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  Deoxyribozyme-mediated ligation for incorporating EPR spin labels and reporter groups into RNA.

Wawrzyniak-Turek, K., & Höbartner, C. (2014). Deoxyribozyme-mediated ligation for incorporating EPR spin labels and reporter groups into RNA. In D. Burke-Aguero (Ed.), Riboswitch discovery, structure and function (pp. 85-104). Amsterdam: Elsevier. doi:10.1016/B978-0-12-801122-5.00004-0.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0024-4B6A-E Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-CCEF-1
Genre: Book Chapter

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 Creators:
Wawrzyniak-Turek, K.1, Author              
Höbartner, C.1, Author              
Affiliations:
1Research Group of Nucleic Acid Chemistry, MPI for Biophysical Chemistry, Max Planck Society, ou_578605              

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Free keywords: Convertible nucleosides; EPR spectroscopy; Nitroxyls; RNA ligation; Solid-phase synthesis; Spin labels
 Abstract: Preparation of site-specifically labeled RNA for spectroscopic studies is a multistep process and requires handling of delicate samples. This chapter is focused on the synthesis of spin-labeled RNA using convertible nucleosides and the application of the deoxyribozyme 9DB1* for the ligation of RNA fragments. The convertible nucleoside approach enables the attachment of nitroxyls as paramagnetic reporters at the exocyclic amino groups of cytidine, adenosine, and guanosine nucleobases in synthetic RNA. The deoxyribozyme 9DB1* is a synthetic single-stranded DNA with RNA ligase activity that can be used as an alternative to protein enzymes (T4 RNA/DNA ligases) for covalently joining RNA fragments via native 3'-5' phosphodiester bonds. The combination of solid-phase synthesis and DNA-catalyzed RNA ligation provides reliable access to site-specifically labeled functional RNAs for spectroscopic studies. A particular advantage of using deoxyribozymes for RNA ligation lies in the mild reaction conditions that prevent chemical damage to sensitive labels. As an example, we describe a detailed protocol for the synthesis of TEMPO-labeled SAM-I riboswitch RNA.

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Language(s): eng - English
 Dates: 2014-11-252014
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Degree: -

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Title: Riboswitch discovery, structure and function
Source Genre: Book
 Creator(s):
Burke-Aguero, D., Editor
Affiliations:
-
Publ. Info: Amsterdam : Elsevier
Pages: XXIII, 546 Volume / Issue: - Sequence Number: - Start / End Page: 85 - 104 Identifier: ISBN: 9780128011225

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Title: Methods in Enzymology
Source Genre: Series
 Creator(s):
Abelson, J. N., Editor
Affiliations:
-
Publ. Info: -
Pages: - Volume / Issue: 549 Sequence Number: - Start / End Page: - Identifier: -