Literature DB >> 35226325

Preparation of Site-Specifically Spin-Labeled RNA by in Vitro Transcription Using an Expanded Genetic Alphabet.

Lisa Bornewasser1, Stephanie Kath-Schorr2.   

Abstract

Recent advances in pulsed electron paramagnetic resonance (EPR) spectroscopy enable studying structure and folding of nucleic acids. An efficient introduction of spin labels at specific positions within the oligonucleotide sequence is a prerequisite. We here present a step-by-step guide to synthesize long RNA oligonucleotides bearing spin labels at specific positions within the sequence. RNA preparation is achieved enzymatically via in vitro transcription using an expanded genetic alphabet. Highly structured, several hundred nucleotides long RNAs with two nitroxide spin labels at specific positions can be prepared by this method.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Electron paramagnetic resonance (EPR); Expanded genetic alphabet; In vitro transcription; Pulsed electron–electron double resonance (PELDOR); RNA; Spin labeling; Unnatural base pairs

Mesh：

Substances：

Year:  2022        PMID： 35226325     DOI： 10.1007/978-1-0716-2047-2_15

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  33 in total

1.  Nanometer distance measurements on RNA using PELDOR.

Authors:  Olav Schiemann; Axel Weber; Thomas E Edwards; Thomas F Prisner; Snorri T Sigurdsson
Journal:  J Am Chem Soc       Date:  2003-03-26       Impact factor: 15.419

2.  Probing secondary structures of spin-labeled RNA by pulsed EPR spectroscopy.

Authors:  Giuseppe Sicoli; Falk Wachowius; Marina Bennati; Claudia Höbartner
Journal:  Angew Chem Int Ed Engl       Date:  2010-08-23       Impact factor: 15.336

3.  Advanced EPR Methods for Studying Conformational Dynamics of Nucleic Acids.

Authors:  B Endeward; A Marko; V P Denysenkov; S Th Sigurdsson; T F Prisner
Journal:  Methods Enzymol       Date:  2015-07-02       Impact factor: 1.600

4.  Long-range distance measurements on nucleic acids in cells by pulsed EPR spectroscopy.

Authors:  Ivan Krstić; Robert Hänsel; Olga Romainczyk; Joachim W Engels; Volker Dötsch; Thomas F Prisner
Journal:  Angew Chem Int Ed Engl       Date:  2011-04-19       Impact factor: 15.336

5.  Posttranscriptional spin labeling of RNA by tetrazine-based cycloaddition.

Authors:  Christof Domnick; Gregor Hagelueken; Frank Eggert; Olav Schiemann; Stephanie Kath-Schorr
Journal:  Org Biomol Chem       Date:  2019-02-13       Impact factor: 3.876

6.  Post-synthetic Spin-Labeling of RNA through Click Chemistry for PELDOR Measurements.

Authors:  Mark Kerzhner; Dinar Abdullin; Jennifer Więcek; Hideto Matsuoka; Gregor Hagelueken; Olav Schiemann; Michael Famulok
Journal:  Chemistry       Date:  2016-07-14       Impact factor: 5.236

7.  A versatile approach for site-directed spin labeling and structural EPR studies of RNAs.

Authors:  Elena S Babaylova; Anton V Ivanov; Alexey A Malygin; Maria A Vorobjeva; Alia G Venyaminova; Yuliya F Polienko; Igor A Kirilyuk; Olesya A Krumkacheva; Matvey V Fedin; Galina G Karpova; Elena G Bagryanskaya
Journal:  Org Biomol Chem       Date:  2014-05-21       Impact factor: 3.876

8.  Relative orientation of rigid nitroxides by PELDOR: beyond distance measurements in nucleic acids.

Authors:  Olav Schiemann; Pavol Cekan; Dominik Margraf; Thomas F Prisner; Snorri Th Sigurdsson
Journal:  Angew Chem Int Ed Engl       Date:  2009       Impact factor: 15.336

9.  Spin labeling of oligonucleotides with the nitroxide TPA and use of PELDOR, a pulse EPR method, to measure intramolecular distances.

Authors:  Olav Schiemann; Nelly Piton; Jörn Plackmeyer; Bela E Bode; Thomas F Prisner; Joachim W Engels
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

10.  Base-specific spin-labeling of RNA for structure determination.

Authors:  Nelly Piton; Yuguang Mu; Gerhard Stock; Thomas F Prisner; Olav Schiemann; Joachim W Engels
Journal:  Nucleic Acids Res       Date:  2007-04-22       Impact factor: 16.971
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