FfAME - Foundation for Applied Molecular Evolution

Senior Scientist

Luran Manfio

Luran is a senior scientist at FfAME working on basic and applied research on the implementation of SAMRS in next-generation diagnostics. His research explores the application of artificial nucleotides to improve performance and access of healthcare.

Phone Number: (386) 418-8085
Experience: 5+

Research Summary

Nucleic Acid Amplification Tests (NAATs) are essential for patient diagnosis and treatment along with supporting public health surveillance. My work focuses on the development of biochemical solutions to:

Reduce barriers for medical access in low- and middle-income area
Fortify communities from disease by accelerating development and deployment of tests
Improve the overall multiplicity, turn-around-time, and specificity of NAATs
Address the need for plug-and-play tests that can add additional markers to and from existing tests to address the growing emergence and re-emergence of pathogens of interest and concern.

By leveraging the self-avoiding molecular recognition system (SAMRS), we can work to solve key biochemical problems at the core of NAATs to meet these goals and enable better patient outcomes and secure greater global health security.

Research Focus:

Infectious Disease
Nucleic acid-based technologies
Low-resource diagnostics
Public Health

Education:

BAS in Biology, University of Florida, United States (2021)

Publications

Kawabe, H., Manfio, L., Magana Pena, S., Zhou, N., Bradley, K., Chen, C., McLendon, C., Benner, S.A., Levy, K., Yang, Z., Marchand, J., Fuhrmeister, E. Synth. Bio. 14 (2) 470-484 (2025) PMC11419210, doi.org/10.1021/acssynbio.4c00619

Environmental surveillance and clinical diagnostics heavily rely on the polymerase chain reaction (PCR) for target detection. A growing list of microbial threats warrants new PCR-based detection methods that are highly sensitive, specific, and multiplexable. Here, we introduce a PCR-based icosaplex (20-plex) assay for detecting 18 enteropathogen and two antimicrobial resistance genes. This multiplexed PCR assay leverages the self-avoiding molecular recognition system (SAMRS) to avoid primer dimer formation, the artificially expanded genetic information system (AEGIS) for amplification specificity, and next-generation sequencing for amplicon identification. Using parallelized multitarget TaqMan Array Cards (TAC) to benchmark performance of the 20-plex assay on wastewater, soil, and human stool samples, we found 90% agreement on positive calls and 89% agreement on negative calls. Additionally, we show how long-read and short-read sequencing information from the 20-plex can be used to further classify allelic variants of genes and distinguish subspecies. The strategy presented offers sensitive, affordable, and robust multiplex detection that can be used to support efforts in wastewater-based epidemiology, environmental monitoring, and human/animal diagnostics.

Bang Wang, Kevin M. Bradley, Myong-Jung Kim, Roberto Laos, Cen Chen, Dietlind L. Gerloff, Luran Manfio, Zunyi Yang & Steven A. Benner Nat. Commun. 15 (4057), Nature (2024) https://doi.org/10.1038/s41467-024-48408-9

With just four building blocks, low sequence information density, few functional groups, poor control over folding, and difficulties in forming compact folds, natural DNA and RNA have been disappointing platforms from which to evolve receptors, ligands, and catalysts. Accordingly, synthetic biology has created "artificially expanded genetic information systems" (AEGIS) to add nucleotides, functionality, and information density. With the expected improvements seen in AegisBodies and AegisZymes, the task for synthetic biologists shifts to developing for expanded DNA the same analytical tools available to natural DNA. Here we report one of these, an enzyme-assisted sequencing of expanded genetic alphabet (ESEGA) method to sequence six-letter AEGIS DNA. We show how ESEGA analyses this DNA at single base resolution, and applies it to optimized conditions for six-nucleotide PCR, assessing the fidelity of various DNA polymerases, and extending this to AEGIS components with functional groups. This supports the renewed exploitation of expanded DNA alphabets in biotechnology.

All My Publications

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