Pin-point chemical modification of RNA with diverse molecules through the functionality transfer reaction and the copper-catalyzed azide–alkyne cycloaddition reaction

Onizuka, Kazumitsu; Shibata, Atsushi; Taniguchi, Yoshihiro; Sasaki, Shigeki

doi:10.1039/c1cc10582e

Cited by 39 publications

(28 citation statements)

References 16 publications

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“…A high selectivity for rC was clearly shown in Figure 3B. The site-specific labeling of rC in RNA has been demonstrated by using an acetylene-functionalized pyridinyl keto unit ( 8 ) for a Cu-catalyzed click reaction with azido derivatives (Biotin-N 3 and FAM-N 3 ) (31)(Supplementary Scheme S2 and Supplementary Figure S3).…”

Section: Resultsmentioning

confidence: 98%

“…Subsequently, it was found that the transfer reaction was enhanced with selectively for the 2-amino group of the guanine base at alkaline pH or in the presence of NiCl2 at neutral pH (29,30). This method was applied to the site-specific labeling of RNA (31) and O 6 -methyl guanosine-containing DNA (32). The functionality transfer ODN probe (FT-ODN) is advantageous for RNA modification in that the driving force to initiate the transfer reaction is duplex formation with the target RNA.…”

Section: Introductionmentioning

confidence: 99%

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Remarkable acceleration of a DNA/RNA inter-strand functionality transfer reaction to modify a cytosine residue: the proximity effect via complexation with a metal cation

et al. 2014

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Modified nucleosides in natural RNA molecules are essential for their functions. Non-natural nucleoside analogues have been introduced into RNA to manipulate its structure and function. We have recently developed a new strategy for the in situ modification of RNA based on the functionality transfer reaction between an oligodeoxynucleotide probe and an RNA substrate. 2′-Deoxy-6-thioguanosine (6-thio-dG) was used as the platform to anchor the transfer group. In this study, a pyridinyl vinyl ketone moiety was newly designed as the transfer group with the expectation that a metal cation would form a chelate complex with the pyridinyl-2-keto group. It was demonstrated that the (E)-pyridinyl vinyl keto group was efficiently and specifically transferred to the 4-amino group of the opposing cytosine in RNA in the presence of NiCl2 with more than 200-fold accelerated rate compared with the previous system with the use of the diketo transfer group. Detailed mechanistic studies suggested that NiCl2 forms a bridging complex between the pyridinyl keto moiety and the N7 of the purine residue neighboring the cytosine residue of the RNA substrate to bring the groups in close proximity.

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Section: Resultsmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Remarkable acceleration of a DNA/RNA inter-strand functionality transfer reaction to modify a cytosine residue: the proximity effect via complexation with a metal cation

et al. 2014

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“…Functional group transfer has been used to selectively label cytosine and guanine residues in RNA molecules [6,[92][93][94][95] (Fig. 2C).…”

Section: Functionality-transfer Reactionmentioning

confidence: 99%

Specific labeling: An effective tool to explore the RNA world

2015

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Our knowledge about the functional diversity and importance of RNA in biology has grown enormously over the past three decades and has driven efforts to develop better tools to characterize RNAs. Amongst these tools are methods for preparing specifically labeled or chemically modified RNAs, which are essential for basic research, biomedical, and clinical applications. Understanding the potential and limits of these different RNA synthesis and labeling strategies is important in deciding how to approach the preparation of a particular RNA molecule. Here, we review these various labeling methods and future directions of the field.

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“…However, over the last few years several research groups have applied the powerful copper-catalyzed azide-alkyne cycloaddition reaction (i.e. CuAAC or click) (23–25, 29–33) and the strain-promoted azide-alkyne cycloaddition reaction (i.e. SPAAC or copper-free click) to the problem of RNA functionalization (34–35).…”

Section: Introductionmentioning

confidence: 99%

“…Thus the sequence selective binding of the DNA directs the transfer reaction to a specific guanosine in the RNA. They showed this selective reaction could be carried out with a 1,3-diketone transfer group bearing an alkyne to give the guanosine analog 18 (Figure 3) (33). RNA so modified was a substrate for a CuAAC reaction with a fluorescent azide.…”

Section: Introductionmentioning

confidence: 99%

Novel Modifications in RNA

2011

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The last several years have seen numerous reports of new chemical modifications for use in RNA. In addition, in that time period, we have seen the discovery of several previously unknown naturally occurring modifications that impart novel properties on the parent RNAs. In this review, we describe recent discoveries in these areas with a focus on RNA modifications that introduce spectroscopic tags, reactive handles, or new recognition properties.

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Pin-point chemical modification of RNA with diverse molecules through the functionality transfer reaction and the copper-catalyzed azide–alkyne cycloaddition reaction

Cited by 39 publications

References 16 publications

Remarkable acceleration of a DNA/RNA inter-strand functionality transfer reaction to modify a cytosine residue: the proximity effect via complexation with a metal cation

Remarkable acceleration of a DNA/RNA inter-strand functionality transfer reaction to modify a cytosine residue: the proximity effect via complexation with a metal cation

Specific labeling: An effective tool to explore the RNA world

Novel Modifications in RNA

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