title: Delineation of G-Quadruplex Alkylation Sites Mediated by 3,6-Bis(1-methyl-4-vinylpyridinium iodide)carbazole-Aniline Mustard Conjugates.
abstract: A new G-quadruplex (G-4)-directing alkylating agent BMVC-C3M was designed and synthesized to integrate 3,6-bis(1-methyl-4-vinylpyridinium iodide)carbazole (BMVC) with aniline mustard. Various telomeric G-4 structures (hybrid-2 type and antiparallel) and an oncogene promoter, c-MYC (parallel), were constructed to react with BMVC-C3M, yielding 35 % alkylation yield toward G-4 DNA over other DNA categories (<6 %) and high specificity under competition conditions. Analysis of the intact alkylation adducts by electrospray ionization mass spectroscopy (ESI-MS) revealed the stepwise DNA alkylation mechanism of aniline mustard for the first time. Furthermore, the monoalkylation sites and intrastrand cross-linking sites were determined and found to be dependent on G-4 topology based on the results of footprinting analysis in combination with mass spectroscopic techniques and in silico modeling. The results indicated that BMVC-C3M preferentially alkylated at A15 (H26), G12 (H24), and G2 (c-MYC), respectively, as monoalkylated adducts and formed A15-C3M-A21 (H26), G12-C3M-G4 (H24), and G2-C3M-G4/G17 (c-MYC), respectively, as cross-linked dialkylated adducts. Collectively, the stability and site-selective cross-linking capacity of BMVC-C3M provides a credible tool for the structural and functional characterization of G-4 DNAs in biological systems.
authors.affiliation: Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359.
authors.forename: Chien-Han
authors.initials: CH
authors.lastname: Chen
authors.affiliation: Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359.
authors.forename: Tsung-Hao
authors.initials: TH
authors.lastname: Hu
authors.affiliation: Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359.
authors.forename: Tzu-Chiao
authors.initials: TC
authors.lastname: Huang
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 11529 Taiwan (R.O.C.).|Institute of Plant Biology and Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.).
authors.forename: Ying-Lan
authors.initials: YL
authors.lastname: Chen
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 11529 Taiwan (R.O.C.).
authors.forename: Yet-Ran
authors.initials: YR
authors.lastname: Chen
authors.affiliation: Department of Applied Chemistry, Chia-Yi University, No. 300, Xuefu Road, Chiayi City, 60004 Taiwan (R.O.C.), Fax: (+886) 5-2717901. cccheng@mail.ncyu.edu.tw.
authors.forename: Chien-Chung
authors.initials: CC
authors.lastname: Cheng
authors.affiliation: Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359. chenct@ntu.edu.tw.
authors.forename: Chao-Tsen
authors.initials: CT
authors.lastname: Chen
mesh_terms: D000478:Alkylation; D000816:Aniline Mustard / Q000737:chemistry*; D002227:Carbazoles / Q000737:chemistry*; D004247:DNA / Q000737:chemistry; D054856:G-Quadruplexes; D006847:Hydrocarbons, Iodinated / Q000737:chemistry*; D011726:Pyridinium Compounds / Q000737:chemistry*
chemical_list: C520417:1-methyl-4-vinylpyridinium; D002227:Carbazoles; D006847:Hydrocarbons, Iodinated; D011726:Pyridinium Compounds; D004247:DNA; D000816:Aniline Mustard
keywords: DNA recognition; DNA structures; G-quadruplexes; alkylation; molecular recognition