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Literature DB >> 20946766

Metal ion-based RNA cleavage as a structural probe.

Abstract

It is well established that many metal ions accelerate the spontaneous degradation of RNA. This property has been exploited in several ways to garner information about RNA structure, especially in regards to the location of site-specifically bound metal ions, the presence of defined structural motifs, and the occurrence of conformational changes in structured RNAs. In this chapter, we review this information, briefly giving strengths and limitations for each of these approaches. Finally, we provide a general protocol to perform metal ion-mediated cleavage of RNA.

Entities: Chemical

Mesh：

Substances：
Metals
RNA

Year: 2009 PMID： 20946766 DOI： 10.1016/S0076-6879(09)68005-8

Source DB: PubMed Journal: Methods Enzymol ISSN： 0076-6879 Impact factor: 1.600

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Cited

19 in total

1. Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects.

Authors: Haoyuan Chen; Joseph A Piccirilli; Michael E Harris; Darrin M York
Journal: Biochim Biophys Acta Date: 2015-03-23

2. Predicting RNA-Metal Ion Binding with Ion Dehydration Effects.

Authors: Li-Zhen Sun; Shi-Jie Chen
Journal: Biophys J Date: 2018-12-13 Impact factor: 4.033

3. Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core.

Authors: David M Truong; David J Sidote; Rick Russell; Alan M Lambowitz
Journal: Proc Natl Acad Sci U S A Date: 2013-09-16 Impact factor: 11.205

4. Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

Authors: Kyle E Watters; Angela M Yu; Eric J Strobel; Alex H Settle; Julius B Lucks
Journal: Methods Date: 2016-04-12 Impact factor: 3.608

Metal ion-based RNA cleavage as a structural probe.

1. Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects.

2. Predicting RNA-Metal Ion Binding with Ion Dehydration Effects.

3. Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core.

4. Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

5. Direct structural analysis of modified RNA by fluorescent in-line probing.

6. Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs.

7. A targeted DNA substrate mechanism for the inhibition of HIV-1 integrase by inhibitors with antiretroviral activity.

Review 8. Theory Meets Experiment: Metal Ion Effects in HCV Genomic RNA Kissing Complex Formation.

9. Database proton NMR chemical shifts for RNA signal assignment and validation.

Review 10. Tackling structures of long noncoding RNAs.