4mgw

Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence

spinqualitylabelsall models 4mgw, resolution 1.93Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4mgw is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 2GF, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Inflammation-mediated reactive molecules can result in an array of oxidized and halogenated DNA damage products including 5-chlorocytosine (ClC). Previous studies have shown that ClC can mimic 5-methylcytosine (mC) and act as a fraudulent epigenetic signal, promoting the methylation of previously unmethylated DNA sequences. Although the 5-halouracils are good substrates for base excision repair, no repair activity has yet been identified for ClC. Due to the apparent biochemical similarities of mC and ClC, we have investigated the effects of mC and ClC substitution on oligonucleotide structure and dynamics. In this study, we have constructed oligonucleotide duplexes containing C, ClC and mC within a CpG dinucleotide. The thermal and thermodynamic stability of these duplexes are found to be experimentally indistinguishable. Crystallographic structures of duplex oligonucleotides containing mC and ClC were determined to 1.2 and 1.9 A, respectively. Both duplexes are B-form and are superimposable on a previously determined structure of a cytosine-containing duplex with RMSD of approximately 0.25 A. NMR solution studies indicate that all duplexes containing cytosine or the cytosine analogs are normal B-form, and no structural perturbations are observed surrounding the site of each substitution. The magnitude of the base-stacking induced upfield shifts for non-exchangeable base proton resonances are similar for each of the duplexes examined, indicating that neither mC nor ClC significantly alter base stacking interactions. The ClC analog is paired with G in an apparently normal geometry; however the G-imino proton of the ClC-G base pair resonates to higher field relative to mC-G or C-G, indicating a weaker imino hydrogen bond. Using selective 15N-enrichment and isotope-edited NMR, we observe that the amino group of ClC rotates at roughly half the rate of the corresponding amino groups of the C-G or mC-G base pairs. The altered chemical shifts of hydrogen bonding proton resonances for the ClC-G base pair, as well as the slower rotation of the ClC amino group can be attributed to the electron-withdrawing inductive property of the 5-chloro substituent. The apparent similarity of duplexes containing mC and ClC demonstrated here is in accord with results of previous biochemical studies and further suggests that ClC is likely to be an unusually persistent form of DNA damage. Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence.,Theruvathu JA, Yin W, Pettitt BM, Sowers LC Biochemistry. 2013 Oct 22. PMID:24147911 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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