Figure 2.

Sequences and secondary structures of variant deoxyribozymes. (A) Individual DNAs shown above and below the double line were isolated after reselection of mutagenized pools based on the sequence of the original class II deoxyribozyme (II) or the class II variant HD2, respectively. Depicted are the nucleotide sequences for the mutagenized core of the parent DNAs (asterisks) and the number (in parentheses) and type of nucleotide changes for each variant deoxyribozyme. HD1 and HD2 were recovered from a mutagenized pool based on II after five rounds of reselection with 50 or 5 mM histidine, respectively. HD3 was isolated from a mutagenized pool of truncated HD2 deoxyribozymes. (B) Each deoxyribozyme was reorganized to create a bimolecular complex, whereby separate substrate molecules are recognized by two regions of base complementation (stems I and II) with the enzyme domain. Nucleotides corresponding to the mutagenized core are numbered as in Fig. 1 and A.