Robust, specific ratiometric biosensing using a copper-free clicked quantum dot-DNA aptamer sensor

We report herein the successful preparation of a compact, functional CdSe/ZnS core/shell quantum dot (QD)-DNA conjugate via the highly efficient copper-free “click chemistry” (CFCC) between a dihydro-lipoic acid-polyethylene glycol-azide (DHLA-PEG-N3) capped QD and a cyclooctyne modified DNA. This represents an excellent balance between the requirements of high sensing sensitivity, robustness and specificity for the QD-FRET (Förster resonance energy transfer) based sensor as confirmed by a detailed FRET analysis on the QD-DNA conjugate, yielding a relatively short donor-acceptor distance of ~5.8 nm. We show not only is this CFCC clicked QD-DNA conjugate able to retain the native fluorescence quantum yield (QY) of the parent DHLA-PEG-N3 capped QD, but also is well-suited for robust, specific biosensing: it can directly quantitate pM level of both labelled and unlabelled complementary DNA probes with good SNP (single-nucleotide polymorphism) discrimination ability in complex media, e.g. 10% human serum via target-binding induced FRET changes between the QD donor and dye accepter. Further, this sensor has also been successfully exploited for the detection of pM level of a specific protein target (thrombin) via the encoded anti-thrombin aptamer sequence in the QD-DNA conjugate.