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Oxidative damage
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Formation of strand breaks (single-stranded nicks)
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Cleavage of the phosphodiester backbone
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PCR of overlapping fragments of short length
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Depurination resulting in a baseless site
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Multiple independent PCR Cloning and sequencing of several clones
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Breakage of the sugar backbone through b-elimination
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Uracil-N-glycolase treatment
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Results in lesions blocking the polymerase enzyme, and promoting chimeric sequences through ‘jumping’ PCR
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Blocking primers Single primer extension or Spex
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Degradation by microorganisms’ nucleases in the post mortem cell
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Strand breaks
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Short fragment length
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PCR of overlapping fragments of short length
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DNA crosslinks
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Inter-strand crosslinks by alkylation
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May prevent the amplification of endogenous template molecules
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PTB (N-phenylacyl thiazolium bromide)
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Intermolecular crosslinks by Maillard reaction
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Increases the risk of contamination
| |
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Hydrolysis damage
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Results in miscoding lesions, for example, deamination of cytosine and adenine to uracil and hypoxathine, respectively
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Results in the incorporation of erroneous bases during amplification and change of coding
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Multiple independent PCR Cloning and sequencing of several clones UNG treatment
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