Table 2.
Various 6mA detection methods and their significance.
| Method | Significance |
|---|---|
| SMRT—A Third Generation Sequencing Method | Based on enzyme kinetics, 6mA bases are identified by highly sensitive inter-pulse duration ratios in the sequencing data [69]. |
| MeDIP-seq(Methylated DNA immunoprecipitation sequencing) | The 6mAin DNA is discovered by using specific antibody by applying high throughput DNA sequencing [70]. |
| Dam ID (DNA adenine methyltransferase Identification) | Proteins of interests are fused with Dam and the binding sites are identified by restriction digestion and mapping [71]. |
| Dam IP (DNA adenine methyltransferase Immunoprecipitation) | Combination of a mutant form of DAMT with 6mA antibody to recognize N-6-methylated DNA followed by IP based enrichment and detection by qRT-PCR with sequence specific primers [72]. |
| UHPLC-TQMS (Ultra High-Performance Liquid Chromatography-Triple Quadrupole Mass Spectrometry) | Sensitive detection and quantification of 6mA by high performance liquid chromatography coupled with mass spectrometry [73] |
| MEME-ChIP (Multiple EM for motif elicitation-Chromatin immunoprecipitation) | Identification and analysis of 6mA motif from the large set of sequence, which were obtained from ChIP [74]. |
| 6mA CLIP Exo (Immunoprecipitation, Photo Crosslinking-Exonuclease Digestion). | Detection of 6mA motifs in genomic DNA fragments incubated with 6mA antibodies followed by UV cross-linking, immunoprecipitation and exonuclease digestion [58]. |
| 6mA-RE(Restriction Endonuclease). | Restriction digestion of unmethylated 6mA motif with CviAII (CATG) or DpnII (GATC) leaves methylated fragments which can be amplified by PCR [58]. |
| Metal ion mediated replication and Rolling Circle Amplification. | This method is able to differentiate the methylated and non-methylated sequences. The non-methylated sequences are ligated and circularized with Ag2+ padlock probes where mismatches are stabilized by metal ions and primer extension processed by polymerases [75]. |
| Dot blot | Detection of 6mA abundance using specific antibodies and distinction of changes in 6mA level in different tissue or same tissue at different time point [46,76]. |
| MCSeEd (Methylation content sensitive enzyme double-digest restriction-site-associated DNA (ddRAD) technique) | Identification of 6mA motif using parallel restrictions carried out by combinations of methylation insensitive and sensitive endonucleases, followed by next-generation sequencing [77]. |
| Nanopore | Identification of DNA methylation at specific genomic position by Nanopore signals where it shows the electric spikes [78]. |