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The assessment of the integrity of the DNA primary structure and the identification of canonical and modified bases are useful tools in medical, pharmaceutical, and forensic applications.
Methyltransferase genes are carried by many bacteriophages [22] [24], and modified bases are common in phage genomes [25], [26].
We also show that the CMS adduct tends to stall DNA polymerases during PCR, especially if these modified bases are adjacent to one another or spaced 1 2 nucleotides apart; this result suggests that genomic regions containing closely-spaced 5-hmC could be missed or underrepresented in quantitative methylation analyses.
The positions of the modified bases are highlighted as red bars.
The Ogg1 gene encodes the enzyme 8-oxoguanine DNA glycosylase, by which oxidatively modified bases are repaired [ 24, 25].
Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function.
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The modified bases were identified using SMRT Analysis Server v. 1.4.0 (Pacific Biosciences).
It is still not entirely clear whether one or both of these modified bases is the endogenous substrate/s for FTO.
Custom oligonucleotides containing modified bases were synthesized on-site or purchased from Trilink BioTechnologies (San Diego, CA, USA) and Integrated DNA Technologies Coralvillee, IA, USA).
Geometric restraint libraries, used in refinement for modified bases, were generated using CCP4 programs Library Sketcher and libchek to create dictionary files.
If this modified base is not repaired, it can lead to G C to A T transition mutations during replication Tan [ 17, 18].
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