Detection of N6-Methyladenine in Eukaryotes

Liu, Baodong; Wang, Hailin

doi:10.1007/978-3-030-51652-9_6

Cited by 5 publications

(2 citation statements)

References 53 publications

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“…Thereafter the digested DNA can be effectively separated in the chromatographic separation system due to the different physical and chemical properties of each component. Next, they are ionized by atmospheric pressure ionization (API) techniques and then entered into the mass spectrometer, identified by MS/MS based on mass-to-charge ratio (m/z) (Vogeser and Seger, 2008;Liu and Wang, 2021) (Figure 1B). HPLC-MS/MS can accurately quantify the signal of each nucleoside even if the samples are contaminated by RNA (Song et al, 2005).…”

Section: Hplc-ms/msmentioning

confidence: 99%

DNA N6-Methyladenine Modification in Eukaryotic Genome

Zhang

Wang

et al. 2022

Front. Genet.

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DNA methylation is treated as an important epigenetic mark in various biological activities. In the past, a large number of articles focused on 5 mC while lacking attention to N6-methyladenine (6 mA). The presence of 6 mA modification was previously discovered only in prokaryotes. Recently, with the development of detection technologies, 6 mA has been found in several eukaryotes, including protozoans, metazoans, plants, and fungi. The importance of 6 mA in prokaryotes and single-celled eukaryotes has been widely accepted. However, due to the incredibly low density of 6 mA and restrictions on detection technologies, the prevalence of 6 mA and its role in biological processes in eukaryotic organisms are highly debated. In this review, we first summarize the advantages and disadvantages of 6 mA detection methods. Then, we conclude existing reports on the prevalence of 6 mA in eukaryotic organisms. Next, we highlight possible methyltransferases, demethylases, and the recognition proteins of 6 mA. In addition, we summarize the functions of 6 mA in eukaryotes. Last but not least, we summarize our point of view and put forward the problems that need further research.

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Section: Hplc-ms/msmentioning

confidence: 99%

DNA N6-Methyladenine Modification in Eukaryotic Genome

Zhang

Wang

et al. 2022

Front. Genet.

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“…4mdC is formed by adding an exocyclic CH 2 group to the nitrogen-4 position of cytosine, and it is also a part of R–M systems and functions in host DNA protection, foreign DNA discrimination, and DNA replication error correction 6mdA and 4mdC have widely existed in prokaryotes and lower eukaryotes. , Accumulating evidence reveal that 6mdA is abundantly present in several higher eukaryotes (e.g., vertebrates, mouse embryonic stem cells, and even human genome), − and 4mdC is detectable in eukaryotes (e.g., bdelloid rotifers and tiny freshwater invertebrates) . Therefore, the simultaneous and selective monitoring of 6mdA and 4mdC at any specific site is of great significance for fundamental studies and epigenetic diagnostics.…”

Section: Introductionmentioning

confidence: 99%

Silver-Coordinated Watson–Crick Pairing-Driven Three-Dimensional DNA Walker for Locus-Specific Detection of Genomic N⁶-Methyladenine and N⁴-Methylcytosine at the Single-Molecule Level

Wang,

Liu,

et al. 2024

Anal. Chem.

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N 6 -Methyladenine (6mdA) and N 4 -methylcytosine (4mdC) are the two most dominant DNA modifications in both prokaryotes and eukaryotes, but standard hybridizationbased techniques cannot be applied for the 6mdA/4mdC assay. Herein, we demonstrate the silver-coordinated Watson−Crick pairing-driven three-dimensional (3D) DNA walker for locus-specific detection of genomic 6mdA/4mdC at the single-molecule level. 6mdA-DNA and 4mdC-DNA can selectively hybridize with the binding probes (BP1 and BP2) to form 6mdA-DNA-BP1 and 4mdC-DNA-BP2 duplexes. The 6mdA-C/4mdC-A mismatches cannot be stabilized by Ag I , and thus, 18-nt BP1/BP2 cannot be extended by the catalysis of KF exonuclease. Through toehold-mediated strand displacement (TMSD), the signal probe (SP1/ SP2) functionalized on the gold nanoparticles (AuNPs) can competitively bind to BP1/BP2 in 6mdA-DNA-BP1/4mdC-DNA-BP2 duplex to obtain SP1−18-nt BP1 and SP2−18-nt BP2 duplexes. The resulting DNA duplexes can act as the substrates of lambda exonuclease, leading to the cleavage of SP1/SP2 and the release of Cy3/Cy5 and 18-nt BP1/BP2. The released 18nt BP1/BP2 can subsequently serve as the walker DNA, moving along the surface of the AuNP to activate dynamic 3D DNA walking and releasing abundant Cy3/Cy5. The released Cy3/Cy5 can be quantified by single-molecule imaging. This nanosensor exhibits high sensitivity with a limit of detection (LOD) of 9.80 × 10 −15 M for 6mdA-DNA and 9.97 × 10 −15 M for 4mdC-DNA. It can discriminate 6mdA-/4mdC-DNA from unmodified genomic DNAs, distinguish 0.01% 6mdA-/4mdC-DNA from excess unmethylated DNAs, and quantify 6mdA-/4mdC-DNA at specific sites in genomic DNAs of liver cancer cells and Escherichia coli plasmid cloning vector, providing a new platform for locus-specific analysis of 6mdA/4mdC in genomic DNAs.

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Identification and quantification of DNA N6-methyladenine modification in mammals: A challenge to modern analytical technologies

Lyu

Wang

Lai

et al. 2023

Current Opinion in Chemical Biology

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Detection of N6-Methyladenine in Eukaryotes

Cited by 5 publications

References 53 publications

DNA N6-Methyladenine Modification in Eukaryotic Genome

DNA N6-Methyladenine Modification in Eukaryotic Genome

Silver-Coordinated Watson–Crick Pairing-Driven Three-Dimensional DNA Walker for Locus-Specific Detection of Genomic N⁶-Methyladenine and N⁴-Methylcytosine at the Single-Molecule Level

Identification and quantification of DNA N6-methyladenine modification in mammals: A challenge to modern analytical technologies

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Detection of N6-Methyladenine in Eukaryotes

Cited by 5 publications

References 53 publications

DNA N6-Methyladenine Modification in Eukaryotic Genome

DNA N6-Methyladenine Modification in Eukaryotic Genome

Silver-Coordinated Watson–Crick Pairing-Driven Three-Dimensional DNA Walker for Locus-Specific Detection of Genomic N6-Methyladenine and N4-Methylcytosine at the Single-Molecule Level

Identification and quantification of DNA N6-methyladenine modification in mammals: A challenge to modern analytical technologies

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Silver-Coordinated Watson–Crick Pairing-Driven Three-Dimensional DNA Walker for Locus-Specific Detection of Genomic N⁶-Methyladenine and N⁴-Methylcytosine at the Single-Molecule Level