Eliminating the secondary structure of targeting strands for enhancement of DNA probe based low-abundance point mutation detection

Ming, Zhihao; Chen, Qianzhi; Chen, Na; Lin, Ming Hwai; Liu, Na; Hu, Junbo; Xiao, Xianjin

doi:10.1016/j.aca.2019.05.015

Cited by 4 publications

(6 citation statements)

References 21 publications

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“…We also tested the BRCA2 rs80359065 mutation, which is associated with ovarian cancer, (using MT-3, WT-3, Guiding-3L, Guiding-3R, Probe-3, and Blocker-3) using an APE-1-assisted target recycling system. The limit of detection was 0.05% (Figure S4c,d), consistent with previous reports . These results indicate that the guiding strands can be used to detect low-abundance point mutations, especially with extensive undesired nuclease activity.…”

Section: Resultssupporting

confidence: 93%

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Guiding-Strand-Controlled DNA Nucleases with Enhanced Specificity and Tunable Kinetics for DNA Mutation Detection

et al. 2021

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Nucleases are powerful tools in various biomedical applications, such as genetic engineering, biosensing, and molecular diagnosis. However, the commonly used nucleases (endonuclease IV, apurinic/apyrimidinic endonuclease-1, and λ exonuclease) are prone to the nonspecific cleavage of single-stranded DNA, making the desired reactions extremely low-yield and unpredictable. Herein, we have developed guiding-strand-controlled nuclease systems and constructed theoretical kinetic models to explain their mechanisms of action. The models displayed excellent agreement with the experimental results, making the kinetics highly predictable and tunable. Our method inhibited the nonspecific cleavage of single-stranded probes while maintaining highly efficient cleavage of double-stranded DNA. We also demonstrated the clinical practicability of the method by detecting a lowfrequency mutation in a genomic DNA sample extracted from the blood of a patient with cancer. The limit of detection could be 0.01% for PTEN rs121909219. We believe that our findings provide a powerful tool for the field and the established model provides us a deeper understanding of the enzymatic activities of DNA nucleases.

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Section: Resultssupporting

confidence: 93%

“…The limit of detection was 0.05% (Figure S4c,d), consistent with previous reports. 31 These results indicate that the guiding strands can be used to detect low-abundance point mutations, especially with extensive undesired nuclease activity.…”

Section: ■ Results and Discussionmentioning

confidence: 94%

Guiding-Strand-Controlled DNA Nucleases with Enhanced Specificity and Tunable Kinetics for DNA Mutation Detection

et al. 2021

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“…All in all, the applications of fluorescent biosensors and imaging technologies are increasingly widespread. However, there are some defects that need to be improved: i) The nucleic acid probes might lose the ability to hybridize with target strands when the target sequences form secondary structures such as hairpins or quadruplexes, subsequently disturbing the surrounding sequences ( Ming et al, 2019 ). Thus, an open strand–based model is required for eliminating the influence of complicated secondary structures.…”

Section: Discussionmentioning

confidence: 99%

The Application of Nucleic Acid Probe–Based Fluorescent Sensing and Imaging in Cancer Diagnosis and Therapy

Huang

Wang

et al. 2021

Front. Chem.

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It is well known that cancer incidence and death rates have been growing, but the development of cancer theranostics and therapeutics has been a challenging work. Recently, nucleic acid probe–based fluorescent sensing and imaging have achieved remarkable improvements in a variety of cancer management techniques, credited to their high sensitivity, good tolerance to interference, fast detection, and high versatility. Herein, nucleic acid probe–based fluorescent sensing and imaging are labeled with advanced fluorophores, which are essential for fast and sensitive detection of aberrant nucleic acids and other cancer-relevant molecules, consequently performing cancer early diagnosis and targeted treatment. In this review, we introduce the characteristics of nucleic acid probes, summarize the development of nucleic acid probe–based fluorescent sensing and imaging, and prominently elaborate their applications in cancer diagnosis and treatment. In discussion, some challenges and perspectives are elaborated in the field of nucleic acid probe–based fluorescent sensing and imaging.

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“…Eliminating the secondary structure of the target sequence can improve the working efficiency of the probe. Ming et al 42 introduced 2 additional single-stranded DNAs to the target strand that will form the secondary structure. These 2 single-stranded DNAs match a part of the probe's target region and open the secondary structure formed ( Figure 4C ).…”

Section: Gene Detection Methods For Early Diagnosis Of Ovarian Cancer...mentioning

confidence: 99%

“…This strategy is applied to detect the plasma BRCA2 rs80359065 mutation in patients with ovarian cancer and reduce the detection limit to 0.05%. 42 The probe designed based on the principle of strand migration reaction is simple and highly selective and can distinguish between mutant and wild-type DNA.…”

Section: Gene Detection Methods For Early Diagnosis Of Ovarian Cancer...mentioning

confidence: 99%

The Progress of the Specific and Rapid Genetic Detection Methods for Ovarian Cancer Diagnosis and Treatment

Dong

Zhang

Cheng

et al. 2022

Technol Cancer Res Treat

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Cancer is a public health problem that threatens human health. Due to the lack of specific and rapid diagnosis and treatment methods, the 5-year survival rate of patients has not been effectively improved in the past 10 years. Abnormal gene expression is closely related to the occurrence and development of cancer. Cancer diagnosis and treatment methods based on genetic testing have received extensive attention in recent years. It is essential to explore specific and rapid cancer genetic testing methods. Taking ovarian cancer as an example, we reviewed the progress of specific and rapid nucleic acid detection methods related to cancer risk assessment, low-abundance mutation detection, and methylation detection, to provide new strategies and ideas for related research.

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Eliminating the secondary structure of targeting strands for enhancement of DNA probe based low-abundance point mutation detection

Cited by 4 publications

References 21 publications

Guiding-Strand-Controlled DNA Nucleases with Enhanced Specificity and Tunable Kinetics for DNA Mutation Detection

Guiding-Strand-Controlled DNA Nucleases with Enhanced Specificity and Tunable Kinetics for DNA Mutation Detection

The Application of Nucleic Acid Probe–Based Fluorescent Sensing and Imaging in Cancer Diagnosis and Therapy

The Progress of the Specific and Rapid Genetic Detection Methods for Ovarian Cancer Diagnosis and Treatment

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