Snap and detect: smartphone-enabled paper-based colorimetric tool for nucleic acid sequence-specific analysis

A/T-rich sequences are vital for genomic stability and gene regulation. One key motif, the TATA box, is a conserved core promoter element in eukaryotic genes, consisting of alternating adenine (A) and thymine (T) bases (TATA[A/T]). Located ∼30 base pairs upstream, it plays a crucial role in transcription and is linked to cancer and neurodegenerative diseases. However, conventional detection methods are often costly and complex, limiting accessibility. This study introduces a simple, cost-effective, and portable colorimetric paper-based assay for nucleic acid detection. Using the sequence-specific cyanine dye DiSC2(5), our method eliminates the need for surface modifications or complex labeling. The platform integrates a paper-based substrate with a 3D-printed dark chamber and smartphone-based image capture analyzed via ImageJ. The paper disk porosity enables easy sample storage and direct colorimetric analysis. TATA-containing sequences induced a blue color shift upon dye binding, with intensity correlating to target concentration. Specificity studies confirmed the assay’s ability to distinguish between alternating and random A/T sequences. Applied to synthetic polymerase chain reaction products, the smartphone-enabled tool achieved a 5.15 nM detection limit within 15 min using just 8 µl of sample. With frugal materials and simple design, this user-friendly platform enhances accessibility, sustainability, and affordability. Its rapid and portable nature makes it ideal for point-of-care diagnostics in decentralized and resource-limited settings.