Evolution of an inhibitory RNA aptamer against T7 RNA polymerase

Highly specific aptamer trap for extremophilic RNA polymerases

During transcription initiation, the holoenzyme of bacterial RNA polymerase (RNAP) specifically recognizes promoters using a dedicated σ factor. During transcription elongation, the core enzyme of RNAP interacts with nucleic acids mainly nonspecifically, by stably locking the DNA template and RNA transcript inside the main cleft. Here, we present a synthetic DNA aptamer that is specifically recognized by both core and holoenzyme RNAPs from extremophilic bacteria of the Deinococcus-Thermus phylum. The aptamer binds RNAP with subnanomolar affinities, forming extremely stable complexes even at high ionic strength conditions, blocks RNAP interactions with the DNA template and inhibits RNAP activity during transcription elongation. We propose that the aptamer binds at a conserved site within the downstream DNA-binding cleft of RNAP and traps it in an inactive conformation. The aptamer can potentially be used for structural studies to reveal RNAP conformational states, affinity binding of RNAP and associated factors, and screening of transcriptional inhibitors.

Plasmids for Controlled and Tunable High-Level Expression in E. coli

Genetic systems for protein overexpression are required tools in microbiological and biochemical research. Ideally, these systems include standardized genetic parts with predictable behavior, enabling the construction of stable expression systems in the host organism.

Autoinhibited transient, gated, and cascaded dynamic transcription of RNAs

Following transient spatiotemporal misregulation of gene expression programs by native transcription machineries, we introduce a versatile biomimetic concept to design transient dynamic transcription machineries, revealing gated and cascaded temporal transcription of RNAs. The concept is based on the engineering of the reaction module consisting of malachite green (MG) and/or DFHBI {(5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylene]-3,5-dihydro-2,3-dimethyl-4H-imidazol-4-one} DNA scaffolds, T7 RNA polymerase (RNAP) aptamer transcription scaffold, and the inhibited T7 RNAP-aptamer complex. In the presence of the counter RNAP aptamer strand and ribonucleoside triphosphates, the triggered activation of the three transcription scaffolds are activated, leading to the transcription of the MG and/or DFHBI RNA aptamer and to the transcription of the RNAP aptamer acting as an autoinhibitor that leads to the transient temporal, dissipative, and blockage of all transcription. By appropriate design of the transcription scaffolds and the inhibitors/coupler, transient gated and cascaded transcription processes are demonstrated, and a bimodal transcription module synthesizing a transient operating ribozyme is introduced.

Lead-start isothermal polymerase amplification controlled by DNAzymatic switches

As DNA polymerases are even active at ambient temperature, there is inevitable non-specific amplification; to avoid the undesired amplification of analytes, a heat activation-based polymerase chain reaction (PCR), called hot-start PCR, is widely used to be highly precise and quantitative in detection. Unlike thermocycling amplification, isothermal amplification, compatible for point-of-care (PoC) tests, cannot be benefited by the heat-activation technique, making the method qualitative rather than quantitative. In this work, we newly developed a lead ion (Pb²⁺) activation technique, called lead-start isothermal amplification, allowing on-demand activation or deactivation of DNA polymerases at room temperature. We systematically correlated the DNA polymerase inhibition by the TQ30 aptamer with Pb²⁺-responsive strand cleavage by the GR5 DNAzyme, and relying on the type of interconnectors, Pb²⁺ successfully served as an initiator or a terminator of isothermal DNA amplification. Our lead-start isothermal amplification was exceptionally Pb²⁺-specific, dramatically increasing the enzymatic activity of DNA polymerase (>25 times) only by Pb²⁺ introduction. Despite one-by-one sample preparation, a number of reactions can begin and end at the same time, sharing the identical amplification conditions, and thereby allowing their quantitative analysis and comparison. Using a portable UV lamp and a smartphone camera, we also succeeded in quantifying the amounts of clinically important and human papillomavirus type 16 genes in human serum and SARS-CoV-2's nucleocapsid genes in human serum and saliva, and the limit of detection was as low as 0.1 nM, highly applicable for actual PoC tests in the field with no purification process.

Building an RNA-Based Toggle Switch Using Inhibitory RNA Aptamers

Synthetic RNA systems offer unique advantages such as faster response, increased specificity, and programmability compared to conventional protein-based networks. Here, we demonstrate an in vitro RNA-based toggle switch using RNA aptamers capable of inhibiting the transcriptional activity of T7 or SP6 RNA polymerases. The activities of both polymerases are monitored simultaneously by using Broccoli and malachite green light-up aptamer systems. In our toggle switch, a T7 promoter drives the expression of SP6 inhibitory aptamers, and an SP6 promoter expresses T7 inhibitory aptamers. We show that the two distinct states originating from the mutual inhibition of aptamers can be toggled by adding DNA sequences to sequester the RNA inhibitory aptamers. Finally, we assessed our RNA-based toggle switch in degrading conditions by introducing controlled degradation of RNAs using a mix of RNases. Our results demonstrate that the RNA-based toggle switch could be used as a control element for nucleic acid networks in synthetic biology applications.

Synthetic logic circuits using RNA aptamer against T7 RNA polymerase

Recent advances in nucleic acids engineering introduced several RNA-based regulatory components for synthetic gene circuits, expanding the toolsets to engineer organisms. In this work, we designed genetic circuits implementing an RNA aptamer previously described to have the capability of binding to the T7 RNA polymerase and inhibiting its activity in vitro. We first demonstrated the utility of the RNA aptamer in combination with programmable synthetic transcription networks in vitro. As a step to quickly assess the feasibility of aptamer functions in vivo, we tested the aptamer and its sequence variants in the cell-free expression system, verifying the aptamer functionality in the cell-free testbed. The expression of aptamer in E. coli demonstrated control over GFP expression driven by T7 RNA polymerase, indicating its ability to serve as building blocks for logic circuits and transcriptional cascades. This work elucidates the potential of T7 RNA polymerase aptamer as regulators for synthetic biological circuits and metabolic engineering.

Ultrasensitive molecular controllers for quasi-integral feedback

Feedback control has enabled the success of automated technologies by mitigating the effects of variability, unknown disturbances, and noise. While it is known that biological feedback loops reduce the impact of noise and help shape kinetic responses, many questions remain about how to design molecular integral controllers. Here, we propose a modular strategy to build molecular quasi-integral feedback controllers, which involves following two design principles. The first principle is to utilize an ultrasensitive response, which determines the gain of the controller and influences the steady-state error. The second is to use a tunable threshold of the ultrasensitive response, which determines the equilibrium point of the system. We describe a reaction network, named brink controller, that satisfies these conditions by combining molecular sequestration and an activation/deactivation cycle. With computational models, we examine potential biological implementations of brink controllers, and we illustrate different example applications.

Current Advances in the Development of Diagnostic Tests based on Aptamers in Parasitology: A Systematic Review

Aptamers are single-stranded DNA or RNA sequences of 20–80 nucleotides that interact with different targets such as: proteins, ions, viruses, or toxins, through non-covalent interactions and their unique three-dimensional conformation. They are obtained in vitro by the systematic evolution of ligands by exponential enrichment (SELEX). Because of their ability of target recognition with high specificity and affinity, aptamers are usually compared to antibodies. However, they present many advantages that make them promising molecules for the development of new methods for the diagnosis and treatment of human diseases. In medical parasitology, aptamers also represent an attractive alternative for the implementation of new parasite detection methods, easy to apply in endemic regions. The aim of this study was to describe the current advances in the development of diagnostic tests based on aptamers in parasitology. For this, articles were selected following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, with specific inclusion and exclusion criteria. The 26 resulting articles deal with the use of aptamers for the detection of six important protozoa that affect human health. This systematic review clearly demonstrates the specificity, sensitivity and selectivity of aptamers and aptasensors, that certainly will soon become standard methods in medical parasitology.

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.

Enzyme-Driven Assembly and Disassembly of Hybrid DNA-RNA Nanotubes

Living cells have the ability to control the dynamics of responsive assemblies such as the cytoskeleton by temporally activating and deactivating inert precursors. While DNA nanotechnology has demonstrated many synthetic supramolecular assemblies that rival biological ones in size and complexity, dynamic control of their formation is still challenging. Taking inspiration from nature, we developed a DNA-RNA nanotube system whose assembly and disassembly can be temporally controlled at physiological temperature using transcriptional programs. Nanotubes assemble when inert DNA monomers are directly and selectively activated by RNA molecules that become embedded in the structure, producing hybrid DNA-RNA assemblies. The reactions and molecular programs controlling nanotube formation are fueled by enzymes that produce or degrade RNA. We show that the speed of assembly and disassembly of the nanotubes can be controlled by tuning various reaction parameters in the transcriptional programs. We anticipate that these hybrid structures are a starting point to build integrated biological circuits and functional scaffolds inside natural and artificial cells, where RNA produced by gene networks could fuel the assembly of nucleic acid components on demand.

Promoter RNA sequencing (PRSeq) for the massive and quantitative promoter analysis in vitro

Analysis of promoter strength and specificity is important for understanding and engineering gene regulation. Here, we report an in vitro promoter analysis method that can achieve both massiveness and quantitativeness. In this approach, a pool of single-stranded DNA with a partially randomized promoter sequence to be analyzed is chemically synthesized. Through enzymatic reactions, the randomized sequence will be copied to the downstream region, resulting in a template DNA pool that carries its own promoter information on its transcribed region. After in vitro transcription of the DNA pool with an RNA polymerase of interest, the sequences of the resulting transcripts will be analyzed. Since the promoter strength linearly correlates to the copy number of transcript, the strength of each promoter sequence can be evaluated. A model experiment of T7 promoter variants demonstrated the quantitativeness of the method, and the method was applied for the analysis of the promoter of cyanophage Syn5 RNA polymerase. This method provides a powerful approach for analyzing the complexity of promoter specificity and discrimination for highly abundant and often redundant alternative sigma factors such as the extracellular function (ECF) sigma factors.

Altered stoichiometry of an evolved RNA aptamer

Inhibitory aptamers against a protein are promising as antagonistic reagents and repressive genetic components. Typically, improvement of such aptamers is achieved by acquiring higher binding affinity. Here, we report an alternative mechanism for the improvement of aptamer activity. Recently, we reported a transcriptional activator based on an inhibitory RNA aptamer against lambda cI repressor. We improved the aptamer through in vitro selection (SELEX) from a randomly mutagenized aptamer pool, followed by in vivo screening and truncation. Biochemical analyses indicated that the activity improvement was achieved by alteration of the complex formation stoichiometry, rather than by higher affinity or expression. Our results suggest an alternative strategy for improving aptamer activity.

A Robust Molecular Network Motif for Period-Doubling Devices

Life is sustained by a variety of cyclic processes such as cell division, muscle contraction, and neuron firing. The periodic signals powering these processes often direct a variety of other downstream systems, which operate at different time scales and must have the capacity to divide or multiply the period of the master clock. Period modulation is also an important challenge in synthetic molecular systems, where slow and fast components may have to be coordinated simultaneously by a single oscillator whose frequency is often difficult to tune. Circuits that can multiply the period of a clock signal (frequency dividers), such as binary counters and flip-flops, are commonly encountered in electronic systems, but design principles to obtain similar devices in biological systems are still unclear. We take inspiration from the architecture of electronic flip-flops, and we propose to build biomolecular period-doubling networks by combining a bistable switch with negative feedback modules that preprocess the circuit inputs. We identify a network motif and we show it can be "realized" using different biomolecular components; two of the realizations we propose rely on transcriptional gene networks and one on nucleic acid strand displacement systems. We examine the capacity of each realization to perform period-doubling by studying how bistability of the motif is affected by the presence of the input; for this purpose, we employ mathematical tools from algebraic geometry that provide us with valuable insights on the input/output behavior as a function of the realization parameters. We show that transcriptional network realizations operate correctly also in a stochastic regime when processing oscillations from the repressilator, a canonical synthetic in vivo oscillator. Finally, we compare the performance of different realizations in a range of realistic parameters via numerical sensitivity analysis of the period-doubling region, computed with respect to the input period and amplitude. Our mathematical and computational analysis suggests that the motif we propose is generally robust with respect to specific implementation details: functionally equivalent circuits can be built as long as the species-interaction topology is respected. This indicates that experimental construction of the circuit is possible with a variety of components within the rapidly expanding libraries available in synthetic biology.

Dynamic Control of Aptamer-Ligand Activity Using Strand Displacement Reactions

Nucleic acid aptamers are an expandable toolkit of sensors and regulators. To employ aptamer regulators within nonequilibrium molecular networks, the aptamer-ligand interactions should be tunable over time, so that functions within a given system can be activated or suppressed on demand. This is accomplished through complementary sequences to aptamers, which achieve programmable aptamer-ligand dissociation by displacing the aptamer from the ligand. We demonstrate the effectiveness of our simple approach on light-up aptamers as well as on aptamers inhibiting viral RNA polymerases, dynamically controlling the functionality of the aptamer-ligand complex. Mathematical models allow us to obtain estimates for the aptamer displacement kinetics. Our results suggest that aptamers, paired with their complement, could be used to build dynamic nucleic acid networks with direct control over a variety of aptamer-controllable enzymes and their downstream pathways.

An aptamer-based biosensor for detection of doxorubicin by electrochemical impedance spectroscopy

An aptamer-based biosensor was developed for the detection of doxorubicin using electrochemical impedance spectroscopy. Doxorubicin and its 14-dehydroxylated version daunorubicin are anthracyclines often used in cancer treatment. Due to their mutagenic and cardiotoxic effects, detection in groundwater is desirable. We developed a biosensor using the daunorubicin-binding aptamer as biological recognition element. The aptamer was successfully co-immobilized with mercaptohexanol on gold and a density of 1.3*10¹³ ± 2.4*10¹² aptamer molecules per cm² was achieved. The binding of doxorubicin to the immobilized aptamer was detected by electrochemical impedance spectroscopy. The principle is based on the inhibition of electron transfer between electrode and ferro-/ferricyanide in solution caused by the binding of doxorubicin to the immobilized aptamer. A linear relationship between the charge transfer resistance (R _ct ) and the doxorubicin concentration was obtained over the range of 31 nM to 125 nM doxorubicin, with an apparent binding constant of 64 nM and a detection limit of 28 nM. With the advantages of high sensitivity, selectivity, and simple sensor construction, this method shows a high potential of impedimetric aptasensors in environmental monitoring. Graphical abstract Measurement chamber and immobilization principle for the detection of doxorubicin by electrochemical impedance spectroscopy.

Identification of RNA aptamers against recombinant proteins with a hexa-histidine tag

Artificial riboswitches that respond to the concentrations of intracellular proteins are a promising tool with a variety of applications. They can be designed and engineered using existing RNA aptamers that target proteins. Aptamers are generated via an iterative selection-amplification process, known as systematic evolution of ligands by exponential enrichment (SELEX). This chapter describes a SELEX procedure for the identification of RNA aptamers against hexa-histidine-tagged proteins. For the efficient enrichment of higher affinity aptamers, the selection stringency should be gradually increased. Undesired RNA species that bind to affinity resins can be eliminated from the pool by using a negative selection step and alternating different types of resins.