DNA-catalyzed DNA cleavage by a radical pathway with well-defined products

Yujeong Lee, Paul C. Klauser, Benjamin M. Brandsen, Cong Zhou, Xinyi Li, Scott K Silverman

Research output: Contribution to journalArticle

Abstract

We describe an unprecedented DNA-catalyzed DNA cleavage process in which a radical-based reaction pathway cleanly results in excision of most atoms of a specific guanosine nucleoside. Two new deoxyribozymes (DNA enzymes) were identified by in vitro selection from N40 or N100 random pools initially seeking amide bond hydrolysis, although they both cleave simple single-stranded DNA oligonucleotides. Each deoxyribozyme generates both superoxide (O2 or HOO·) and hydrogen Peroxide (H2O2) and leads to the same set of products (3'-phosphoglycoIate, 5'-phosphate, and base propenal) as formed by the natural product bleomycin, with product assignments by mass spectrometry and colorimetric assay. We infer the same mechanistic pathway, involving formation of the C4' radical of the guanosine nucleoside that is subsequently excised. Consistent with a radical pathway, glutathione fully suppresses catalysis. Conversely, adding either superoxide or H2O2 from the outset strongly enhances catalysis. The mechanism of generation and involvement of superoxide and H2O2 by the deoxyribozymes is not yet defined. The deoxyribozymes do not require redox-active metal ions and function with a combination of Zn2+ and Mg2+, although including Mn2+ increases the activity, and Mn2+ alone also supports catalysis. In contrast to all of these observations, unrelated DNA-catalyzed radical DNA cleavage reactions require redox-active metals and lead to mixtures of products. This study reports an intriguing example of a well-defined, DNA-catalyzed, radical reaction process that cleaves single-stranded DNA and requires only redox-inactive metal ions.

Original languageEnglish (US)
Pages (from-to)255-261
Number of pages7
JournalJournal of the American Chemical Society
Volume139
Issue number1
DOIs
StatePublished - Jan 11 2017

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Catalytic DNA
DNA Cleavage
cleavage
DNA
Catalysis
Superoxides
Oxidation-Reduction
Guanosine
Single-Stranded DNA
Metals
Nucleosides
catalysis
Ions
Metal ions
Bleomycin
Biological Products
Amides
Oligonucleotides
Hydrogen Peroxide
Glutathione

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

DNA-catalyzed DNA cleavage by a radical pathway with well-defined products. / Lee, Yujeong; Klauser, Paul C.; Brandsen, Benjamin M.; Zhou, Cong; Li, Xinyi; Silverman, Scott K.

In: Journal of the American Chemical Society, Vol. 139, No. 1, 11.01.2017, p. 255-261.

Research output: Contribution to journalArticle

Lee, Yujeong ; Klauser, Paul C. ; Brandsen, Benjamin M. ; Zhou, Cong ; Li, Xinyi ; Silverman, Scott K. / DNA-catalyzed DNA cleavage by a radical pathway with well-defined products. In: Journal of the American Chemical Society. 2017 ; Vol. 139, No. 1. pp. 255-261.
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