Simulation-assisted Design Of Localized DNA Probe For Cancer Biomarkers Detection And Imaging

The occurrence and incidence of tumors seriously affect the life span and quality of life of the population,and the accurate early diagnosis of tumors can significantly optimize the therapeutic effect.Tumor biomarkers are molecular targets for early diagnosis.However,currently the main detection technologies usually have a single target or limited sensitivity.DNA nanostructured components,as tumor biomarker probes,have significant advantages of high confidence and high sensitivity in realizing accurate early diagnosis of tumors.However,this type of probe depends on the intramolecular chain hybridization reaction,and the mechanism of this kind of reaction is still lack of in-depth understanding,so the detection efficiency of DNA nanoprobes is limited.In this paper,a coarse-grained model was used to simulate immobilized DNA circuit’s intramolecular hybridization reaction to carry out immobilized probe design and explore its detection and imaging effects on various types of cancer-related biomarkers.Simulating-assisted MDC probes can simultaneously detect multiple biomarkers,such as adenosine triphosphate(ATP),Micro RNA(mi RNA),and Apurinic-Apyrimidinic Endonuclease I(APE1).MDC probes can realize logical gated responses of three types of biomarkers in vitro.Fluorescence analysis showed that the sensitivity of the simulation-assisted MDC was 9.3times higher than that of the non-immobilized similar probe,which was in good agreement with the simulation results.Live cell imaging results showed that the MDC probe successfully distinguished cancer cells from normal cells by detecting three tumor biomarkers simultaneously.ADC was reasonably introduced into the mi RNA detection tool and immobilized with the aid of simulation.Meanwhile,lock-in nucleic acid modification was added to the functional module to inhibit signal leakage generated by spontaneous action,further improving the detection sensitivity and accuracy.The in vitro detection results showed that the detection limit of the ADC probe with analog aided design was 29 times lower than that of the same type of probe with irrational design.Cell detection showed that the combination of fluorescently labeled ADC probes could simultaneously detect and distinguish different intracellular mi RNAs.The results of this paper show that the MDC and ADC probes designed with the aid of simulation optimize the actual detection and imaging performance of DNA nanoprobes for tumor biomarkers,and obtain a good agreement with the simulation results.In addition,this study has improved the understanding of the mechanism of intramolecular hybridization.