S1 nuclease digestion-based rational truncation of PD-L1 aptamer and establishment of a signal dual amplification aptasensor.

A simply novel S1 nuclease digestion-based strategy was proposed to rationally truncate the PD-L1 aptamer Apt80. Based on this novel strategy, Apt38 with lower K d value and higher PD-L1 binding-associated conformational change superior to Apt80 was successfully truncation optimized. Moreover, the fabricated signal dual amplification aptasensor based on the truncated Apt38 has slighted higher detection sensitivity, wider linear range, lower detection cost and less time for detection of PD-L1 in human sample than ELISA assay. • S1 nuclease digestion-based strategy can rationally truncate PD-L1 aptamer Apt80. • S1 nuclease digestion-based strategy can directly identify the core aptamer sequence. • Truncated Apt38 had higher PD-L1 binding affinity and conformational change. • A signal dual amplification fluorescence aptasensor was fabricated based on Apt38. • The aptasensor had high sensitivity, specificity and low cost for detection of PD-L1. Truncation optimization of aptamers can improve both specificity and robustness. At present, aptamer truncation is mainly performed based on predictions from molecular docking simulations, but this usually requires tedious trial-and-error and may result in false predictions. Here, we propose a strategy based on digestion by S1 nuclease to rationally truncate the aptamer, using the PD-L1-binding aptamer Apt80 as an example. Due to steric hindrance, recognition and binding regions between Apt80 and PD-L1 are not digested by the enzyme. The truncated form, Apt38, shows higher affinity and larger conformational change after binding, when compared to Apt80. The truncated Apt38 was used as a platform for developing a signal dual amplification fluorescence aptasensor using targeted recycling assisted by exonuclease I and qRT-PCR analysis. This aptasensor exhibited a high sensitivity toward PD-L1 with a limit of detection of 0.076 ng/mL in buffer system and 0.3625 ng/mL in human serum. Owing to its high sensitivity, specificity, ease operation and low cost for detection of PD-L1, this aptasensor should be useful in assisting clinicians to evaluate the status of cancer patient and to decide whether inhibitor drugs are needed. [ABSTRACT FROM AUTHOR]