Undergradute Researcher: Theodora Stefan - Junior Biochemistry and Pre-Medical Studies Major

Faculty Mentor: Dr. Kevin Yehl

Abstract

Purpose: The purpose of this project is to develop a DNAzyme-based array to detect and distinguish bacterial species through unique fluorescence pattern responses. By analyzing kinetic fluorescence signals and pattern-based readouts, this system will enable rapid, specific, and multiplexed bacterial detection for field applications.

Expected Outcomes: We anticipate that the DNAzyme array will produce distinct fluorescence kinetic patterns in response to different bacterial lysates. These patterns should allow for the differentiation of bacterial species and strains, demonstrating the array’s specificity and sensitivity. Additionally, unknown sample validation is expected to confirm the platform’s diagnostic potential.

Significance: This pattern-based detection method provides a low-cost, quicker alternative to traditional diagnostics. Its simplicity and adaptability make it promising for use in underprivileged areas, where access to laboratory equipment is limited. Additionally, the ability to distinguish between bacterial strains could aid in monitoring the spread of antibiotic resistance and support more targeted treatment strategies.

Background

Antibiotic Resistance

Antibiotic resistance is a growing global health crisis, with an estimated 1.27 million deaths directly attributed to resistant infections in 2019 alone and nearly 5 million associated deaths worldwide [1]. This issue disproportionately impacts low-resource settings, where diagnostic technology is often inaccessible or slow. Rapid and specific bacterial detection is essential to guide appropriate antibiotic use and limit the spread of resistance. The DNAzyme array described in this project offers a promising tool for early identification of bacterial strains without requiring culture-based methods or expensive equipment. By providing immediate, pattern-based readouts, this platform could help inform treatment decisions and reduce the misuse of broad antibiotics, contributing to global healthcare improvement.

Effects on Food and Water

Contaminated food and water are major sources of bacterial infections globally, causing an estimated 600 million cases of foodborne illness and 420,000 deaths each year, according to the World Health Organization [2]. Waterborne diseases alone account for over 485,000 deaths annually due to contaminated drinking water [3]. Quick and accurate identification of harmful bacteria is critical for preventing outbreaks and ensuring public health, particularly in under-resourced areas. The DNAzyme array platform developed in this project enables pattern-based detection of bacterial strains for a point-of-care device. Its portability and low-cost design make it ideal for field deployment in food safety testing and water quality monitoring, where access to advanced diagnostics may be limited.

Pattern-Based Detection

Pattern-based sensing mimics the olfactory system by generating unique response patterns for different analytes instead of relying on specific molecular recognition. This approach enables discrimination between related bacterial strains using a limited number of cross-reactive elements [4,5]. It is valuable for detecting unknown pathogens and testing for a high number of analytes at once. In this project, the DNAzyme array produces distinct fluorescence patterns in response to bacterial lysates, allowing for rapid identification. 

DNAzymes

DNAzymes, or deoxyribozymes, are catalytic DNA molecules capable of cleaving specific RNA or DNA substrates. They are highly stable, cost-effective, and can be easily engineered for sequence-specific recognition, making them attractive for biosensor development [6,7]. In biosensing, DNAzymes have been widely applied for detecting metal ions, nucleic acids, and pathogens by linking target recognition to signal output, such as fluorescence [8]. In this project, we developed a DNAzyme array to detect bacterial lysates, generating unique fluorescence patterns for each strain. This pattern-based sensing approach enables rapid, cost-effective, and portable detection, suitable for diagnostics and environmental monitoring.

Hypothesis

A fluorescence-based DNAzyme array will produce distinct pattern-based responses to bacterial lysates from E. coli enabling selective and accurate identification of each species based on their fingerprints. 

References

[1] World Health Organization. (2020). Antimicrobial resistance. https://www.who.int/news-room/fact-sheets/detail/antimicrobial-resistance

[2]World Health Organization. (2015). Estimates of the global burden of foodborne diseases. https://www.who.int/publications/i/item/9789241565165
[3] World Health Organization. (2019). Drinking-water. https://www.who.int/news-room/fact-sheets/detail/drinking-water

[4] You, M., Zhang, Y., Han, C., et al. (2011). Array-based sensing using nanoparticles: an alternative approach for cancer diagnostics. Nanomedicine (Lond), 10(17), 2981–2990. https://doi.org/10.2217/nnm.14.104

[5]Rotello, V. M., et al. (2002). Array-based sensing of proteins using gold nanoparticles and fluorogenic polymers. Journal of the American Chemical Society, 124(10), 2904–2905. https://doi.org/10.1021/ja017705d

[6]Silverman, S. K. (2009). Deoxyribozymes: Selection design and serendipity in the development of DNA catalysts. Accounts of Chemical Research, 42(10), 1521–1531. https://doi.org/10.1021/ar900029f

[7]Liu, J., & Lu, Y. (2007). Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. Angewandte Chemie, 119(5), 773–776. https://doi.org/10.1002/ange.200603617