Identification of the Same Na+-Specific DNAzyme Motif from Two In Vitro Selections Under Different Conditions
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.
KeywordsDNAzyme (deoxyribozyme) In vitro selection Sodium Lanthanides Functional motif
We thank Claire E. McGhee for critical reading of the manuscript. This work was supported by US National Institutes of Health (Grant R01ES016865).