Detecting and typing target DNA with a novel CRISPR-typing PCR (ctPCR) technique

Abstract

This study develops a new method for detecting and typing the interested DNAs based on CRISPR, which was named as ctPCR3.0, representing CRISPR- or Cas9/sgRNA-typing PCR, version 3.0. This technique detects target DNA in just one homogeneous step: quantitative PCR (qPCR) amplifying the Cas9/sgRNA-cleaved DNA samples. By directly adding Cas9 and sgRNA into the qPCR reaction and giving an additional isothermal incubation before qPCR program, the target DNA can be homogeneously detected in as few as 2 h. Without opening the detecting tube in the whole detection process, ctPCR3.0 can be used to detect target DNA as the traditional qPCR detection. The technique was fully verified by detecting the cloned HPV L1 genes of 10 high-risk human papillomavirus (HPV) subtypes. The technique also successfully detected the L1 and E6-E7 genes of two highest-risk HPVs, HPV16 and HPV18, in the genomic DNA of two HPV-positive cervical carcinoma cells, HeLa and SiHa. Finally, the ctPCR3.0 method was validated by successfully detecting HPVs in many clinical samples. By performing these detections, this study thus provides a new CRISPR-based DNA detection and typing platform and a ready-to-use HPV clinical detection technique. The platform has wide application in clinical diagnosis.