Aptamer-based regulation of transcription circuits

Using CIVT-SELEX to Select Aptamers as Genetic Parts to Regulate Gene Circuits in a Cell-Free System

The complexity of genetic circuits has not seen a significant increase over the last decades, even with the rapid development of synthetic biology tools. One of the bottlenecks is the limited number of orthogonal transcription factor-operator pairs. Researchers have tried to use aptamer-ligand pairs as genetic parts to regulate transcription. However, most aptamers selected using traditional methods cannot be directly applied in gene circuits for transcriptional regulation. To that end, we report a new method called CIVT-SELEX to select DNA aptamers that can not only bind to macromolecule ligands but also undergo significant conformational changes, thus affecting transcription. The single-stranded DNA library with affinity to our example ligand human thrombin protein is first selected and enriched. Then, these ssDNAs are inserted into a genetic circuit and tested in the in vitro transcription screening to obtain the ones with significant inhibitory effects on downstream gene transcription when thrombins are present. These aptamer-thrombin pairs can inhibit the transcription of downstream genes, demonstrating the feasibility and robustness of their use as genetic parts in both linear DNAs and plasmids. We believe that this method can be applied to select aptamers of any target ligands and vastly expand the genetic part library for transcriptional regulation.

A mass-tagged MOF nanoprobe approach for ultra-sensitive protein quantification in tumor-educated platelets

A mass-tagged metal-organic framework (MOF) nanoprobe approach was developed for ultra-sensitive quantification of platelet protein CD44 by integrating activable aptamer recognition and MOF nanoprobe signal amplification with mass spectrometric detection. This approach offered high sensitivity and quantitative capability for low abundant protein analysis in tumor-educated platelets (TEPs), exhibiting great potential in cancer diagnosis and management.

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.

A strategy for programming the regulation of in vitro transcription with application in molecular circuits

In vitro transcription is a convenient platform for fabricating nanodevices and has been used for assembling synthetic networks. However, it remains challenging to regulate synthetic cell-free in vitro transcription by multiple stimuli in a simple and programmable way. We proposed a strategy to regulate in vitro transcription by controlling the transcription templates' promoter domain via variable DNA inputs. To demonstrate the utility of this strategy, various logic circuits and cascading circuits were implemented. With the advantage of simplicity, modularity, programmability, and extensibility, the proposed strategy has potential in biocomputing, bioanalytical, and therapeutic applications.

Translational control of enzyme scavenger expression with toxin-induced micro RNA switches

Biological computation requires in vivo control of molecular behavior to progress development of autonomous devices. miRNA switches represent excellent, easily engineerable synthetic biology tools to achieve user-defined gene regulation. Here we present the construction of a synthetic network to implement detoxification functionality. We employed a modular design strategy by engineering toxin-induced control of an enzyme scavenger. Our miRNA switch results show moderate synthetic expression control over a biologically active detoxification enzyme molecule, using an established design protocol. However, following a new design approach, we demonstrated an evolutionarily designed miRNA switch to more effectively activate enzyme activity than synthetically designed versions, allowing markedly improved extrinsic user-defined control with a toxin as inducer. Our straightforward new design approach is simple to implement and uses easily accessible web-based databases and prediction tools. The ability to exert control of toxicity demonstrates potential for modular detoxification systems that provide a pathway to new therapeutic and biocomputing applications.

Monodirectional Tissue P Systems With Promoters

Tissue P systems with promoters provide nondeterministic parallel bioinspired devices that evolve by the interchange of objects between regions, determined by the existence of some special objects called promoters. However, in cellular biology, the movement of molecules across a membrane is transported from high to low concentration. Inspired by this biological fact, in this article, an interesting type of tissue P systems, called monodirectional tissue P systems with promoters, where communication happens between two regions only in one direction, is considered. Results show that finite sets of numbers are produced by such P systems with one cell, using any length of symport rules or with any number of cells, using a maximal length 1 of symport rules, and working in the maximally parallel mode. Monodirectional tissue P systems are Turing universal with two cells, a maximal length 2, and at most one promoter for each symport rule, and working in the maximally parallel mode or with three cells, a maximal length 1, and at most one promoter for each symport rule, and working in the flat maximally parallel mode. We also prove that monodirectional tissue P systems with two cells, a maximal length 1, and at most one promoter for each symport rule (under certain restrictive conditions) working in the flat maximally parallel mode characterizes regular sets of natural numbers. Besides, the computational efficiency of monodirectional tissue P systems with promoters is analyzed when cell division rules are incorporated. Different uniform solutions to the Boolean satisfiability problem (SAT problem) are provided. These results show that with the restrictive condition of "monodirectionality," monodirectional tissue P systems with promoters are still computationally powerful. With the powerful computational power, developing membrane algorithms for monodirectional tissue P systems with promoters is potentially exploitable.

Switching the activity of Taq polymerase using clamp-like triplex aptamer structure

In nature, allostery is the principal approach for regulating cellular processes and pathways. Inspired by nature, structure-switching aptamer-based nanodevices are widely used in artificial biotechnologies. However, the canonical aptamer structures in the nanodevices usually adopt a duplex form, which limits the flexibility and controllability. Here, a new regulating strategy based on a clamp-like triplex aptamer structure (CLTAS) was proposed for switching DNA polymerase activity via conformational changes. It was demonstrated that the polymerase activity could be regulated by either adjusting structure parameters or dynamic reactions including strand displacement or enzymatic digestion. Compared with the duplex aptamer structure, the CLTAS possesses programmability, excellent affinity and high discrimination efficiency. The CLTAS was successfully applied to distinguish single-base mismatches. The strategy expands the application scope of triplex structures and shows potential in biosensing and programmable nanomachines.

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.

Nucleic Acid Aptamers for Molecular Diagnostics and Therapeutics: Advances and Perspectives

The advent of SELEX (systematic evolution of ligands by exponential enrichment) technology has shown the ability to evolve artificial ligands with affinity and specificity able to meet growing clinical demand for probes that can, for example, distinguish between the target leukemia cells and other cancer cells within the matrix of heterogeneity, which characterizes cancer cells. Though antibodies are the conventional and ideal choice as a molecular recognition tool for many applications, aptamers complement the use of antibodies due to many unique advantages, such as small size, low cost, and facile chemical modification. This Minireview will focus on the novel applications of aptamers and SELEX, as well as opportunities to develop molecular tools able to meet future clinical needs in biomedicine.

NIR Remote-Controlled "Lock-Unlock" Nanosystem for Imaging Potassium Ions in Living Cells

Despite great achievements in sensitive and selective detection of important biomolecules in living cells, it is still challenging to develop smart and controllable sensing nanodevices for cellular studies that can be activated at desired time in target sites. To address this issue, we have constructed a remote-controlled "lock-unlock" nanosystem for visual analysis of endogenous potassium ions (K⁺), which employed a dual-stranded aptamer precursor (DSAP) as recognition molecules, SiO₂ based gold nanoshells (AuNS) as nanocarriers, and near-infrared ray (NIR) as the remotely applied stimulus. With the well-designed and activatable DSAP-AuNS, the deficiencies of traditional aptamer-based sensors have been successfully overcome, and the undesired response during transport has been avoided, especially in complex physiological microenvironments. While triggered by NIR, the increased local temperature of AuNS induced the dehybridiztion of DSAP, realized the "lock-unlock" switch of the DSAP-AuNS nanosystem, activated the binding capability of aptamer, and then monitored intracellular K⁺ via the change of fluorescence signal. This DSAP-AuNS nanosystem not only allows us to visualize endogenous ions in living cells at a desired time but also paves the way for fabricating temporal controllable nanodevices for cellular studies.

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.