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===Conclusion=== * In these experiments, oxidation alone, oxidation with bisulfite conversion, and bisulfite conversion alone did not fragment all or most of the DNA. Based on QUBIT quantification of the amount DNA yielded, >50% less DNA was obtained from oxidation bisulfite than from bisulfite alone, which means that oxidation bisulfite do fragment the DNA more than bisulfite. We did not observe, qualitatively or quantitatively, that 5hmC were fragmented more than 5mC or C amplicons. * It was possible to amplify the single stranded DNA from oxidation bisulfite and bisulfite conversion. We did observe significantly, that the B amplicons containing 5hmC were much less amplifiable than the F amplicons (containing C) and the E amplicons (containing 5mC). The order of amplification was 5mC > C > 5hmC. This may be due to more extensive DNA damage to the 5hmC containing amplicons. The amplification efficiency cannot be due to differences in primer efficiencies because under the same conditions, B,E,F primers have similar amplification. * We found that the PreCR Repair mix may be able to repair the damage to 5hmC containing amplicons, as we saw that the DNA that was diluted to 0.2X in the repair mix, was able to amplify almost as well as the DNA undiluted. * The no repair control (where the DNA was diluted and incubated with water and ThermoPol buffer), shows what the amplification might looks like if there was no repair. Since the no repair control could not amplify well, this further supports that the PreCR repair mix helped the damaged DNA.
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