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Literature DB >> 28984884

Debranchase-resistant labeling of RNA using the 10DM24 deoxyribozyme and fluorescent modified nucleotides.

Tucker J Carrocci¹, Lea Lohe², Matthew J Ashton¹, Claudia Höbartner³, Aaron A Hoskins¹.

Abstract

The 10DM24 deoxyribozyme can site-specifically label RNAs with fluorophore-GTP conjugates; however, the 2',5'-branched RNA linkage is readily cleaved by debranchase. To prevent loss of labels upon cleavage, we synthesized phosphorothioate-modified, fluorescent GTP derivatives and elaborated conditions for their incorporation by 10DM24. RNAs labeled with fluorescent derivatives of Sp-GTPS were found to be resistant to debranchase.

Entities: Chemical Disease Gene Species

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Year: 2017 PMID： 28984884 PMCID： PMC5668183 DOI： 10.1039/c7cc06703h

Source DB: PubMed Journal: Chem Commun (Camb) ISSN： 1359-7345 Impact factor: 6.222

21 in total

1. Engineering a selective small-molecule substrate binding site into a deoxyribozyme.

Authors: Claudia Höbartner; Scott K Silverman
Journal: Angew Chem Int Ed Engl Date: 2007 Impact factor: 15.336

Review 2. Nucleoside phosphorothioates.

Authors: F Eckstein
Journal: Annu Rev Biochem Date: 1985 Impact factor: 23.643

Review 3. RNA labeling, conjugation and ligation.

Authors: Eduardo Paredes; Molly Evans; Subha R Das
Journal: Methods Date: 2011-02-24 Impact factor: 3.608

Review 4. Enzyme-mediated tagging of RNA.

Authors: Lea Anhäuser; Andrea Rentmeister
Journal: Curr Opin Biotechnol Date: 2017-04-08 Impact factor: 9.740

Review 5. Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes.

Authors: Scott K Silverman
Journal: Trends Biochem Sci Date: 2016-05-25 Impact factor: 13.807

6. Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain.

Authors: S Basu; S A Strobel
Journal: RNA Date: 1999-11 Impact factor: 4.942

7. Synthesis, characterization, and biological properties of small branched RNA fragments containing chiral (Rp and Sp) 2',5'-phosphorothioate linkages.

Authors: Rawan Mourani; Masad J Damha
Journal: Nucleosides Nucleotides Nucleic Acids Date: 2006 Impact factor: 1.381

Debranchase-resistant labeling of RNA using the 10DM24 deoxyribozyme and fluorescent modified nucleotides.

1. Engineering a selective small-molecule substrate binding site into a deoxyribozyme.

Review 2. Nucleoside phosphorothioates.

Review 3. RNA labeling, conjugation and ligation.

Review 4. Enzyme-mediated tagging of RNA.

Review 5. Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes.

6. Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain.

7. Synthesis, characterization, and biological properties of small branched RNA fragments containing chiral (Rp and Sp) 2',5'-phosphorothioate linkages.

8. Functional Hallmarks of a Catalytic DNA that Makes Lariat RNA.

9. Site-specific labeling of RNA at internal ribose hydroxyl groups: terbium-assisted deoxyribozymes at work.

10. Functional identification of catalytic metal ion binding sites within RNA.

Review 1. Coming Together: RNAs and Proteins Assemble under the Single-Molecule Fluorescence Microscope.

2. Repurposing Antiviral Drugs for Orthogonal RNA-Catalyzed Labeling of RNA.

Review 3. Strategies for Covalent Labeling of Long RNAs.