DNAmoreDB - A Database of Deoxyribozymes

Published on 2015 in Nucleic Acids Res. volume 43 issue 1.

PubMed ID: 25488814

DOI:10.1093/nar/gku1296

Abstract:

In vitro selection of RNA-cleaving DNAzymes was performed using three heavy lanthanide ions (Ln3+): Ho3+, Er3+ and Tm3+. The resulting sequences were aligned together and about half of the library contained a new family of DNAzyme. These DNAzymes have a simple loop structure, and they are active only with the seven heavy Ln3+. Among the tested non-lanthanide ions, only Y3+ induced cleavage and even Pb2+ failed to cleave, suggesting a very high specificity. A representative DNAzyme, Tm7, has a sigmoidal metal binding curve with a Hill coefficient of 3, indicating that three metal ions are involved in the catalytic step. Its pH-rate profile has a slope of 1, suggesting a single deprotonation step is involved in the rate-limiting step. Tm7 has a cleavage rate of 1.6 min−1 at pH 7.8 with 10 μM Er3+. Phosphorothioate substitution at the cleavage junction completely inhibits the activity, which cannot be rescued by Cd2+ alone, or by a mixture of Er3+ and Cd2+, suggesting that two interacting metal ions are involved in direct bonding to both non-bridging oxygen atoms. A new model involving three lanthanide ions is proposed based on this study. A biosensor is engineered using Tm7 to detect Dy3+ down to 14 nM.



DNAzymes linked to this article:

Name Isolated sequence Length Reaction
Tm32 CTGCAGAATTCTAATACGAGTCACTATAGGAAGARGGCGAAACATCTTAAGAGCCGTCAGGTATGCCCTGTCAAAAACTCGTATAGTCGGTAAGCTTG      98 RNA cleavage
Tm7 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCGATACTCTCTTTGACGTTCGTATAAACGAGACAATAGTCGGTAAGCTTG      98 RNA cleavage
Ho7 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTAGAAATTTTCTATAACGAGTTTGATCATGTACCGTTAGTCGGTAAGCTTG      98 RNA cleavage
Ho13 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTAGAAATTTTCTATAACGAGTTTGATCATGTACCGTTAGTCGGTAAGCTTG      98 RNA cleavage
Ho14 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTAGAAATTTTCTATAACGAGTTTGATCATGTACCGTTAGTCGGTAAGCTTG      98 RNA cleavage
Er5 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTGGCAAATCTCTTTAACGAATTTAGTAGTGTACCGTAGTCGGTAAGCTTG      98 RNA cleavage
Er1 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCGAGATGATTTATATAACGAGTAAAGGACCGATTGTAGTCGGTAAGCTTG      98 RNA cleavage
Er16 CTGCAGAATTCTAATACSAGTCACYMTAGGAAGATGGCGAAACATCTTAGACAAATTATATAACGAGTATAGGAGCGAGCACATAGTCGGTAAGCTTG      98 RNA cleavage
Er18 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTGATTCTCTCTTTAACGAGTATCAGTGGCTRCAACGTAGTCGGTAAGCTTG      98 RNA cleavage
Er39 CTGCAGAATTCTAATACCTATAGGAAGATGGCGAAACATCTTGATTCTCTCTTTAACGAGTATCAGTGGCTCCAACGTAGTCGGTAAGCTTG      92 RNA cleavage
Er11 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTGATTCTCTCTCTAACGAGTATCAGTGGCTCCACCGTAGTCGGTAAGCTTG      98 RNA cleavage
Tm4 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCAAAATTCAGTCTGACGCGGTAGGTGGGTCCACCATAGTCGGTAAGCTTG      98 RNA cleavage
Tm26 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTAAATATAATCTTTAACGAGTAACCCAGACACATATAGTCGGTAAGCTTG      97 RNA cleavage
Ho12 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTATATGATATCTTTTAACGAGTATTAAACCATAAGATAGTCGGTAAGCTTG      98 RNA cleavage
Tm27 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCTATGTTACTATCTAACGAGAAGAGAACCATAACTAGCGGTAAGCTTG      96 RNA cleavage
Ho9 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCAGTACCATCAATCTAACGAGTGTTAGAACGCAAATAGTCGGTAAGCTTG      98 RNA cleavage
Er34 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCGAAAGCAAATTTATTTGACGAGAATGCATACAAACAGTCGGTAAGCTTG      98 RNA cleavage
Tm14 CTGCAGAATTCTAATAGAGTCACTATGGAAGATGGCGAAACATCTTCAAAATTTACTATAACGAGTGTTTAACGTGGAAATTAGCGGTAAGCTTG      95 RNA cleavage
Ho2 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTAGCTCAATCAGCACGCATGCGTGATTATAGTGAAGTAGTCGGTAAGCTTG      98 RNA cleavage
Er22 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCTAGAATCATTTATTTGACCACGGATTGCAGATTATAGCGGTAAGCTTG      97 RNA cleavage
Ho6 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTAATAACTTTATCTAACGAAGTATTACTCAAAGAGGTAGTCGGTAAGCTTG      98 RNA cleavage
Er32 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTTGTACATTGATCTGACTCACTCATGCTGTGGACCTAGTCGGTAAGCTTG      98 RNA cleavage
Er24 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTAAACAGGAATTTCTTTAACTCGCTGTAGGTGGACTAGTCGGTAAGCTTG      98 RNA cleavage
Er30 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTAAAACTTTATTTGACTCGGAGGAAGAGAATTGGTAGTCGGTAAGCTTG      97 RNA cleavage
Ho4 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCAATTTATTCTTTGATGAGAAAAAGGTGGAACTATTAGTCGGTAAGCTTG      98 RNA cleavage
Ho11 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCTAAAATTCCCTCTAACTCGTACAATGACCCTTGTTAGTCGGTAAGCTTG      98 RNA cleavage
Er36 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTAAACGTACATCATCTCTAACTCGTTGATAGAACTTAGTCGGTAAGCTTG      98 RNA cleavage
Er4 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTAGTACCCAAAGGGAGGATGTTATAACTCGTATCTCTAGTCGGTAAGCTTG      98 RNA cleavage
Tm16 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTAAGAGCCGTCAGGTATGCCCTGTCAAAAACTCGTATAGTCGGTAAGCTTG      98 RNA cleavage
Er23 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCCTCAAACTGATATCAGAAGATCAACTCCTATAACTCGTAGTCGGTAAGCTTG      98 RNA cleavage
Ho15 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCTAATAATTCTTTTAACTCGATTATGTAGCGTATATAGCGGTAAGCTTG      97 RNA cleavage
Tm8 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCATACACGTTTTTTTAACTCGCTATGTATGGAAGGTAGCGGTAAGCTTG      97 RNA cleavage
Ho1 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTAGAGGTACGTATAGAGACGAGGTGACGCAATTGAGTAGTCGGTAAGCTTG      98 RNA cleavage
Er6 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTAGATATGGAAACGATTGTGAGGCTATATGACGAGGTAGCGGTAAGCTTG      97 RNA cleavage
Er13 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCGAAAAAGGTATCTGAGTTTATTTGATTCGTTGATTAGTCGGTAAGCTTG      98 RNA cleavage
Er31 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTATAGGTAATGGAAACTAATATTTGACTCGCTGATATAGTCGGTAAGCTTG      98 RNA cleavage
Er25 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTGGAGAGAGAAACTCAATTTATTTGACTCAATGGGTTAGTCGGTAAGCTTG      98 RNA cleavage
Er35 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTAGGGGTAGTGCGTAGGACGAGATTTATTTGGCTCGTAGCGGTAAGCTTG      97 RNA cleavage
Tm17 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTGAGAAGCACGAAGTGCAGGTTTATTTGACAAATAATAGTCGGTAAGCTTG      98 RNA cleavage
Er12 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTGTATAACTTAAGTAGGTTATTTTAACGAGTATTATTAGTCGGTAAGCTTG      98 RNA cleavage
Er26 CTGCAGAATTTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCGACATAACGAATGTTACCCCCTTTAACGAGTAATTAGCCGGTAAGCTTG      97 RNA cleavage
Er27 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTTATAGATCGATAGAGGATTTATTTGACAGGTATTTAGTCGGTAAGCTTG      98 RNA cleavage
Er33 CGCCCTTAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTTATAGATCGATAGAGGATTTATTTGACAGGTATTAGTCGGTAAGCTTG      98 RNA cleavage
Tm1 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTGTACAAGAACGGGAGAGGGTATATTTAAATCGTAGTAGCGGTAAGCTTG      97 RNA cleavage
Er9 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTG      96 RNA cleavage
Er20 CTGCAGAATTCTAATACGATCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTG      95 RNA cleavage
Er10 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTG      96 RNA cleavage
Tm3 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTG      96 RNA cleavage
Tm22 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTG      96 RNA cleavage
Er37 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAGATGCGGTTATAGTGACGGTAAGCTTG      96 RNA cleavage
Ho3 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCACAAATAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTG      96 RNA cleavage
Ho10 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCACCGGACAAACTATGGGAGGAGCGGTTATAGTCGGTAAGCTTG      98 RNA cleavage
Er2 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGGGTCCACTATGCACAACGGTTATAGTGACGGTAAGCTTG      97 RNA cleavage
Er17 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGGGTCCACTATGCACAACGGTTATAGTGACGGTAAGCTTG      97 RNA cleavage
Er28 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGGGTCCACTATGCACAACGGTTACAGTGACGGTAAGCTTG      97 RNA cleavage
Ho8 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGGGTCCACTATGCACAACGGTTGTAGTGACGGTAAGCTTG      97 RNA cleavage
Er19 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGGGTCCACTATGCACAACGGTTATAGTGGCGGTAAGCTTG      97 RNA cleavage
Er38 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGTGTCCACTATGCACAACGGTTATAGTGACGGTAAGCTTG      97 RNA cleavage
Ho5 CTGCAGAATTCCAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACGAGATAGAATGTTGTACAGTCTAGCGGTTATAGTCGGTAAGCTTG      96 RNA cleavage
Er15 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTGTATACCGGAAAGGTAAAATTAATTTAACGAGAGTAGTCGGTAAGCTTG      98 RNA cleavage
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