DNAmoreDB - A Database of Deoxyribozymes

Published on 2013 in J. Am. Chem. Soc. volume 135 issue 43.

PubMed ID: 24127695

DOI:10.1021/ja4077233

Abstract:

We previously reported that DNA catalysts (deoxyribozymes) can hydrolyze DNA phosphodiester linkages, but DNA-catalyzed amide bond hydrolysis has been elusive. Here we used in vitro selection to identify DNA catalysts that hydrolyze ester linkages as well as DNA catalysts that hydrolyze aromatic amides, for which the leaving group is an aniline moiety. The aromatic amide-hydrolyzing deoxyribozymes were examined using linear free energy relationship analysis. The hydrolysis reaction is unaffected by substituents on the aromatic ring (ρ ≈ 0), suggesting general acid-catalyzed elimination as the likely rate-determining step of the addition–elimination hydrolysis mechanism. These findings establish that DNA has the catalytic ability to achieve hydrolysis of esters and aromatic amides as carbonyl-based substrates, and they suggest a mechanism-based approach to achieve DNA-catalyzed aliphatic amide hydrolysis.



DNAzymes linked to this article:

Name Isolated sequence Length Reaction
10ZA8 CACACGAGCGAAAGATTAGGCTGAGCTCCTGGGGACCTGC      40 Ester hydrolysis
10ZA5 GCCGATAAGCAAAGCATCAGGAGTACGAACAGGTCCAAAT      40 Ester hydrolysis
10ZA7 CCCGCATAAGGAGGGGTCTTCGAGAGGGATCCATGCATCT      40 Ester hydrolysis
10ZA13 ACACACAGGGTGGAATTATTATGCCTCAGGGTGCCGCCTC      40 Ester hydrolysis
10ZA15 CCCCACGCACGCTGACAAAGGTCGAGGTAATCAGGGGTAG      40 Ester hydrolysis
10ZA19 GGGCCGGCAGGGAGTTAGGGGGTCGGATTCCTGGGCCGAT      40 Ester hydrolysis
10ZA20 TCCCGGGTTGCACGAGCTATAATCGAGGACTTCGAAGTCA      40 Ester hydrolysis
10ZA22 AAAGGGCGGTTTACAAACAAGTTTCACGAGTGAAGGACCC      40 Ester hydrolysis
10ZA23 CACGGCCCCAACACAGCAACGGAGGACTTTACGGGGGGCA      40 Ester hydrolysis
13ZB38 GGGCGGCGAACAGGATGGGAGGAGGGACCTGGCAATACCG      40 Ester hydrolysis
13ZB44 GGGGGCGCGTCATCATCGAAAGGGGGTCCTGCATTACGCC      40 Ester hydrolysis
8ZC9 ACAGGTCGGGAAGTTACATGCATGTCAATGTAACGGGTAC      40 Amide hydrolysis
8ZC4 CACCGGTCGGAAAAACGAGGATTAAGCACGATATTGGTCG      40 Amide hydrolysis
8ZC8 ACGGGACGGGAAGCGTCACGAAAAGTCTAGACGCGGGTAA      40 Amide hydrolysis
8ZC41 ACGGGCCGGGAAGCGAGTCAAAAGCGTTTGAATGCGGGTAT      41 Amide hydrolysis
6AP102 ACGGGCCGGGAAGAAACAAGCTATACGAAGTTTCGGGTCA      40 Amide hydrolysis
6AP103 ACAGGCCGGGAAGTGACGAGCAAGACGAGGAAACGGGTTC      40 Amide hydrolysis
6AP108 ACAGGCCGGGAAGTGAGGAGCAAGACAACGAAACGGGTCC      40 Amide hydrolysis
6AP112 ACGGGCCGGGAAGCAGTCAAAAGCGTTTGAATGCGGGTAT      40 Amide hydrolysis
6AP122 ACAGGCCGGGAAGGAACAAGCAAGACTTAGTTCCGGGTGC      40 Amide hydrolysis
6AP134 ACGGGCCGGGAAGGAACAAGTCACAACGAGAGACGGGTAA      40 Amide hydrolysis
6AP136 ACAGGACGGGAAGGAGCAAGTAACACAACGCGACGGGTAC      40 Amide hydrolysis
6AP138 ACAGGTCGGGAAGAGACAAGCAAAGCACAAACTCGGGTCC      40 Amide hydrolysis
6AP139 ACAGGACGGGAAGCAACGAGCAAGACGAGGAAGCGGGTGC      40 Amide hydrolysis
6AP143 ACAGGTCGGGAAGATTCATGCTAGACATAGAATCGGGTCG      40 Amide hydrolysis
6AP144 ACAGGACGGGAAGATTCTAGCTTGCCAAAGAATCGGGTAC      40 Amide hydrolysis
6AP145 ACGGGCCGGGAAGATACAAGCAAGACATTGTATCGGGTAC      40 Amide hydrolysis
6AP146 ACAGGTCGGGAAGAAACTAGCTAGACACAGTTTCGGGTAC      40 Amide hydrolysis
9BN101 GCAGTGCGGACCAGGGCGGA      20 Amide hydrolysis
9BN102 CAAAGGCGGACTAGGGCGGA      20 Amide hydrolysis
9BN105 GCAAGGCGGACTAGGGCGGA      20 Amide hydrolysis
9BN107 CGAGTGCGGACCAGGGCGGA      20 Amide hydrolysis
9BN112 GGAAGGCGGACTAGGGCGGA      20 Amide hydrolysis
9BN113 ACAGTGCGGACCAGGGCGGA      20 Amide hydrolysis
9BN119 GAAAGGCGGACTAGGGCGGA      20 Amide hydrolysis
9BN121 GCAATGCGGACTAGGGCGGA      20 Amide hydrolysis
8BQ102 ACGGGTCGGGAAGAATACATATTCGGGTTA      30 Amide hydrolysis
8BQ103 ACAGGCCGGGAAGCAGGAACATGCGGGTCC      30 Amide hydrolysis
8BQ117 ACAGGTCGGGAAATCTGACAAGATGGGTCA      30 Amide hydrolysis
8BQ118 ACGGGCCGGGAAGCATCTCGGATGCGGGTA      30 Amide hydrolysis
8BQ119 CGGGTCGGGAAGGACTACAAGGACGGGTCA      30 Amide hydrolysis
8BQ128 ACAGGCCGGGAAAGGCGACAGCCTGGGTAA      30 Amide hydrolysis
8BQ131 CGGGCCGGACACCCAAAAAGGGATGGTGTT      30 Amide hydrolysis
8BQ136 ACAGGTCGGGAAGAGTGAAGACTCGGGTTA      30 Amide hydrolysis
10ZA1 CACCCCGAATGTGTCATAGCTGGGGGAGGTTTCTTGAGTA      40 Ester hydrolysis
10ZA18 CCCCACGCGTAATGGGCACAATTCTTTGAGCTGTAATGCT      40 Ester hydrolysis
13ZB37 GGGGCAGCGAGCGTAAGCTGGGGGACCTGCTATTAGCTGC      40 Ester hydrolysis
8ZC30 ACGGGTCGGGAAGTCCCCTCCTAGGAGGTGGACGGGTCTA      40 Amide hydrolysis
9BN114 CGAAGGCGGACCAGGGCGGA      20 Amide hydrolysis
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