Microenvironment‐Guided Evolution of ssDNA‐SWCNT Probes for Selective Recognition of Aggressive Prostate Cancer Phenotypes

ABSTRACT Despite advances in prostate cancer detection, distinguishing indolent from aggressive phenotypes remains challenging. We report a microenvironment‐guided strategy for evolving phenotype‐specific molecular probes using single‐stranded DNA‐functionalized single‐walled carbon nanotubes (ssDNA‐SWCNTs). Our approach employs 3D tumor models that recapitulate complex cancer microenvironments, enabling identification of ssDNA sequences with differential binding properties. We developed two distinct probes for prostate cancer cells: PC3D2, which preferentially binds hypoxia‐adapted stem‐like cells associated with treatment resistance, and PC2D2, which shows enhanced binding to mesenchymal‐like cells. These probes exhibit characteristic second near‐infrared (NIR‐II, 1000‐1700 nm) fluorescence, enabling non‐invasive detection of aggressive phenotypes in heterogeneous tumors using NIR‐II optical imaging. We demonstrate their utility for selective drug delivery to prostate cancer spheroids, resulting in enhanced therapeutic efficacy. This platform represents a significant advancement in precision diagnostics and theranostics, potentially transforming prostate cancer management through phenotype‐specific targeting. The methodology offers a generalizable approach for developing nanoprobes that recognize clinically relevant cancer phenotypes based on their unique microenvironmental signatures rather than individual biomarkers.