the conformational variability of the thymidine linkers due to the increased flexibility of each helix. Hence, the double helices become the important factors on the structural stability of total cages with the DNA twisting number, and also give the signification contributions to the sizes of these cages conferring the larger spaces of the 2TD and 3TD cages than the 1TD cage. Our result provides an insight into which roles the double helix edges play in assembling DNA polyhedron, and also contribute to improving the loading capacity of DNA tetrahedron in drug delivery.

Engineering a responsive DNA triple helix into an octahedral DNA nanostructure for a reversible opening/closing switching mechanism: a computational and experimental integrated study

We propose an experimental and simulative approach to study the effect of integrating a DNA functional device into a large-sized DNA nanostructure. We selected, as a test bed, a well-known and characterized pH-dependent clamp-switch, based on a parallel DNA triple helix, to be integrated into a truncated octahedral scaffold. We designed, simulated and experimentally characterized two different functionalized DNA nanostructures, with and without the presence of a spacer between the scaffold and the functional elements. The experimental and simulative data agree in validating the need of a spacer for the occurrence of the pH dependent switching mechanism. The system is fully reversible and the switching can be monitored several times without any perturbation, maintaining the same properties of the isolated clamp switch in solution.

Probing the Functional Topology of a pH-Dependent Triple Helix DNA Nanoswitch Family through Gaussian Accelerated MD Simulation

The topology of a pH-dependent triple helix DNA nanoswitch family has been characterized through simulative analysis to evaluate the efficiency of the switching mechanism varying the length of the loop connecting the two strands forming the double helix portion. In detail, the system is formed by a double helix made by two six base complementary sequences, connected by one loop having an increasing number of thymidines, namely 5, 7, or 9. The triplex-forming sequence made by six bases, connected to the double helix through a constant 25 base loop, interacts at pH 5.0 through Hoogsteen hydrogen bonds with one strand of the double helical region. We demonstrate, through molecular dynamics simulation, that the thymidine loop length exerts a fine regulatory role for the stability of the triple helix structure and is critical in modulating the switching mechanism triggered by the pH increase.

Simulative and Experimental Characterization of a pH-Dependent Clamp-like DNA Triple-Helix Nanoswitch

Here we couple experimental and simulative techniques to characterize the structural/dynamical behavior of a pH-triggered switching mechanism based on the formation of a parallel DNA triple helix. Fluorescent data demonstrate the ability of this structure to reversibly switch between two states upon pH changes. Two accelerated, half microsecond, MD simulations of the system having protonated or unprotonated cytosines, mimicking the pH 5.0 and 8.0 conditions, highlight the importance of the Hoogsteen interactions in stabilizing the system, finely depicting the time-dependent disruption of the hydrogen bond network. Urea-unfolding experiments and MM/GBSA calculations converge in indicating a stabilization energy at pH 5.0, 2-fold higher than that observed at pH 8.0. These results validate the pH-controlled behavior of the designed structure and suggest that simulative approaches can be successfully coupled with experimental data to characterize responsive DNA-based nanodevices.

Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model

DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs). The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis. The dynamics profiles derived from ENMs have then been evaluated and compared with previous classical molecular dynamics simulation trajectories. The results presented here revealed that ENMs can provide useful insights into the intrinsic dynamics of large DNA nanocages and represent a useful tool in the field of structural DNA nanotechnology.

Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model

We use oxDNA, a coarse-grained model of DNA at the nucleotide level, to simulate large nanoprisms that are composed of multi-arm star tiles, in which the size of bulge loops that have been incorporated into the tile design is used to control the flexibility of the tiles. The oxDNA model predicts equilibrium structures for several different nanoprism designs that are in excellent agreement with the experimental structures as measured by cryoTEM. In particular we reproduce the chiral twisting of the top and bottom faces of the nanoprisms, as the bulge sizes in these structures are varied due to the greater flexibility of larger bulges. We are also able to follow how the properties of the star tiles evolve as the prisms are assembled. Individual star tiles are very flexible, but their structures become increasingly well-defined and rigid as they are incorporated into larger assemblies. oxDNA also finds that the experimentally observed prisms are more stable than their inverted counterparts, but interestingly this preference for the arms of the tiles to bend in a given direction only emerges after they are part of larger assemblies. These results show the potential for oxDNA to provide detailed structural insight as well as to predict the properties of DNA nanostructures and hence to aid rational design in DNA nanotechnology.

A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra

A semiautomatic procedure to build complex atomistic covalently linked DNA nanocages has been implemented in a user-friendly, free, and fast program. As a test set, seven different truncated DNA polyhedra, composed by B-DNA double helices connected through short single-stranded linkers, have been generated. The atomistic structures, including a tetrahedron, a cube, an octahedron, a dodecahedron, a triangular prism, a pentagonal prism, and a hexagonal prism, have been probed through classical molecular dynamics and analyzed to evaluate their structural and dynamical properties and to highlight possible building faults. The analysis of the simulated trajectories also allows us to investigate the role of the different geometries in defining nanocages stability and flexibility. The data indicate that the cages are stable and that their structural and dynamical parameters measured along the trajectories are slightly affected by the different geometries. These results demonstrate that the constraints imposed by the covalent links induce an almost identical conformational variability independently of the three-dimensional geometry and that the program presented here is a reliable and valid tool to engineer DNA nanostructures.

The Potential of Nucleic Acid-Based Nanoparticles for Biomedical Application

The recent development of biomedical nanotechnology is providing the appropriate know-how to build novel nanocarriers/nanocapsules to be used in the pharmaceutical industry for delivery of drugs and/or therapeutic payloads to specific cells. DNA is an extremely suitable polymer for the generation of nanocapsules being biocompatible, stable and chemically modifiable. Moreover, the simple four bases mechanism allows the auto-assembly of geometrically defined systems. In this review, we describe the general properties of DNA nanocarriers, how they can be functionalized for different tasks, their interaction with cellular systems and we provide an outlook of their use in a therapeutic perspective.

Comparative simulative analysis of single and double stranded truncated octahedral DNA nanocages

Spacefill view of double (DSL) and single (SSL) stranded linkers DNA cages. The blue atoms represent the shared cages scaffold, while the yellow atoms show the single stranded DNA oligonucleotides shaping the double stranded linkers of the DSL cage.

Multiscale modelling of DNA mechanics

Mechanical properties of DNA are important not only in a wide range of biological processes but also in the emerging field of DNA nanotechnology. We review some of the recent developments in modeling these properties, emphasizing the multiscale nature of the problem. Modern atomic resolution, explicit solvent molecular dynamics simulations have contributed to our understanding of DNA fine structure and conformational polymorphism. These simulations may serve as data sources to parameterize rigid base models which themselves have undergone major development. A consistent buildup of larger entities involving multiple rigid bases enables us to describe DNA at more global scales. Free energy methods to impose large strains on DNA, as well as bead models and other approaches, are also briefly discussed.