Advances in detection and quantification of methylcytosine and its derivatives

Asenso, James; Wang, Liang; Du, Yan; Liu, Qinghua; Xu, Bing‐ju; Guo, Mengzhe; Tang, Daoquan

doi:10.1002/jssc.201801100

Cited by 2 publications

(3 citation statements)

References 109 publications

(155 reference statements)

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“…It frequently occurs at cytosine–phosphate–guanine (CpG) islands, which are found at or near transcription start sites. As a result, DNA methylation can cause a wide range of diseases, including genetic diseases, diabetes, and cancer. − The modified bases can be released into the bloodstream and eventually manifest in the urine after DNA excision. , Consequently, urine samples could be used to noninvasively assess the epigenetic status of the entire body. − The measurement and quantification of 5-mC and its oxidation products in urine may aid in the comprehension of the association between DNA methylation and disease.…”

Section: Introductionmentioning

confidence: 99%

Optically Responsive Glutathione-Decorated Gold Nanoclusters for the Detection of Cytosine and 5-Methylcytosine Revealed by Multiscale Simulation

Phanchai,

Thonghlueng,

Puangmali

2024

ACS Appl. Nano Mater.

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The abnormal concentrations of cytosine (C) and 5methylcytosine (5-mC) in human plasma and urine have been closely linked to various human diseases, including cancer. Thus, they have become significant biomarkers for the diagnosis and prognosis of these diseases. In this work, we study the signature response between C/5-mC and glutathione-protected gold nanoclusters [Au 25 (GSH) 18 − ]. We have used molecular dynamics (MD) simulation and density functional theory (DFT) calculations to uncover this complicated interaction and acquire insights into complex interactions. Our finding shows that GSH ligand attains the most stable conformation when the values of distance (d Au-γ-Glu ) and angle (θγ-Glu-Cys-Gly) fall within the range of 0.45−0.54 nm and 85−95°, respectively. Once in stable states, the number of hydrogen bonds between the GSH ligand and water molecules decreased slightly, possibly because the GSH ligands could form hydrogen bonds with each other, potentially competing with the hydrogen bonds between the GSH ligand and water molecules. The C has a higher affinity for the GSH ligand than the 5-mC. The HOMO−LUMO gap of Au 25 (GSH) 18− can be affected by surface ligands, and it is significantly different when bound with C and 5-mC. It was discovered that both C and 5-mC had an effect on the HOMO−LUMO gap, causing a reduction of 0.13 and 0.44 eV in the gap, respectively. The 5-mC possesses an electron-donating group, a methyl group, which has an increased capability to channel electron density toward the Au core via the S−Au bond through a ligand-to-metal charge transfer mechanism, which leads to effectively enhanced fluorescence intensity. This suggests that the fluorescence of Au 25 (GSH) 18− can be more effectively enhanced through ligands possessing electron-rich and donating groups. The present study opens the door for the detection of C/5-mC.

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Section: Introductionmentioning

confidence: 99%

Optically Responsive Glutathione-Decorated Gold Nanoclusters for the Detection of Cytosine and 5-Methylcytosine Revealed by Multiscale Simulation

Phanchai,

Thonghlueng,

Puangmali

2024

ACS Appl. Nano Mater.

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“…Anomalies in the normal levels of 5-mCpG dinucleotides have been associated with a variety of pathological processes, such as tumors, , Alzheimer’s, Parkinson’s, depression, and various cancers. , Following DNA excision, the modified bases can be released into the bloodstream and eventually appear in the urine . Thus, whole-body epigenetic status could be assessed noninvasively using urine samples. , The measurement and quantification of 5-mC and its oxidation products in urine may aid in understanding the relationship between DNA methylation and disease.…”

Section: Introductionmentioning

confidence: 99%

“…7 Thus, whole-body epigenetic status could be assessed noninvasively using urine samples. 8,9 The measurement and quantification of 5-mC and its oxidation products in urine may aid in understanding the relationship between DNA methylation and disease.…”

Section: Introductionmentioning

confidence: 99%

Dual-Responsive Carbon Quantum Dots for the Simultaneous Detection of Cytosine and 5-Methylcytosine Interpreted by a Machine Learning-Assisted Smartphone

Thonghlueng

Ngernpimai

Chuaephon

et al. 2023

ACS Appl. Mater. Interfaces

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DNA methylation is an epigenetic alteration that results in 5-methylcytosine (5-mC) through the addition of a methyl group to the fifth carbon of a cytosine (C) residue. The methylation level, the ratio of 5-mC to C, in urine might be related to the whole-body epigenetic status and the occurrence of common cancers. To date, never before have any nanomaterials been developed to simultaneously determine C and 5-mC in urine samples. Herein, a dual-responsive fluorescent sensor for the urinary detection of C and 5-mC has been developed. This assay relied on changes in the optical properties of nitrogen-doped carbon quantum dots (CQDs) prepared by microwave-assisted pyrolysis. In the presence of C, the blue-shifted fluorescence intensity of the CQDs increased. However, fluorescence quenching was observed upon the addition of 5-mC. This was primarily due to photoinduced electron transfer as confirmed by the density functional theory calculation. In urine samples, our sensitive fluorescent sensor had detection limits for C and 5-mC of 43.4 and 74.4 μM, respectively, and achieved satisfactory recoveries ranging from 103.5 to 115.8%. The simultaneous detection of C and 5-mC leads to effective methylation level detection, achieving recoveries in the range of 104.6−109.5%. Besides, a machine learningenabled smartphone was also developed, which can be effectively applied to the determination of methylation levels (0−100%). These results demonstrate a simple but very effective approach for detecting the methylation level in urine, which could have significant implications for predicting the clinical prognosis.

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Advances in detection and quantification of methylcytosine and its derivatives

Cited by 2 publications

References 109 publications

Optically Responsive Glutathione-Decorated Gold Nanoclusters for the Detection of Cytosine and 5-Methylcytosine Revealed by Multiscale Simulation

Optically Responsive Glutathione-Decorated Gold Nanoclusters for the Detection of Cytosine and 5-Methylcytosine Revealed by Multiscale Simulation

Dual-Responsive Carbon Quantum Dots for the Simultaneous Detection of Cytosine and 5-Methylcytosine Interpreted by a Machine Learning-Assisted Smartphone

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