9ly4 | pdb_00009ly4

Photo-crosslinkable oligonucleotodes which have a trioxsalen conjugated to C2' position of guanosine

spinqualitylabelsall models 9ly4, resolution 3.11Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9ly4 is a 2 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.11Å Ligands: 5CM, A1L7U, GMP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Transcription is tightly regulated by epigenetic modifications that control the expression of specific genes. One such modification is 5-methylcytosine (5mC) that is formed by cytosine methylation via DNA methyltransferases and functions as a transcriptional silencer of gene promoters. Dynamically regulated subsequent modifications by ten-eleven translocation (TET) enzymes catalyze the sequential oxidation of 5mC for generating 5-hydroxymethylcytosine, 5-formylcytosine (5fC), and 5-carboxylcytosine. Recently, these oxidized cytosine derivatives were indicated as not merely intermediates in the demethylation process; however, each derivative plays a unique biologically relevant role. A photo-crosslinkable oligonucleotide probe for detecting these cytosine modifications could support the spatiotemporal functional analysis of cytosine derivatives via a light stimulus. Herein, we designed novel photoreactive nucleosides by conjugating a psoralen (Ps) derivative, trioxsalen, to the C2' position of guanosine (GPs and GPs2) and developed photo-crosslinkable oligonucleotides (GPs-Oligo and GPs2-Oligo). In particular, GPs-Oligo demonstrated an intriguing and unique ability of photo-crosslinking with 5fC. GPs-Oligo was employed to detect 5fC using a DNA chip glass plate, which demonstrated the potential of GPs-Oligo for future investigation of the function of 5fC inside cells. Detection of Epigenetically Important 5-Formylcytosine Modifications Using Novel Photoreactive Oligonucleotides Containing a Trioxsalen-Conjugated Guanosine.,Mikame Y, Shirahama H, Doi K, Maekawa N, Kanazawa H, Yamamoto T, Dohno C, Kondo J, Wada T, Yamayoshi A J Am Chem Soc. 2026 Jan 21;148(2):2220-2228. doi: 10.1021/jacs.5c11463. Epub 2026 , Jan 7. PMID:41498324 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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