Biology subjects

Jurado, Z.

Publications and source records attributed to Jurado, Z..

4 recordsLinked to original sources

bioRxiv2026

Towards interoperable modeling of toehold-mediated strand exchange circuits across DNA nanotechnology and engineering biology

Originally developed for DNA nanotechnology, toehold-mediated strand exchange (TMSE) circuits are gaining traction in synthetic biology due to their high programmability, seamless integration with biological components, and robust operation across diverse environments and cell types. However, while forward-engineering in synthetic biology has benefited from automated genetic circuit modeling pipelines, there is currently a lack of accessible, automated tools for the mechanistic modeling of TMSE circuits integrated with these systems, hindering the development of new biotechnologies. The TMSE-BioCRNpyler Library allows TMSE molecules to be transcribed RNAs or fixed-concentration nucleic acids while leveraging existing BioCRNpyler features, such as upstream transcription regulation and downstream gene regulation. We demonstrate this librarys applicability by modeling published applications of TMSE circuits spanning a wide range of applications, including simple in vitro reactions, cell-free biosensors, and in vivo microbial and mammalian systems. Additionally, we validated that models compiled using the TMSE-BioCRNpyler Library produced results with < 0.2 % relative error compared to multiple models of TMSE previously developed in the literature. Finally, to streamline interoperability with existing models, we developed txt2biocrnpyler. This accompanying tool converts chemical reaction networks from the literature into a BioCRNpyler-ready source script and a Systems Biology Markup Language XML file -- a standard data format for sharing and simulating biological models. The TMSE-BioCRNpyler Library serves as a powerful new resource for the rational, automated design of molecular information processing systems.

bioengineering↗

bioRxiv2026

Nucleotide-level chemical reaction network modeling enables quantitative prediction of reconstituted cell-free expression system

Cell-free expression systems offer a method for rapid prototyping of DNA circuits and functional protein synthesis. While crude extracts remain a black box with many components carrying out unknown reactions, PURE contains only the required transcription and translation components for protein production. All proteins and small molecules are at known concentrations, enabling detailed modeling for reliable computational predictions. However, there is little to no experimental data supporting the expression of target proteins for PURE-based models. In this work, we generalized the PURE detailed translation model for proteins with arbitrary amino acid compositions and lengths. We then built a chemical reaction network for transcription in PURE, validating the transcription models using DNA expression for the malachite-green aptamer (MGapt) to measure mRNA production. Lastly, we coupled the transcription and the generalized translation models to create a PURE protein synthesis model built purely of mass-action reactions. We used the combined model to capture the kinetics of MGapt and deGFP expressed from plasmids at varying concentrations.

synthetic biology↗

bioRxiv2024

Impact of Chemical Dynamics of Commercial PURE Systems on Malachite Green Aptamer Fluorescence

The malachite green aptamer (MGapt) is known for its utility in RNA measurement in vivo and lysate-based cell-free protein systems. However, MGapt fluorescence dynamics do not accurately reflect mRNA concentration. Our study finds that MGapt fluorescence is unstable in commercial PURE systems. We discovered that the chemical composition of the cell-free reaction strongly influences MGapt fluorescence, which leads to inaccurate RNA calculations. Specific to the commercial system, we posit that MGapt fluorescence is significantly affected by the systems chemical properties, governed notably by the presence of dithiothreitol (DTT). We propose a model that, on average, accurately predicts MGapt measurement within a 10% margin, leveraging DTT concentration as a critical factor. This model sheds light on the complex dynamics of MGapt in cell-free systems and underscores the importance of considering environmental factors in RNA measurements using aptamers.

synthetic biology↗

bioRxiv2023

A chemical reaction network model of PURE

Cell-free expression systems provide a method for rapid DNA circuit prototyping and functional protein synthesis. While crude extracts remain a black box with many components carrying out unknown reactions, the PURE system contains only the required transcription and translation components for protein production. All proteins and small molecules are at known concentrations, opening up the possibility of detailed modeling for reliable computational predictions. However, there is little to no experimental data supporting the expression of target proteins for detailed protein models PURE models. In this work, we build a chemical reaction network transcription model for PURE protein synthesis. We compare the transcription models using DNA encoding for the malachite-green aptamer (MGapt) to measure mRNA production. Furthermore, we expand the PURE detailed translation model for an arbitrary set of amino acids and length. Lastly, we combine the transcription and the expanded translation models to create a PURE protein synthesis model built purely from mass-action reactions. We use the combined model to capture the translation of a plasmid encoding MGapt and deGFP under a T7-promoter and a strong RBS. The model accurately predicts the MGapt mRNA production for the first two hours, the dynamics of deGFP expression, and the total protein production with an accuracy within 10 %.

synthetic biology↗