Metal ion as both a cofactor and a probe of metal-binding sites in a uranyl-specific DNAzyme: A uranyl photocleavage study

Marjorie Cepeda-Plaza, Eric L. Null, Yi Lu

Resultado de la investigación: Article

19 Citas (Scopus)

Resumen

DNAzymes are known to bind metal ions specifically to carry out catalytic functions. Despite many studies since DNAzymes were discovered nearly two decades ago, the metal-binding sites in DNAzymes are not fully understood. Herein, we adopt uranyl photocleavage to probe specific uranyl-binding sites in the 39E DNAzyme with catalytically relevant concentrations of uranyl. The results indicate that uranyl binds between T23 and C25 in the bulge loop, G11 and T12 in the stem loop of the enzyme strand, as well as between T2.4 and G3 close to the cleavage site in the substrate strand. Control experiments using two 39E DNAzyme mutants revealed a different cleavage pattern of the mutated region. Another DNAzyme, the 8-17 DNAzyme, which has a similar secondary structure but shows no activity in the presence of uranyl, indicated a different uranyl-dependent photocleavage as well. In addition, a close correlation between the concentration-dependent photocleavage and enzymatic activities is also demonstrated. Together, these experiments suggest that uranyl photocleavage has been successfully used to probe catalytically relevant uranyl-binding sites in the 39E DNAzyme. As uranyl is the cofactor of the 39E DNAzyme as well as the probe, specific uranyl binding has now been identified without disruption of the structure.

Idioma originalEnglish
Páginas (desde-hasta)9361-9370
Número de páginas10
PublicaciónNucleic Acids Research
Volumen41
N.º20
DOI
EstadoPublished - nov 2013

Huella dactilar

Catalytic DNA
Metals
Binding Sites
Ions

ASJC Scopus subject areas

  • Genetics

Citar esto

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Metal ion as both a cofactor and a probe of metal-binding sites in a uranyl-specific DNAzyme : A uranyl photocleavage study. / Cepeda-Plaza, Marjorie; Null, Eric L.; Lu, Yi.

En: Nucleic Acids Research, Vol. 41, N.º 20, 11.2013, p. 9361-9370.

Resultado de la investigación: Article

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AB - DNAzymes are known to bind metal ions specifically to carry out catalytic functions. Despite many studies since DNAzymes were discovered nearly two decades ago, the metal-binding sites in DNAzymes are not fully understood. Herein, we adopt uranyl photocleavage to probe specific uranyl-binding sites in the 39E DNAzyme with catalytically relevant concentrations of uranyl. The results indicate that uranyl binds between T23 and C25 in the bulge loop, G11 and T12 in the stem loop of the enzyme strand, as well as between T2.4 and G3 close to the cleavage site in the substrate strand. Control experiments using two 39E DNAzyme mutants revealed a different cleavage pattern of the mutated region. Another DNAzyme, the 8-17 DNAzyme, which has a similar secondary structure but shows no activity in the presence of uranyl, indicated a different uranyl-dependent photocleavage as well. In addition, a close correlation between the concentration-dependent photocleavage and enzymatic activities is also demonstrated. Together, these experiments suggest that uranyl photocleavage has been successfully used to probe catalytically relevant uranyl-binding sites in the 39E DNAzyme. As uranyl is the cofactor of the 39E DNAzyme as well as the probe, specific uranyl binding has now been identified without disruption of the structure.

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