Development of a DNA‐Templated Peptide Probe for Photoaffinity Labeling and Enrichment of the Histone Modification Reader Proteins

Bai, Xue; Lu, Congcong; Jin, Jin; Tian, Shanshan; Guo, Zhenchang; Chen, Pu; Zhai, Guijin; Zheng, Shiyou; He, Xiwen; Fan, Enguo; Zhang, Yukui; Zhang, Kai

doi:10.1002/ange.201602558

Cited by 12 publications

(10 citation statements)

References 41 publications

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“…[36] A third strategy in this category of DNA-templated protein modification uses peptides to guide a hybridized reactive DNA strand to a specific protein (Figure 1). [37,38] Using a DNA temp that contained a trimethylated histone H3 peptide as a guiding moiety, proteins reading histone modification could be selectively bound within complex protein mixtures. [37] Then, the diazirine-bearing DNA react was hybridized.…”

Section: Protein Modification By Dna Templationmentioning

confidence: 99%

DNA‐assisted site‐selective protein modification

Keijzer

Albada

2021

Biopolymers

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Protein modification is important for various types of biomedical research, including proteomics and therapeutics. Many methodologies for protein modification exist, but not all possess the required level of efficiency and site selectivity. This review focuses on the use of DNA to achieve the desired conversions and levels of accuracy in protein modification by using DNA (i) as a template to help concentrate dilute reactants, (ii) as a guidance system to achieve selectivity by binding specific proteins, and (iii) even as catalytic entity or construct to enhance protein modification reactions.

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Section: Protein Modification By Dna Templationmentioning

confidence: 99%

DNA‐assisted site‐selective protein modification

Keijzer

Albada

2021

Biopolymers

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“…DNA-templated peptide probes have been developed by the Kai Zhang group [ 71 ]. They developed a DNA-templated peptide probe for PAL and enrichment of the histone modification reader proteins (Fig.…”

Section: Diazirine-based Probesmentioning

confidence: 99%

“…Figure reproduced from ref. [ 71 ] with permission from Wiley-WCH publication. ( Right ) structure of a D A phosphoramidite unit …”

Section: Diazirine-based Probesmentioning

confidence: 99%

Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs)

et al. 2016

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Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific proteins, including affinity chromatography, activity-based probes, affinity-based probes and photo-affinity labeling (PAL). PAL has become one of the most powerful strategies to study PPIs. Traditional photocrosslinkers are used in PAL, including benzophenone, aryl azide, and diazirine. Upon photoirradiation, these photocrosslinkers (Pls) generate highly reactive species that react with adjacent molecules, resulting in a direct covalent modification. This review introduces recent examples of chemical proteomics study using PAL for PPIs.

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“…However, the attached crosslinking group might cause potential steric hindrance and thus alter the recognized motif in mRNA, which eventually may affect the binding and identification of reader proteins. To resolve the issue, we introduced DNA templated technique that can guide the desired groups in a site-specific manner through the self-assembly of complementary double-stranded DNA, which has been applied in the screening interaction of protein-small molecule ( Li et al., 2013 ), protein-protein ( Bai et al., 2016 ) and protein-DNA ( Liu et al., 2015b ). As far as structure is concerned, single-stranded mRNA is easier to integrate with DNA than protein or small molecule, and therefore this technique is highly expected to be suitable for the design of mRNA modification probes.…”

Section: Introductionmentioning

confidence: 99%

DNA-guided photoactivatable probe-based chemical proteomics reveals the reader protein of mRNA methylation

et al. 2021

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Summary Chemical modification on mRNA can recruit specific binding proteins (readers/partners) to determine post-transcriptional gene regulation. However, the identification of the reader is extremely limited owing to the rather weak and highly dynamic non-covalent interactions between mRNA modification and reader, and therefore the sensitive and robust approaches are desirable. Here, we report a DNA-guided photoactivatable-based chemical proteomic approach for profiling the readers of mRNA methylation. By use of N 6 -methyladenosine (m 6 A), we illustrated that this method can be successfully utilized for labelling and enriching the readers of mRNA modification, as well as for the discovery of new partners. Thus we applied this strategy to a new modification 2′-O-methyladenosine. As a result, DDX1 was identified and verified as a potential binding protein. Our study therefore provides a powerful chemical proteomics tool for identifying the binding factors of mRNA modification and reveals the underlying function of mRNA modification.

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Development of a DNA‐Templated Peptide Probe for Photoaffinity Labeling and Enrichment of the Histone Modification Reader Proteins

Cited by 12 publications

References 41 publications

DNA‐assisted site‐selective protein modification

DNA‐assisted site‐selective protein modification

Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs)

DNA-guided photoactivatable probe-based chemical proteomics reveals the reader protein of mRNA methylation

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