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DNA-catalyzed sequence-specific hydrolysis of DNA


Deoxyribozymes (DNA catalysts) have been reported for cleavage of RNA phosphodiester linkages, but cleaving peptide or DNA phosphodiester linkages is much more challenging. Using in vitro selection, here we identified deoxyribozymes that sequence-specifically hydrolyze DNA with multiple turnover and with a rate enhancement of 108 (possibly as high as 1014). The new DNA catalysts require both Mn2+ and Zn2+, which is noteworthy because many natural DNA nucleases are bimetallic protein enzymes.

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Figure 1: In vitro selection of deoxyribozymes that cleave a substrate with both amide and DNA phosphodiester linkages.
Figure 2: Hydrolysis of DNA phosphodiester bonds by the new deoxyribozymes.

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This research was supported by the US National Institutes of Health (GM065966), the US Defense Threat Reduction Agency (BRBAA08-l-2-0001) and the David and Lucile Packard Foundation. A.S. was partially supported by the US National Institutes of Health (National Institute of General Medical Sciences) under the Ruth L. Kirschstein National Research Service Award T32 GM070421. We thank D. Ghosh and P. Bevilacqua (Pennsylvania State University) for independently verifying the cleavage activity of the 10MD5 deoxyribozyme with an all-DNA substrate. We thank L.A. Furgerson Ihnken and W. van der Donk for expert assistance with and access to the ESI mass spectrometer for the 18O-water experiment.

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M.C. performed in vitro selections using substrates synthesized by A.S. M.C. and A.S. characterized the deoxyribozymes. S.K.S. conceived the project, assisted M.C. and A.S. with analysis of experimental data and wrote the manuscript with input from M.C. and A.S.

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Correspondence to Scott K Silverman.

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Chandra, M., Sachdeva, A. & Silverman, S. DNA-catalyzed sequence-specific hydrolysis of DNA. Nat Chem Biol 5, 718–720 (2009).

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