Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding

Simulation-Guided Rational Design of DNA Walker-Based Theranostic Platform

Biomolecule-functionalized nanoparticles represent a type of promising biomaterials in biomedical applications owing to their excellent biocompatibility and versatility. DNA-based reactions on nanoparticles have enabled emerging applications including intelligent biosensors, drug delivery, and biomimetic devices. Among the reactions, strand hybridization is the critical step to control the sensitivity and specificity of biosensing, and the efficiency of drug delivery. However, a comprehensive understanding of DNA hybridization on nanoparticles is still lacking, which may differ from the process in homogeneous solutions. To address this limitation, coarse-grained model-based molecular dynamic simulation is harnessed to disclose the critical factors involved in intermolecular hybridization. Based on simulation guidance, DNA walker-based smart theranostic platform (DWTP) based on "on-particle" hybridization is developed, showing excellent consistency with simulation. DWTP is successfully applied for highly sensitive miRNA 21 detection and tumor-specific miRNA 21 imaging, driven by tumor-endogenous APE 1 enzyme. It enables the precise release of antisense oligonucleotide triggered by tumor-endogenous dual-switch miRNA 21 and APE 1, facilitating effective gene silencing therapy with high biosafety. The simulation of "on-particle" DNA hybridization has improved the corresponding biosensing performance and the release efficiency of therapeutic agents, representing a conceptually new approach for DNA-based device design.

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.

Lattice model on the rate of DNA hybridization

We develop a lattice model on the rate of hybridization of the complementary single-stranded DNAs (c-ssDNAs). Upon translational diffusion mediated collisions, c-ssDNAs interpenetrate each other to form correct (cc), incorrect (icc), and trap correct contacts (tcc) inside the reaction volume. Correct contacts are those with exact registry matches, which leads to nucleation and zipping. Incorrect contacts are the mismatch contacts which are less stable compared to tcc, which can occur in the repetitive c-ssDNAs. Although tcc possess registry match within the repeating sequences, they are incorrect contacts in the view of the whole c-ssDNAs. The nucleation rate (k_{N}) is directly proportional to the collision rate and the average number of correct contacts (〈n_{cc}〉) formed when both c-ssDNAs interpenetrate each other. Detailed lattice model simulations suggest that 〈n_{cc}〉∝L/V where L is the length of c-ssDNAs and V is the reaction volume. Further numerical analysis revealed the scaling for the average radius of gyration of c-ssDNAs (R_{g}) with their length as R_{g}∝sqrt[L]. Since the reaction space will be approximately a sphere with radius equals to 2R_{g} and V∝L^{3/2}, one obtains k_{N}∝1/sqrt[L]. When c-ssDNAs are nonrepetitive, the overall renaturation rate becomes as k_{R}∝k_{N}L, and one finally obtains k_{R}∝sqrt[L] in line with the experimental observations. When c-ssDNAs are repetitive with a complexity of c, earlier models suggested the scaling k_{R}∝sqrt[L]/c, which breaks down at c=L. This clearly suggests the existence of at least two different pathways of renaturation in the case of repetitive c-ssDNAs, viz., via incorrect contacts and trap correct contacts. The trap correct contacts can lead to the formation of partial duplexes which can keep the complementary strands in the close proximity for a prolonged timescale. This is essential for the extended 1D slithering, inchworm movements, and internal displacement mechanisms which can accelerate the searching for the correct contacts. Clearly, the extent of slithering dynamics will be inversely proportional to the complexity. When the complexity is close to the length of c-ssDNAs, the pathway via incorrect contacts will dominate. When the complexity is much less than the length of c-ssDNA, pathway via trap correct contacts would be the dominating one.