Detection of DNA methylation by hyperbranched rolling circle amplification and DNA microarray

Zhao, Hong; Zhang, Lu

doi:10.1016/j.cclet.2014.09.010

Cited by 11 publications

(3 citation statements)

References 25 publications

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“…DNA cytosine methylation (5-methyl-2′-deoxycytidine, 5-mdC) is one of the most important epigenetic marks that play critical roles in a variety of cellular processes, including cell differentiation, genome imprinting, and X-chromosome inactivation . Maintaining proper DNA methylation status is critical for the normal functions of cells. , Abnormal DNA methylation can cause many human diseases, such as diabetes, neurological disorders, and cancers. , …”

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confidence: 99%

Determination of DNA and RNA Methylation in Circulating Tumor Cells by Mass Spectrometry

et al. 2016

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DNA methylation (5-methylcytosine, 5-mC) is the best characterized epigenetic mark that has regulatory roles in diverse biological processes. Recent investigation of RNA modifications also raises the possible functions of RNA adenine and cytosine methylations on gene regulation in the form of "RNA epigenetics." Previous studies demonstrated global DNA hypomethylation in tumor tissues compared to healthy controls. However, DNA and RNA methylation in circulating tumor cells (CTCs) that are derived from tumors are still a mystery due to the lack of proper analytical methods. In this respect, here we established an effective CTCs capture system conjugated with a combined strategy of sample preparation for the captured CTCs lysis, nucleic acids digestion, and nucleosides extraction in one tube. The resulting nucleosides were then further analyzed by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). With the developed method, we are able to detect DNA and RNA methylation (5-methyl-2'-deoxycytidine, 5-methylcytidine, and N(6)-methyladenosine) in a single cell. We then further successfully determined DNA and RNA methylation in CTCs from lung cancer patients. Our results demonstrated, for the first time, a significant decrease of DNA methylation (5-methyl-2'-deoxycytidine) and increase of RNA adenine and cytosine methylations (N(6)-methyladenosine and 5-methylcytidine) in CTCs compared with whole blood cells. The discovery of DNA hypomethylation and RNA hypermethylation in CTCs in the current study together with previous reports of global DNA hypomethylation in tumor tissues suggest that nucleic acid modifications play important roles in the formation and development of cancer cells. This work constitutes the first step for the investigation of DNA and RNA methylation in CTCs, which may facilitate uncovering the metastasis mechanism of cancers in the future.

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confidence: 99%

Determination of DNA and RNA Methylation in Circulating Tumor Cells by Mass Spectrometry

et al. 2016

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“…PP is usually used to detect some nucleic sequences, such as microRNA [ 26 , 27 ], methylated DNA sequences [ 28 , 29 , 30 , 31 ], and exosomes [ 32 ], but it has not been previously used to detect DNA MTase activity. To sensitively detect MTase, PP with RCA was designed as illustrated in Scheme 1 .…”

Section: Resultsmentioning

confidence: 99%

Simple Detection of DNA Methyltransferase with an Integrated Padlock Probe

Wang

Han

Zhou³

et al. 2022

Biosensors

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DNA methyltransferases (MTases) can be regarded as biomarkers, as demonstrated by many studies on genetic diseases. Many researchers have developed biosensors to detect the activity of DNA MTases, and nucleic acid amplification, which need other probe assistance, is often used to improve the sensitivity of DNA MTases. However, there is no integrated probe that incorporates substrates and template and primer for detecting DNA MTases activity. Herein, we first designed a padlock probe (PP) to detect DNA MTases, which combines target detection with rolling circle amplification (RCA) without purification or other probe assistance. As the substrate of MTase, the PP was methylated and defended against HpaII, lambda exonuclease, and ExoI cleavage, as well as digestion, by adding MTase and the undestroyed PP started RCA. Thus, the fluorescent signal was capable of being rapidly detected after adding SYBRTM Gold to the RCA products. This method has a detection limit of approximately 0.0404 U/mL, and the linear range was 0.5–110 U/mL for M.SssI. Moreover, complex biological environment assays present prospects for possible application in intricacy environments. In addition, the designed detection system can also screen drugs or inhibitors for MTases.

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“…For instance, rolling circle amplification (RCA) is one of the most widely used strategies for nucleic acid signal amplification, benefiting from its simplicity, robustness, and high efficiency. 49 Huang et al took advantage of the properties of RCA to develop a fast aptamer-based method for quantitative measurement of gastric cancer exosomes (Fig. 2A).…”

Section: Aptamer-based Diagnosismentioning

confidence: 99%