Figure 4.

Representative MALDI mass spectra to assign cleavage reactions and sites for deoxyribozymes from the initial N₂₀ and N₃₀ selections for DNA cleavage. All mass spectra data and precise cleavage-site assignments are tabulated in Tables S1 and S2. The indicated C nucleotide of the substrate was not base-paired with either deoxyribozyme binding arm (see Figure 1). (A) 8VB4 deoxyribozyme, which hydrolyzes the DNA substrate at a specific phosphodiester linkage and forms 3′-phosphate and 5′-hydroxyl products. Some of the new DNA-hydrolyzing deoxyribozymes lead instead to 3′-hydroxyl and 5′-phosphate products. (B) 8VB5 deoxyribozyme, which deglycoyslates the DNA substrate at a specific guanosine. After two subsequent β-elimination reactions, the products are missing the entire G nucleoside and have 3′-phosphate and 5′-phosphate groups. Some of the new DNA-deglycosylating deoxyribozymes are not site-specific and deglycosylate the substrate at either of two adjacent nucleotide positions. In the spectrum of panel B, the asterisk denotes the peak for uncleaved substrate with z = 2.