Small molecule-linked programmable DNA for washing-free imaging of cell surface biomarkers

Detection of specific biomarkers in cell membranes is critical for cell biology and disease theranostics. Here we develop a versatile terminal protection assay strategy for wash-free quantification and imaging of cell surface proteins using small molecule-linked DNA with programmable signal sequences. DNA probes are designed to link to a small molecule ligand at 3' end for specific recognition of the cell surface protein and a programmable signal sequence at 5' terminal for delivering detectable responses. Binding of the small molecule ligand to target protein enables protection of the DNA probes from exonuclease I mediated degradation, leaving the surface-binding probes intact while the non-binding probes degraded. This strategy thus allows wash-free detection of the cell surface protein via the selectively protected signal sequence. By programming the signal sequences as peroxidase-like DNAzyme, quantitative polymerase chain reaction (qPCR) targeting DNA and Ag nanoclusters (AgNCs) forming DNA template based on our new finding that the exonuclease I is able to quench the fluorescence of AgNCs, we can develop this strategy into a versatile platform for colorimetric detection, qPCR quantification and fluorescence imaging of the cell surface protein. This platform is demonstrated using a folate-linked DNA probe for folate receptor detection on tumor cell surface. The results revealed that this strategy enables highly selective and sensitive detection of the tumor cells as well as quantification and localization of the membrane protein on the cells, implying its potential in membrane protein based biomedical and clinical applications.