We reported the design of the genetic regulatory network that detects proteolysis over digit -specific cleavage of the HIV-1 protease , which activates gene transcription , which may be linked to the expression of the gene of the selected effector . This method of construction of the logic circuit is designed on the basis of the identification of the essential functions of the virus , and is independent of the mutation. This principle could be used for the detection of other viral or microbial proteases as well as other essential functions and represents a good example of the application of the principle of synthetic biology .
COBISS.SI-ID: 5607450
We have described a new principle of regulation of gene transcription via cyclization TALE domains being topologically locks to the DNA or by cyclization prevent them from binding to DNA. We have shown that the absolute level of activation is significantly higher over the two-hybrid principle and reached more than 300 - fold increase in gene transcription.
COBISS.SI-ID: 5839898
Transcriptional activator-like effector (TALE)- and CRISPR/Cas9-based designable recognition domains represent a technological breakthrough not only for genome editing but also for building designed genetic circuits. Both platforms are able to target rarely occurring DNA segments, even within complex genomes. TALE and dCas9 domains, genetically fused to transcriptional regulatory domains, can be used for the construction of engineered logic circuits. Here we benchmarked the performance of the two platforms, targeting the same DNA sequences, to compare their advantages for the construction of designed circuits in mammalian cells. Optimal targeting strands for repression and activation of dCas9-based designed transcription factors were identified; both platforms exhibited good orthogonality and were used to construct functionally complete NOR gates. Although the CRISPR/dCas9 system is clearly easier to construct, TALE-based activators were significantly stronger, and the TALE-based platform performed better, especially for the construction of layered circuits.
COBISS.SI-ID: 5948442
Biological oscillators present a fundamental part of several regulatory mechanisms that control the response of various biological systems. Several analytical approaches for their analysis have been reported recently. They are, however, limited to only specific oscillator topologies and/or to giving only qualitative answers, i.e., is the dynamics of an oscillator given the parameter space oscillatory or not. Here, we present a general analytical approach that can be applied to the analysis of biological oscillators. It relies on the projection of biological systems to classical mechanics systems. The approach is able to provide us with relatively accurate results in the meaning of type of behavior system reflects (i.e., oscillatory or not) and periods of potential oscillations without the necessity to conduct expensive numerical simulations. We demonstrate and verify the proposed approach on three different implementations of amplified negative feedback oscillator.
COBISS.SI-ID: 1536851139
Bistable switches are fundamental regulatory elements of complex systems, ranging from electronics to living cells. Designed genetic toggle switches have been constructed from pairs of natural transcriptional repressors wired to inhibit one another. The complexity of the engineered regulatory circuits can be increased using orthogonal transcriptional regulators based on designed DNA-binding domains. However, a mutual repressor-based toggle switch comprising DNA-binding domains of transcription-activator-like effectors (TALEs) did not support bistability in mammalian cells. Here, the challenge of engineering a bistable switch based on monomeric DNA-binding domains is solved via the introduction of a positive feedback loop composed of activators based on the same TALE domains as their opposing repressors and competition for the same DNA operator site. This design introduces nonlinearity and results in epigenetic bistability. This principle could be used to employ other monomeric DNA-binding domains such as CRISPR for applications ranging from reprogramming cells to building digital biological memory.
COBISS.SI-ID: 5564186