Amplification-free in situ KRAS point mutation detection at 60 copies per mL in urine in a background of 1000-fold wild type

An exonuclease III-amplified 4-way strand migration system for low-abundance deletion mutation

A 4-way strand exchange competitive DNA testing system based on Holliday junction has an advantage in realizing high sensitivity and specificity simultaneously. However, the kinetics is limited without enzyme assisting. Herein, we constructed a method that combined a 4-way strand migration system and exonuclease III (Exo III). For the properties of Exo III that has high catalytic effects and no specific recognition site, a DNA probe assisted by Exo III is easy to design and synthesize. We applied the system to detect different lengths of deletion mutation, and the results showed that the time to differentiate wild-type DNA and mutant-type DNA was so short within 5-20 min. Besides, the discrimination factor (DF) was as high as 1177.88 for EGFR-15-nt deletion, and the mutation detection limit was as low as 0.02% for PBRM1-8-nt deletion. Without adding any other specific label, the Exo III-amplified 4-way strand migration system is a simple, sensitive, selective, and cost-effective method that suggests a potential possibility for the diagnosis of cancers.

Installing CRISPR-Cas12a sensors in a portable glucose meter for point-of-care detection of analytes

Integrating CRISPR-Cas12a sensors with a portable glucose meter (PGM) was developed based on the target-induced activation of the collateral cleavage activity of Cas12a. Considering the portability, low cost and facile incorporation of the PGM system with suitable Cas12a sensors to recognize many targets, the CRISPR/Cas12a-PGM system demonstrated here paves a way to further broaden the POC applications of CRISPR-based diagnostics.

Developing a Low-Cost, Simple-to-Use Electrochemical Sensor for the Detection of Circulating Tumour DNA in Human Fluids

It is well-known that two major issues, preventing improved outcomes from cancer are late diagnosis and the evolution of drug resistance during chemotherapy, therefore technologies that address these issues can have a transformative effect on healthcare workflows. In this work we present a simple, low-cost DNA biosensor that was developed specifically to detect mutations in a key oncogene (KRAS). The sensor employed was a screen-printed array of carbon electrodes, used to perform parallel measurements of DNA hybridisation. A DNA amplification reaction was developed with primers for mutant and wild type KRAS sequences which amplified target sequences from representative clinical samples to detectable levels in as few as twenty cycles. High levels of sensitivity were demonstrated alongside a clear exemplar of assay specificity by showing the mutant KRAS sequence was detectable against a significant background of wild type DNA following amplification and hybridisation on the sensor surface. The time to result was found to be 3.5 h with considerable potential for optimisation through assay integration. This quick and versatile biosensor has the potential to be deployed in a low-cost, point-of-care test where patients can be screened either for early diagnosis purposes or monitoring of response to therapy.

In situ, amplification-free double-stranded mutation detection at 60 copies/ml with thousand-fold wild type in urine

We have investigated amplification-free in situ double-stranded mutation detection in urine in the concentration range 10-19 M - 10-16 M using piezoelectric plate sensors (PEPs). The detection was carried out in a close-loop flow with two temperature zones. The 95 °C high-temperature zone served as the reservoir where the sample was loaded and DNA de-hybridized. The heated urine was cooled flowing through a 1 m long tubing immersed in room-temperature water bath at a flow rate of 4 ml/min to reach the detection cell at the desired temperature for the detection to take place. With hepatitis B virus double mutation (HBVDM) and KRAS G12V point mutation as model double mutations, it is shown that PEPS was able to detect double-stranded HBVDM and KRAS with 70% detection efficiency or better at concentration as low as 10-19 M against single-stranded mutation detection at the same concentrations, which was validated by the following in situ fluorescent reporter microspheres (FRMs) detection as well as microscopic visualization of the FRMs bound to the captured mutant on the PEPS surface. Furthermore, the same double-stranded mutation detection efficacy was demonstrated at 10-19 M - 10-16 M in a background of 250-fold wildtype for HBVDM and 1000-fold wildtype for KRAS. Also demonstrated was detection of KRAS mutation at 10-19 M - 10-16 M of SW480 DNA fragments in urine.

Endonuclease IV based competitive DNA probe assay for differentiation of low-abundance point mutations by discriminating stable single-base mismatches

We disclosed the unique discrimination property of Endo IV toward stable single-base mismatches located at the second nucleotide 3' to the AP site. Coupled with thermodynamic differentiation and competitive blocker strands, a highly sensitive and specific detection system was established with discrimination factors of 510-1079 for G:X mismatches and LODs of 0.003-0.005% for KRAS G12A, KRAS G12V and KRAS G12S mutations.

Piezoelectric Plate Sensor (PEPS) for Analysis of Specific KRAS Point Mutations at Low Copy Number in Urine Without DNA Isolation or Amplification

We have examined in situ detection of single-nucleotide KRAS mutations in urine using a (Pb(Mg_1/3Nb_2/3)O₃)_0.65(PbTiO₃)_0.35 (PMN-PT) piezoelectric plate sensor (PEPS) coated with a 17-nucleotide (nt) locked nucleic acid (LNA) probe DNA complementary to the KRAS mutation without DNA isolation and amplification. In situ mutant (MT) DNA in urine in a wild type (WT) background was carried out at a flow rate of 4 mL/min and at 63 °C with the PEPS vertically situated at the center of the flow. Both the temperature and the impingement flow force discriminated the wild type. Under these conditions PEPS was shown to specifically detect KRAS MT in situ within 30 min with an analytical sensitivity of 60 copies/mL in a clinically relevant background of WT with concentrations 1000-fold greater than that of MT without DNA isolation, amplification, or labeling. For validation, detection was performed in a mixture of blue MT fluorescent reporter microspheres (FRMs) (MT FRMs) that bound to only the captured MT, and orange WT FRMs that bound to only the captured WT. The captured blue MT FRMs still outnumbered the orange WT FRMs by a factor of 4-1 even though WT was 1000-fold of MT in urine, illustrating the specificity of the point mutation detection.