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Thymine residues in an oligodeoxyribonucleotide are subject to methylation at N3 by the internucleotide methyl phosphotriester linkages. This alkylation occurs most rapidly in the presence of a strong base such as DBU, but also takes place, at a much slower rate, during oligonucleotide synthesis.
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Gao et al. (1985) studied this question.
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