Taqman-MGB nanoPCR for Highly Specific Detection of Single-Base Mutations

Abstract

Zhenrui Xue,1– 3,* Minli You,2,3,* Ping Peng,1– 3,* Haoyang Tong,2,3 Wanghong He,2– 4 Ang Li,4 Ping Mao,1– 3 Ting Xu,1 Feng Xu,2,3 Chunyan Yao1 1Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Army Medical University, Chongqing, 400038, People’s Republic of China; 2The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China; 3Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China; 4Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China*These authors contributed equally to this workCorrespondence: Chunyan Yao; Feng XuDepartment of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Army Medical University, Chongqing, 400038, People’s Republic of ChinaTel [phone]Email [email protected]; [email protected]: Detection of single-base mutations is important for real-time monitoring of tumor progression, therapeutic effects, and drug resistance. However, the specific detection of single-base mutations from excessive wild-type background sequences with routine PCR technology remains challenging. Our objective is to develop a simple and highly specific qPCR-based single-base mutation detection method.Methods: Using EGRF T790M as a model, gold nanoparticles at different concentrations were separately added into the Taqman-MGB qPCR system to test specificity improvement, leading to the development of the optimal Taqman-MGB nanoPCR system. Then, these optimal conditions were used to test the range of improvement in the specificity of mutant-type and wild-type templates and the detection limit of mutation abundances in a spiked sample.Results: The Taqman-MGB nanoPCR was established based on the traditional qPCR, with significantly suppressed background noise and improved specificity for single-base mutation detection. With EGFR T790M as a template, we demonstrated that our Taqman-MGB nanoPCR system could improve specificity across a wide concentration range from 10− 9 μM to 10 μM and detect as low as 0.95% mutation abundance in spiked samples, which is lower than what the traditional Taqman-MGB qPCR and existing PCR methods can detect. Moreover, we also proposed an experimentally validated barrier hypothesis for the mechanism of improved specificity.Conclusion: The developed Taqman-MGB nanoPCR system could be a powerful tool for clinical single-base mutation detection.Keywords: nanoparticle-assisted PCR, point mutation, gold nanoparticle, specificity

Keywords

• nanoparticle-assisted pcr
• point mutation
• gold nanoparticle
• specificity