About

Andrej Lupták, Ph.D., is a researcher leading a team at the Lupták Lab focused on molecular biology and biochemistry. His research involves exploring the molecular mechanisms underlying biological processes, with a particular emphasis on pharmaceutical sciences. As a faculty member at the University of California, Irvine, he oversees a diverse team of postdoctoral researchers, Ph.D. candidates, and students, all engaged in advancing scientific understanding in these fields. His work contributes to the broader scientific community by investigating fundamental biological questions and developing insights that may inform pharmaceutical and biomedical research.

Research topics

• Biology
• Cell biology
• Biochemistry
• Chemistry
• Molecular biology
• Computational biology
• Biophysics
• Nanotechnology
• Genetics
• Materials science
• Physics
• Ecology

Selected publications

• Bioluminescent Probes for Multiplexed RNA Imaging

  Journal of the American Chemical Society · 2026-03-10

  articleOpen accessSenior authorCorresponding

  A comprehensive understanding of RNA biology requires methods to visualize transcripts and their interactions within physiological environments. However, few technologies can report on multiple RNAs continuously and in living systems. We are addressing this void with bioluminescent probes. Bioluminescence does not require excitation light and can enable sensitive, noninvasive readouts in a variety of settings. Here, we report a panel of structured RNA tags and luciferase fragments (RNA lanterns) for multiplexed RNA detection. The lanterns emit few photons on their own but assemble and emit light when brought into proximity by the RNA tags. Three orthogonal tag-lantern combinations were designed based on known RNA-binding proteins that recognize distinct targets. The probes were optimized in vitro for selective transcript detection. We further applied the tags and lanterns in cultured cells, achieving multitarget imaging with good subcellular resolution. Collectively, the probes expand the toolkit for RNA imaging and will facilitate efforts to trace RNA targets in living systems.

  PublisherDOI

• An Open, Integrated Platform for Multiplexed Bioluminescence Microscopy

  Chemical & Biomedical Imaging · 2025-08-22 · 1 citations

  preprintOpen access

  We report an imaging package to democratize all-in-one bioluminescence and fluorescence microscopy. The platform comprises three tools: PhasorViewer, a visualization suite to design experiments and identify optimal probe combinations; PhasorScope, an open-source, cost-effective microscopy framework to upgrade conventional microscopes; and PhasorAnalysis, a dedicated, user-friendly analysis pipeline to quantify phasor imaging data. We demonstrate the utility of the platform for multiplexed, simultaneous fluorescence and bioluminescence imaging with readily accessible optical reporters.

  PublisherDOI

• Response to Letter Regarding “Accurate Detection of Cerebrospinal Fluid by DNA Aptamers Derived by Clinical Samples”

  International Forum of Allergy & Rhinology · 2025-08-18

  letter

  The basis for this work was supported in part by the UCI Institute for Clinical and Translational Science, International Society of Inflammation and Allergy of the Nose, North American Skull Base Society, UCI School of Medicine, and the American Rhinologic Society (all to ECK). The other authors report no disclosures.

  PublisherDOI

• Rapid discovery of functional RNA domains

  Nucleic Acids Research · 2025-04-10 · 2 citations

  articleOpen accessSenior author

  Many strategies have been implemented to enrich an RNA population for a selectable function, but demarcation of the optimal functional motifs or minimal structures within longer libraries remains a lengthy and tedious process. To overcome this problem, we have developed a technique that isolates minimal active segments from complex heterogeneous pools of RNAs. This method allows for truncations to occur at both 5' and 3' ends of functional domains and introduces independent primer-binding sequences, thereby removing sequence and structure bias introduced by constant-sequence regions. We show examples of minimization for genomic and synthetic aptamers and demonstrate that the method can directly reveal an active RNA assembled from multiple strands, facilitating the development of heterodimeric structures used in cellular sensors. This approach provides a pipeline to experimentally define the boundaries of active domains and accelerate the discovery of functional RNAs.

  PublisherDOI

• Electrochemical aptamer-based sensor for cerebrospinal fluid detection

  Analytical Methods · 2025-01-01

  article

  , meningitis). Current diagnostic methods rely on immunofixation electrophoresis or nephelometry for detecting beta-2 transferrin or beta-trace protein, respectively, but these techniques are time-consuming, require specialized laboratory equipment, and may yield false-negative results due to sample contamination. To address these limitations, we developed a novel electrochemical aptamer-based (E-AB) biosensor for rapid, sensitive, and point-of-care detection of CSF leaks. The biosensor provides a conformation-switching aptamer system, building on our prior work through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX), to enable a "switch-off" mechanism upon target binding. This electrochemical transduction strategy facilitates reagent-free, real-time detection with a response time as short as 20 minutes. The sensor was optimized through square wave voltammetry (SWV) to achieve high specificity and signal suppression in CSF samples. Notably, the E-AB sensor demonstrated significant differentiation between CSF and serum, minimizing interference from blood contamination - a common issue in clinical sample collection. By streamlining the transition from aptamer discovery to biosensor development, this platform not only enhances the diagnostic workflow for CSF leaks but also establishes a versatile framework for future biosensing applications in neurology and emergency medicine. Further optimization and adaptation to portable electrochemical systems could position this technology as a clinically viable, point-of-care diagnostic tool for rapid CSF leak detection.

  PublisherDOI

• Accurate Detection of Cerebrospinal Fluid by DNA Aptamers Derived by Clinical Samples

  International Forum of Allergy & Rhinology · 2025-06-24 · 2 citations

  articleOpen access

  KEY POINTS: Novel DNA aptamers CSF-APT-1 and CSF-APT-2 accurately detected cerebrospinal fluid (CSF) in 19 patient samples. Sequencing confirmed CSF-APT-1 and CSF-APT-2 as superior CSF detection probes over other candidates from the same in vitro selection. Use of CSF-APT-1 and CSF-APT-2, which are specific to CSF, may offer improvements in speed and accuracy compared to current CSF diagnostics.

  PublisherOA PDFDOI

• Discovery of a Novel Cerebrospinal Fluid-Specific DNA Aptamer

  Journal of Neurological Surgery Part B Skull Base · 2025-02-01

  article
  PublisherDOI

• Inhibition of Cpeb3 ribozyme elevates CPEB3 protein expression and polyadenylation of its target mRNAs and enhances object location memory

  eLife · 2024-02-06 · 8 citations

  articleOpen accessSenior author

  A self-cleaving ribozyme that maps to an intron of the cytoplasmic polyadenylation element-binding protein 3 ( Cpeb3 ) gene is thought to play a role in human episodic memory, but the underlying mechanisms mediating this effect are not known. We tested the activity of the murine sequence and found that the ribozyme’s self-scission half-life matches the time it takes an RNA polymerase to reach the immediate downstream exon, suggesting that the ribozyme-dependent intron cleavage is tuned to co-transcriptional splicing of the Cpeb3 mRNA. Our studies also reveal that the murine ribozyme modulates maturation of its harboring mRNA in both cultured cortical neurons and the hippocampus: inhibition of the ribozyme using an antisense oligonucleotide leads to increased CPEB3 protein expression, which enhances polyadenylation and translation of localized plasticity-related target mRNAs, and subsequently strengthens hippocampal-dependent long-term memory. These findings reveal a previously unknown role for self-cleaving ribozyme activity in regulating experience-induced co-transcriptional and local translational processes required for learning and memory.

  PublisherDOI

• Multimodal diagnosis of cerebrospinal fluid rhinorrhea: State of the art review and emerging concepts

  Laryngoscope Investigative Otolaryngology · 2024-05-27 · 7 citations

  articleOpen access

  Objective: Currently, diagnosis of cerebrospinal fluid (CSF) rhinorrhea relies on a multimodal approach, increasing costs and ultimately delaying diagnosis. In the United States and internationally, the crux of such a diagnosis relies on confirmation testing (via biomarkers) and localization (e.g., imaging). Biomarker testing may require analysis at an outside facility, resulting in delays diagnosis and treatment. In addition, specialized imaging may be nonspecific and often requires an active leak for diagnosis. There remains a clear need for innovative new technology. Methods: A comprehensive review was conducted on both foundational and innovative scholarly articles regarding current and emerging diagnosis modalities for CSF. Results: Current modalities in CSF rhinorrhea diagnosis and localization include laboratory tests (namely, B2T immunofixation), imaging (CT and/or MRI) with or without intrathecal administration, and surgical exploration. Each of these modalities carry flaws, risks, and benefits, ultimately contributing to delays in diagnosis and morbidity. Promising emerging technologies include lateral flow immunoassays (LFI) and biologically functionalized field-effect transistors (BioFET). Nevertheless, these carry some drawbacks of their own, and require further validation. Conclusion: CSF rhinorrhea remains a challenging diagnosis, requiring a multimodal approach to differentiate from nonpathologic causes of rhinorrhea. Current methods in diagnosis are imperfect, as the ideal test would be a readily accessible, inexpensive, rapid, highly accurate point-of-care test without the need for excess fluid or specialized processing. Critical work is being done to develop promising, new, improved tests, though a clear successor has not yet emerged. Level of Evidence: N/A.

  PublisherOA PDFDOI

• Engineering a ribozyme with aminoacyl-tRNA synthetase activity

  bioRxiv (Cold Spring Harbor Laboratory) · 2024

  • Chemistry
  • Computational biology
  • Biochemistry

  A ribozyme that can charge a tRNA with amino acids and discriminate between cognate and non-cognate tRNAs is of interest because an RNA with this ability may have been a critical for translation in the transition from the RNA world. In addition, it could provide a tool for incorporating non-canonical amino acids for biotechnology applications. Here, we rationally engineer a ribozyme by fusing a tRNA binding module derived from a T-box riboswitch with a catalytic module (a flexizyme) to generate a ribozyme that can amino acylate a target tRNA. We demonstrate that this ribozyme be readily redesigned to alter tRNA specificity. This ribozyme is compatible with an in vitro translation system and could be used to recode a protein sequence to site-specifically incorporate a non-canonical amino acid.

  PublisherOA PDFDOI

Recent grants

• RNA photonics: Light-responsive RNAs for precise manipulation of the transcriptome

  NSF · $400k · 2018–2021

• NIH Grant R01GM094929

  NIH · $1.2M · 2014

• Aptamers in model organisms

  NSF · $510k · 2013–2017

Frequent coauthors

• Jack W. Szostak

  18 shared

• Luiz F. M. Passalacqua

  California Lutheran University

  12 shared

• Nathan Riccitelli

  10 shared

• Alexander Litovchick

  9 shared

• Kourosh Salehi‐Ashtiani

  New York University Abu Dhabi

  9 shared

• Elise Digga

  Brigham and Women's Hospital

  8 shared

• Benjamin A. Teply

  University of Nebraska Medical Center

  8 shared

• Randi M. Jimenez

  University of California, Irvine

  8 shared

Labs

• Lupták LabPI

Education

• Ph.D., Biophysical Chemistry

  Yale University

  2002

• M.S., Chemistry

  University of Pennsylvania

  1996

• B.A., Biochemistry and Biophysics

  University of Pennsylvania

  1996

Awards & honors

• Benjamin Franklin Scholar (1992-1996)
• Pew Scholar (2010)
• Guggenheim Fellow (2020)
• W. M.. Keck Foundation grantee (2021)
• Chancellor's Fellow (2024)