Unnatural Base Pair Enables Alphabet-Expanded DNA Self-Assembly.

Self-assembly properties and diversity in higher-order structures of DNA enable programmable tools to be used to construct algorithms at the molecular level. However, the utility of DNA-based programmable tools is hampered by the low orthogonality to natural nucleic acids, especially in complex molecular systems. To address this challenge, we report here the orthogonal regulation of DNA self-assembly by using an unnatural base pair (UBP) formation.

DNA-friendly Cu(ii)/TEMPO-catalyzed 5-hydroxymethylcytosine-specific oxidation.

The mixture of copper(ii) perchlorate and 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) mildly and specifically oxidized 5-hydroxymethylcytosine to yield 5-formylcytosine because of its allyl alcohol specificity. The genomic DNA oxidized at 5-hydroxymethylcytosine by the copper(ii)/TEMPO oxidation was efficiently analyzed using various practical methods: DNA cleavage by piperidine, specific functionalization by hydrazone formation, and genome-wide high-resolution microarray.