Quantification and mapping of DNA modifications

Abstract

Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows DNA modifications can regulate diverse biological processes. Dynamic and reversible modification of DNA...

RNA‐Cleaving Deoxyribozymes Differentiate Methylated Cytidine Isomers in RNA

“…[13] AN05 cleaved hm 5 C-containing RNA slightly slower but to a similar extent as m 5 C RNA, while f 5 C was comparable to unmodified RNA (Figure S9). Surprisingly, this result is in line with bisulfite sequencing, which is unable to distinguish m 5 C from hm 5 C, and f 5 C from C. [14] Given the functional importance of hm 5 C and f 5 C in natural RNA, [13] future in vitro selection experiments may be directed to evolve deoxyribozymes specific for the individual oxidized m 5 C variants.…”

Labeling and sequencing nucleic acid modifications using bio-orthogonal tools

“…Chemical labeling methods are specific for target DNA modifications, the results of sequencing only for target modification. As part of the chemical labeling approach induce base conversion of the DNA modifications, base resolution sequencing information be obtained by sequencing, 12,111 including bio-orthogonal tools This journal is © The Royal Society of Chemistry 20xx…”

“…9, 10 Numerous methods have been developed for detecting and mapping nucleic acid modifications, including liquid chromatography, immunostaining-based detection, and chemically labeled sequencing technologies. 11,12 Due to the selectivity, biocompatibility, and biological inertness of the bio-orthogonal reaction, it has been used to label distinct biomacromolecules within cells and then track their synthesis, metabolism, and interactions with other biomacromolecules within cells. [13][14][15] Click chemistry plays a critical role in bio-orthogonal reactions such as Diels-Alder reactions, copper(I)-catalyzed azide-alkyne cycloadditions, and strain-promoted azide-alkyne cycloadditions.…”

Genome-wide mapping of N4-methylcytosine at single-base resolution by APOBEC3A-mediated deamination sequencing

“…Mass spectrometry has been established as an effective technique for qualitative and quantitative analysis of nuclei acid modications. [23][24][25][26][27][28] However, it is unable to achieve genome-wide mapping of DNA modications.…”