DNAzyme-seq: a single-cell metal ion and transcriptome profiling platform

Background

Metal ions such as zinc, copper, and calcium play indispensable roles in nearly every facet of cellular physiology, from enzymatic catalysis to signal trans­duction. However, conventional single-cell transcriptomics has largely over­looked the contribution of metal cofactors to gene expression, metabolism, and disease progression. With metal homeostasis increasingly implicated in cancer, neurodegenerative conditions, and immune responses, there is a growing need for tools that can provide simultaneous insight into both metal ion distributions and cellular transcriptomes at the single-cell level.
Current methods for metal ion detection, such as ICP–MS, require cell destruction and lack spatial or temporal resolution. Fluorescent probes and genetically encoded sensors often deliver only qualitative signals, suffer from off-target binding or cellular perturbation, and cannot robustly quantify intracellular ion levels. These limitations make it difficult to correlate metal ion dynamics with transcriptional activity and obscure key biological insights.

Technology overview

DNAzyme-Seq is a high-throughput platform that enables simultaneous quantification of intracellular metal ions and gene expression in single, live cells. It uses engineered, metal-specific DNAzymes—nucleic acid enzymes that cleave in response to specific metal ions—to generate cleavage products that are uniquely barcoded and sequenced along with mRNA. This dual profiling approach allows precise mapping of metal ion concentrations and their direct correlation with transcriptional programs across diverse cell populations.
Unlike traditional methods that rely on cell lysis or fluorescent dyes, DNAzyme-Seq operates in vivo, preserving spatial integrity and avoiding artifacts from sample processing. The method achieves single-base resolution through next-generation sequencing, enabling accurate cleavage detection without false positives from degradation. Inactive DNAzyme controls serve as built-in calibration tools to further enhance specificity. By integrating metal ion sensing with transcriptomic profiling in the same cell, DNAzyme-Seq offers an unprecedented view into how metal homeostasis influences cell fate, disease mechanisms, and therapeutic response.

Benefits

  • Simultaneously measures intracellular metal ions and transcriptomes in single, live cells
  • Provides quantitative, high-throughput readouts with single-base resolution
  • Avoids artifacts associated with cell lysis or external perturbation
  • Includes internal controls to distinguish specific cleavage from background degradation
  • Enables discovery of metal-regulated genes and pathways in native biological contexts

Applications

  • Single-cell transcriptomics
  • Cancer and neurodegeneration research
  • Metal homeostasis profiling
  • Drug target discovery
  • Live-cell molecular diagnostics

Opportunity

  • Fills a critical gap in single-cell omics by integrating metal sensing and mRNA profiling
  • Enables new diagnostics and biomarker discovery for metal-linked diseases
  • Compatible with existing sequencing platforms and scalable to clinical studies
  • Available for exclusive licensing

Intellectual property

PCT/US2025/028075
Patent Information:
Direct Link:
https://canberra-ip.technologypublisher.com/tech?title=DNAzyme-seq%3a_a_singl e-cell_metal_ion_and_transcriptome_profiling_platform
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For Information, Contact:
Cory Lago
Intellectual Property Specialist
University of Texas at Austin
cory.lago@austin.utexas.edu