DNAmoreDB - A Database of Deoxyribozymes

Published on 2014 in Anal. Chem. volume 86 issue 19.

PubMed ID: 25199650

DOI:10.1021/ac5029962

Abstract:

Developing biosensors for lanthanides is an important but challenging analytical task. To address this problem, in vitro selection of RNA-cleaving DNAzymes was carried out using a library containing a region of 35 random nucleotides in the presence of Lu3+, since Lu3+ was reported to be the most efficient lanthanide for RNA cleavage. The resulting DNA sequences can be aligned to a single family with two conserved stretches of nucleotides. One of the representative DNAzymes (named Lu12) was further studied. Lu12 is more active with smaller lanthanides and has the lowest activity in the presence of the largest lanthanide (lutetium). Its cleavage rate is 0.12 min–1 in the presence of 10 μM Nd3+ at pH 6.0. This is a new DNAzyme, and a catalytic beacon sensor is designed by attaching a fluorophore/quencher pair, detecting Nd3+ down to 0.4 nM (72 parts-per-trillion). This DNAzyme is highly selective for lanthanides as well, showing cleavage only with two nonlanthanide ions: Y3+ and Pb2+. We previously reported a DNAzyme named Ce13d, which has similar responses to all the trivalent lanthanides. Combining these two allows for a ratiometric assay that identifies a few large lanthanides.



DNAzymes linked to this article:

Name Isolated sequence Length Reaction
Lu12 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAACGGTTATAGTGAAAGGAAACTCGTAGTCGGTAAGCTTGGCAC      99 RNA cleavage
Lu2 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGGGTCCACTATGCACAACGGTTATAGTGACGGTAAGCTTGGCAC      101 RNA cleavage
Lu7 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTCRCAAGGAAGGGCCACTATGCACAACGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu29 (identical to Lu2) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGGGTCCACTATGCACAACGGTTATAGTGACGGTAAGCTTGGCAC      101 RNA cleavage
Lu17 (identical to Lu2) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGGGTCCACTATGCACAACGGTTATAGTGACGGTAAGCTTGGCAC      101 RNA cleavage
Lu1 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGGGTACTATGCACAACGGTTATAGTGACGGTAAGCTTGGCAC      99 RNA cleavage
Lu27 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGGGTCCACTATACACAACGGTTATAGTGACGGTAAGCTTGGCAC      101 RNA cleavage
Lu30 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAAGGGTCCACTACACACAACGGTTATAGTGACGGTAAGCTTGGCAC      101 RNA cleavage
Lu31 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACGAGAGGGAAATACAATGCCCTCGGTTATAGTGACGGTAAGCTTGGCAC      99 RNA cleavage
Lu11 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTTGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu32 CTGTAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu40 (identical to Lu8) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu39 (identical to Lu8) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu35 (identical to Lu8) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu28 (identical to Lu8) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu21 (identical to Lu8) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu20 (identical to Lu8) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu13 (identical to Lu8) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu8 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu14 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATTGGAATGCGGTTATAGTGACGGTAAGCTTGGCAC      99 RNA cleavage
Lu9 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTGGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu37 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCGGTGGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu18 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTCTACAAGCATCAGTTGATTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu22 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGACTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu34 (identical to Lu22) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGACTGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu24 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGATCGGAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu4 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCATCAGTAGGTTGCAAATGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu5 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGTTATATGGTAAGAATATAGCGGTTATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu36 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGAATCCGACATTCAGGATTCGGTTATAGTGACGGTAAGCTTGGCAC      99 RNA cleavage
Lu16 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACAAAAATGTAGACAGCGAGCATTCCGAATTAGGTTAATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu23 (identical to Lu16) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACAAAAATGTAGACAGCGAGCATTCCGAATTAGGTTAATAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu25 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGAAAAATGTCTGACGTTTTTGGTTATAGTGACGGTAAGCTTGGCAC      99 RNA cleavage
Lu38 (identical to Lu12) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAACGGTTATAGTGAAAGGAAACTCGTAGTCGGTAAGCTTGGCAC      99 RNA cleavage
Lu15 (identical to Lu12) CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAACGGTTATAGTGAAAGGAAACTCGTAGTCGGTAAGCTTGGCAC      99 RNA cleavage
Lu6 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAACGGTTATAGTGAAAGGAAACTRGTAGTCGGTAAGCTTGGCAC      99 RNA cleavage
Lu33 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGGAACGGTTATACTGACGAGGGATACTAGTGACGGTAAGCTTGGCAC      100 RNA cleavage
Lu26 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCGGAGCGGTTATAGGAACGAGCGATATAGTCGGTAAGCTTGGCAC      99 RNA cleavage
Lu10 CTGCAGAATTCTAATACGAGTCACTATAGGAAGATGGCGAAACATCTTTACAAGCGAAGCGGTTATGGGGACACGCACTGGTGACGGTAAGCTTGGCAC      99 RNA cleavage
Lu1a TTTCGCCATCTTTACAAGGAAGGATGCACAACGGTTATAGTGACTCGTGAC      51 RNA cleavage
Lu1b TTTCGCCATCTTTACAAGGAACACAACGGTTATAGTGACTCGTGAC      46 RNA cleavage
Lu1c TTTCGCCATCTTTACAAGAAAAAAAAAAAAACGGTTATAGTGACTCGTGAC      51 RNA cleavage
Lu1d TTTCGCCATCTTTACAAGTTTTTTTTTTTTTCGGTTATAGTGACTCGTGAC      51 RNA cleavage
Lu1e TTTCGCCATCTTTACAAGCCCCCCCCCCCCCCGGTTATAGTGACTCGTGAC      51 RNA cleavage
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