A study on a special DNA nanotube assembled from two single-stranded tiles

Diverse Chiral Nanotubes Assembled from Identical DNA Strands

DNA nanotubes with controllable geometries hold a wide range of interdisciplinary applications. When preparing DNA nanotubes of varying widths or distinct chirality, existing methods require repeatedly designing and synthesizing specific DNA sequences, which can be costly and laborious. Here, we proposed an intercalator-assisted DNA tile assembly method which enables the production of DNA nanotubes of diverse widths and chirality using identical DNA strands. Through adjusting the concentration of intercalators during assembly, the twisting direction and extent of DNA tiles could be modulated, leading to the formation of DNA nanotubes featuring controllable widths and chirality. Moreover, through introducing additional intercalators and secondary annealing, right-handed nanotubes could be reconfigured into distinct left-handed nanotubes. We expect that this method could be universally applied to modulating the self-assembly pathways of various DNA tiles and other chiral materials, advancing the landscape of DNA tile assembly.

Active Self-Assembly of Ladder-Shaped DNA Carrier for Drug Delivery

With the advent of nanotechnology, DNA molecules have been transformed from solely genetic information carriers to multifunctional materials, showing a tremendous potential for drug delivery and disease diagnosis. In drug delivery systems, DNA is used as a building material to construct drug carriers through a variety of DNA self-assembly methods, which can integrate multiple functions to complete in vivo and in situ tasks. In this study, ladder-shaped drug carriers are developed for drug delivery on the basis of a DNA nanoladder. We first demonstrate the overall structure of the nanoladder, in which a nick is added into each rung of the nanoladder to endow the nanoladder with the ability to incorporate a drug loading site. The structure is designed to counteract the decrement of stability caused by the nick and investigated in different conditions to gain insight into the properties of the nicked DNA nanoladders. As a proof of concept, we fix the biotin in every other nick as a loading site and assemble the protein (streptavidin) on the loading site to demonstrate the feasibility of the drug-carrying function. The protein can be fixed stably and can be extended to different biological and chemical drugs by altering the drug loading site. We believe this design approach will be a novel addition to the toolbox of DNA nanotechnology, and it will be useful for versatile applications such as in bioimaging, biosensing, and targeted therapy.

DNA origami frame filled with two types of single-stranded tiles

DNA origami and DNA single-stranded tiles (SSTs) are two basic motifs that are widely used in fabricating DNA nanostructures. Typically, DNA origami is self-folded via a long single phage strand (scaffold strand) and this process is aided by a myriad of short oligonucleotides (staple strand). Unlike DNA origami, SSTs construct nanostructures using many unique strands connected with each other to obtain specific shapes. These motifs are material- and labour-consuming, and require multiple different synthetic oligonucleotides, and DNA SSTs tend to remain kinetically trapped in the form of tubes. In this study, we present a new strategy that combines DNA origami with DNA SSTs to construct a DNA nanostructure with a predesigned shape. A rectangular DNA origami frame with ten dozen helper strands was filled with two types of SSTs assembled repeatedly, which avoided the kinetic trap and used fewer synthetic oligonucleotides. The assembly results were identified using atomic force microscopy. The experimental analysis demonstrated the stability and feasibility of the strategy.

Solving 0-1 Integer Programming Problem Based on DNA Strand Displacement Reaction Network

Chemical reaction networks (CRNs) based on DNA strand displacement (DSD) can be used as an effective programming language for solving various mathematical problems. In this paper, we design three chemical reaction modules by using the DNA strand displacement reaction as the basic principle, with a weighted reaction module, sum reaction module, and threshold reaction module. These modules are used as basic elements to form chemical reaction networks that can be used to solve 0-1 integer programming problems. The problem can be solved through the three steps of weighting, sum, and threshold, and then the results of the operations can be expressed through a single-stranded DNA output with fluorescent molecules. Finally, we use biochemical experiments and Visual DSD simulation software to verify and evaluate the chemical reaction networks. The results have shown that the DSD-based chemical reaction networks constructed in this paper have good feasibility and stability.

Stability Based on PI Control of Three-Dimensional Chaotic Oscillatory System via DNA Chemical Reaction Networks

The classical proportional integral (PI) controller of SISO linear system is realized by DNA chemical reaction networks (CRNs) in the previous work. Up to now, few works have been done to realize PI controller of chaotic system through DNA CRNs. In this paper, a three-dimensional chaotic oscillatory system and a PI controller of three-dimensional chaotic oscillatory system are proposed by DNA CRNs. The CRNs of chaotic oscillatory system are made up of catalysis modules, degradation module and annihilation module then chemical reaction equations can be compiled into three-dimensional chaotic oscillatory system by the law of mass action to generate chaotic oscillatory signals. The CRNs of PI controller are designed by an integral module, a proportion module and an addition module, which can be compiled into PI controller for stabilizing chaotic oscillatory signals. The simulations of Matlab and Visual DSD are given to show our design achieving the PI control of a three-variable chaotic oscillatory system.

DNA Computing Model for Satisfiability Problem Based on Hybridization Chain Reaction

Satisfiability problem is a famous nondeterministic polynomial-time complete (NP-complete) problem, which has always been a hotspot in artificial intelligence. In this paper, by combining the advantages of DNA origami with hybridization chain reaction, a computing model was proposed to solve the satisfiability problem. For each clause in the given formula, a DNA origami device was devised. The device corresponding to the clause was capable of searching for assignments that satisfied the clause. When all devices completed the search in parallel, the intersection of these satisfying assignments found must satisfy all the clauses. Therefore, whether the given formula is satisfiable or not was decided. The simulation results demonstrated that the proposed computing model was feasible. Our work showed the capability of DNA origami in architecting automatic computing device. The paper proposed a novel method for designing functional nanoscale devices based on DNA origami.

Constraining DNA Sequences With a Triplet-Bases Unpaired

DNA computing, the combination of computer science and molecular biology, is a burgeoning research field that holds promise for many applications. The accuracy of DNA computing is determined by reliable DNA sequences, the quality of which affects the accuracy of hybridization reactions. Evaluating the sequences obtained from the previous combination constraints in NUPACK for simulation experiments, we find that the concentration of the sequences after entering solution was significantly lower than that before entering solution, which should affect the accuracy of DNA hybridization reactions. Therefore, in this study, we propose a new constraint, a triplet-bases unpaired constraint, which can be combined with other constraints to form a new combination constraint. In addition, we combine the Harmony Search algorithm with the Whale Optimization Algorithm (WOA) to present a new algorithm, termed HSWOA, which we used to design DNA sequences that meet the new combination constraint. Finally, compared with previous findings, our result shows that our algorithm not only improves the efficiency of hybridization reactions but also yields a better fitness value.