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Strategies for Characterization of Enzymatic Nucleic Acids

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Catalytically Active Nucleic Acids

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 170))

Abstract

Practical application of enzymatic nucleic acids has received more attention in recent years. Understanding the mechanism of catalysis and availability of information on potentials and limitations of these enzymes expands their application scope. A general approach for characterization of functional macromolecules including enzymatic nucleic acids is to perturb a specific set of condition and to follow the perturbation effect by biophysical and biochemical methods. This chapter reviews several perturbation strategies for functional nucleic acids, including deletion, mutation, and modifications of backbone and nucleobases, and consequent kinetic analysis, spectroscopic investigations, and probing assays. In addition to single point mutation and modifications, different combinatorial approaches for perturbation interference analysis provide reliable high amounts of data in a time-effective manner. The chapter compares various combinatorial perturbation interference analysis methods, that is, combinatorial mutation interference analysis (CoMA), nucleotide analogue interference mapping for RNA and DNA (NAIM and dNAIM), chemical and enzymatic combinatorial nucleoside deletion scanning (NDS), and dimethyl sulfate interference (DMSi).

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Abbreviations

CoMA:

Combinatorial mutation interference analysis

DMSi:

Dimethyl sulfate interference

dNAIM:

Nucleotide analogue interference mapping of DNA

NAIM:

Nucleotide analogue interference mapping

NDS:

Combinatorial nucleoside deletion scanning

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Author information

Authors and Affiliations

  1. Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran

    Fatemeh Javadi-Zarnaghi

  2. Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Göttingen, Germany

    Claudia Höbartner

Authors
  1. Fatemeh Javadi-Zarnaghi
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  2. Claudia Höbartner
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Corresponding author

Correspondence to Fatemeh Javadi-Zarnaghi .

Editor information

Editors and Affiliations

  1. Branch Bioanalytics and Bioprocesses (IZI-BB) Biomarker Validation and Assay Development, Fraunhofer Institute for Cell Therapy and Immunology, Potsdam, Germany

    Harald Seitz

  2. Institut für Technische Chemie, Leibniz Universität Hannover, Hannover, Germany

    Frank Stahl

  3. Institut für Technische Chemie, Leibniz Universität Hannover, Hannover, Niedersachsen, Germany

    Johanna-Gabriela Walter

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Javadi-Zarnaghi, F., Höbartner, C. (2017). Strategies for Characterization of Enzymatic Nucleic Acids. In: Seitz, H., Stahl, F., Walter, JG. (eds) Catalytically Active Nucleic Acids. Advances in Biochemical Engineering/Biotechnology, vol 170. Springer, Cham. https://doi.org/10.1007/10_2016_59

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