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. 2011 Oct 28;40(4):1778–1786. doi: 10.1093/nar/gkr860

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© The Author(s) 2011. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — The 10MD5 deoxyribozyme, and identification by in vitro selection of new DNA-hydrolyzing deoxyribozymes. (A) 10MD5 and interactions with its DNA substrate (9). Sequence specificity is inherently provided by the Watson-Crick base pairs between deoxyribozyme and substrate. However, the 4-nt ATG^T requirement at the cleavage site means that 10MD5 is not broadly tolerant of different substrate sequences. (B) In vitro selection strategy. The loop on the right side (arrow) enables the selection process but is dispensable for catalysis; its removal enables in trans (intermolecular) assays. The two DNA substrate nucleotides immediately flanking the cleavage site are denoted here generically as X^Z. DNA-catalyzed hydrolysis is sought at or near the XZ region of the substrate.