4MKW

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

4MKW の概要

• エントリーDOI: 10.2210/pdb4mkw/pdb
• 関連するPDBエントリー: 4MGW
• 分子名称: 5methylC DNA dodecamer, MAGNESIUM ION (3 entities in total)
• 機能のキーワード: modified dna dodecamer, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 7379.14

構造登録者

Yin, Y.W. (登録日: 2013-09-05, 公開日: 2013-11-06, 最終更新日: 2024-02-28)

主引用文献

Theruvathu, J.A.,Yin, Y.W.,Pettitt, B.M.,Sowers, L.C.
Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence.
Biochemistry, 52:8590-8598, 2013

PubMed Abstract: Inflammation-mediated reactive molecules can result in an array of oxidized and halogenated DNA-damage products, including 5-chlorocytosine ((Cl)C). Previous studies have shown that (Cl)C can mimic 5-methylcytosine ((m)C) 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 (Cl)C. Because of the apparent biochemical similarities of (m)C and (Cl)C, we have investigated the effects of (m)C and (Cl)C substitution on oligonucleotide structure and dynamics. In this study, we have constructed oligonucleotide duplexes containing C, (Cl)C, and (m)C within a CpG dinucleotide. The thermal and thermodynamic stability of these duplexes were found to be experimentally indistinguishable. Crystallographic structures of duplex oligonucleotides containing (m)C or (Cl)C were determined to 1.2 and 1.9 Å resolution, respectively. Both duplexes are B-form and are superimposable on a previously determined structure of a cytosine-containing duplex with a rmsd of approximately 0.25 Å. NMR solution studies indicate that all duplexes containing cytosine or the cytosine analogues are normal B-form and that no structural perturbations are observed surrounding the site of each substitution. The magnitude of the base-stacking-induced upfield shifts for nonexchangeable base proton resonances are similar for each of the duplexes examined, indicating that neither (m)C nor (Cl)C significantly alter base-stacking interactions. The (Cl)C analogue is paired with G in an apparently normal geometry; however, the G-imino proton of the (Cl)C-G base pair resonates to higher field relative to (m)C-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 (Cl)C rotates at roughly half of the rate of the corresponding amino groups of the C-G and (m)C-G base pairs. The altered chemical shifts of hydrogen-bonding proton resonances for the (Cl)C-G base pair as well as the slower rotation of the (Cl)C amino group can be attributed to the electron-withdrawing inductive property of the 5-chloro substituent. The apparent similarity of duplexes containing (m)C and (Cl)C demonstrated here is in accord with results of previous biochemical studies and further suggests that (Cl)C is likely to be an unusually persistent form of DNA damage.

PubMed: 24147911
DOI: 10.1021/bi400980c

実験手法

X-RAY DIFFRACTION (1.219 Å)