Protein, Nucleic Acid, and Nanomaterial Engineering for Biosensors and Monitoring

Abstract

The engineering of proteins, nucleic acids, and nanomaterials has significantly advanced the development of biosensors for the monitoring of rare diseases. These innovative biosensing technologies facilitate the early detection and management of conditions that often lack adequate diagnostic solutions. By utilizing engineered proteins and functional nucleic acids, such as aptamers and nucleic acid sensors, these biosensors can achieve high specificity in identifying the biomarkers associated with rare diseases. The incorporation of nanomaterials, like nanoparticles and nanosensors, enhances sensitivity and allows for the real-time monitoring of biochemical changes, which is critical for timely intervention. Moreover, integrating these technologies into wearable devices provides patients and healthcare providers with continuous monitoring capabilities, transforming the landscape of healthcare for rare diseases. The ability to detect low-abundance biomarkers in varied sample types, such as blood or saliva, can lead to breakthroughs in understanding disease pathways and personalizing treatment strategies. As the field continues to evolve, the combination of protein, nucleic acid, and nanomaterial engineering will play a crucial role in developing next-generation biosensors that are not only cost-effective but also easy to use, ultimately improving outcomes and the quality of life for individuals affected by rare diseases.

Keywords: DNA; MOF; RNA; biosensor; directed evolution; nanocomposites; rare diseases.

Figure 4

Strategy for evolving bacterial biosensor for measuring cadmium concentration. Dose-dependent response of bacterial biosensors to cadmium in E. coli strain JudeI. Reprinted from ref. [7] with permission. Copyright © 2022 American Chemical Society.

Figure 1

Biomolecular and nanomaterial engineering in the development of biosensors for monitoring.

Figure 2

A strategy for the development of a highly sensitive, PbrR-based biosensor via directed evolution and its application for lead detection. (a) The dose-dependent response of PbrR-WT WCB detected by flow cytometer. (b) The dose-dependent response of PbrR-E3 WCB detected by flow cytometer. Reprinted from ref. [2] with permission. Copyright © 2025 Elsevier B.V.

Figure 3

A schematic of the biosensor platform. (a) Biosensors for small molecules are modularly constructed by replacing the LBD with proteins possessing altered substrate preferences. (b) The activity of the biosensor can be tuned by (1) introducing destabilizing mutations (red Xs), (2) adding a degron, (3) altering the strength of the TAD or DNA binding affinity of the TF, (4) changing the number of TF-binding sites or sequences, and (5) titrating 3-aminotriazole, an inhibitor of His3. (c) Yeast provides a genetically tractable chassis for biosensor development before implementation in more complex eukaryotes, such as mammalian cells and plants. Reprinted from ref. [3]; licensed under a Creative Commons Attribution license (CC-BY).

Figure 5

Strategy for enhancing electrochemical biosensor selectivity with engineered d-amino acid oxidase enzymes for d-serine and d-alanine quantification. RgDAAO WT (A), RgDAAO M213G (B), and hDAAO W209R (C) biosensor calibration in standard solutions of 0–50 μM d-serine and d-alanine. Error bars represent ± S.E.M, (n = 3). The shaded areas represent 95% confidence interval regions. Reprinted from ref. [12] with permission. Copyright © 2022 American Chemical Society.

Figure 6

Strategy for development of colorimetric-based, whole-cell biosensor for organophosphorus compounds by engineering transcription regulator DmpR. (a) Color of liquid cultures of DmpR mutants after overnight exposure to various OP pesticides (fenitrothion, parathion, methyl-parathion, and chlorpyrifos) at concentrations of 25 and 100 μM at 30 °C at 225 rpm. (b) Induction ratios of DmpR mutants after overnight induction to 25 μM OP pesticides at 30 °C at 225 rpm. (c) Induction ratios of DmpR mutants after overnight induction to 100 μM OP pesticides at 30 °C at 225 rpm. Reprinted from ref. [25] with permission. Copyright © 2022 American Chemical Society.