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Identification of the Same Na(+)-Specific DNAzyme Motif from Two In Vitro Selections Under Different Conditions
Seyed-Fakhreddin Torabi1, Yi Lu2,3
1Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Journal of Molecular Evolution
|November 19, 2015
Summary
The Ce13 DNAzyme requires sodium (Na+) as a cofactor, revealing it as a variant of the NaA43 DNAzyme. This discovery enables the design of new allosteric DNAzymes for biotechnological applications.
Area of Science:
- Biochemistry
- Molecular Biology
- Catalysis
Background:
- Two RNA-cleaving DNAzymes, NaA43 and Ce13, exhibit distinct metal ion specificities.
- Despite functional differences, NaA43 and Ce13 share significant sequence similarity (~60% identity).
Purpose of the Study:
- To investigate the functional relationship between NaA43 and Ce13 DNAzymes.
- To elucidate the role of metal ions in the activity of these DNAzymes.
Main Methods:
- In vitro selection techniques were employed for DNAzyme isolation.
- Systematic analysis of DNAzyme activity under varying metal ion conditions.
Main Results:
- Sodium (Na+) was identified as an obligate cofactor for the Ce13 DNAzyme.
- Lanthanides could not initiate cleavage without the presence of Na+.
- Ce13 DNAzyme activity is dependent on Na+, with lanthanides potentially acting as allosteric modulators.
Conclusions:
- The Ce13 DNAzyme is a variant of the NaA43 DNAzyme, functioning optimally with Na+.
- A novel DNAzyme motif with Na+-specificity and potential for allosteric regulation has been identified.
- These findings pave the way for designing novel allosteric DNAzymes for biotechnological applications.
