TY - JOUR
T1 - Identification of the Same Na+-Specific DNAzyme Motif from Two In Vitro Selections Under Different Conditions
AU - Torabi, Seyed Fakhreddin
AU - Lu, Yi
N1 - We thank Claire E. McGhee for critical reading of the manuscript. This work was supported by US National Institutes of Health (Grant R01ES016865).
PY - 2015/12/1
Y1 - 2015/12/1
N2 - We report an investigation of the functional relationship between two independently selected RNA-cleaving DNAzymes, NaA43, and Ce13, through in vitro selection. The NaA43 DNAzyme was obtained through a combination of gel-based and column-based in vitro selection in the presence of Na+ and reported to be highly selective for Na+ over other metal ions. The Ce13 DNAzyme was isolated via a gel-based method in the presence of Ce4+ and found to be active with trivalent lanthanides, Y3+ and Pb2+. Despite completely different activities reported for the two DNAzymes, they share a high level of sequence similarity (~60 % sequence identity). In this work, we systematically analyzed the activity of both DNAzymes to elucidate their potential functional relationship. We found that Na+ is an obligate cofactor of the Ce13 DNAzyme and lanthanides cannot initiate the cleavage reaction in the absence of Na+. Hence, we conclude that the Ce13 DNAzyme is a variant of the NaA43 DNAzyme that catalyzes reaction in the presence Na+ and also utilizes lanthanides in a potentially allosteric manner. These results have identified a new DNAzyme motif that is not only remarkably Na+-specific, but also allows for design of novel allosteric DNAzymes for different biotechnological applications.
AB - We report an investigation of the functional relationship between two independently selected RNA-cleaving DNAzymes, NaA43, and Ce13, through in vitro selection. The NaA43 DNAzyme was obtained through a combination of gel-based and column-based in vitro selection in the presence of Na+ and reported to be highly selective for Na+ over other metal ions. The Ce13 DNAzyme was isolated via a gel-based method in the presence of Ce4+ and found to be active with trivalent lanthanides, Y3+ and Pb2+. Despite completely different activities reported for the two DNAzymes, they share a high level of sequence similarity (~60 % sequence identity). In this work, we systematically analyzed the activity of both DNAzymes to elucidate their potential functional relationship. We found that Na+ is an obligate cofactor of the Ce13 DNAzyme and lanthanides cannot initiate the cleavage reaction in the absence of Na+. Hence, we conclude that the Ce13 DNAzyme is a variant of the NaA43 DNAzyme that catalyzes reaction in the presence Na+ and also utilizes lanthanides in a potentially allosteric manner. These results have identified a new DNAzyme motif that is not only remarkably Na+-specific, but also allows for design of novel allosteric DNAzymes for different biotechnological applications.
KW - DNAzyme (deoxyribozyme)
KW - Functional motif
KW - In vitro selection
KW - Lanthanides
KW - Sodium
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U2 - 10.1007/s00239-015-9715-7
DO - 10.1007/s00239-015-9715-7
M3 - Article
C2 - 26577294
AN - SCOPUS:84948382395
SN - 0022-2844
VL - 81
SP - 225
EP - 234
JO - Journal of Molecular Evolution
JF - Journal of Molecular Evolution
IS - 5-6
ER -