title: Emulsified BMVC derivative induced filtration for G-quadruplex DNA structural separation.
abstract: A novel method based on emulsion/filtration is introduced for G-quadruplex DNA structural separation. We first synthesized a lipophilic analogue of BMVC, 3,6-Bis(1-methyl-4-vinylpyridinium)-9-(12'-bromododecyl) carbazole diiodide (BMVC-12C-Br), which can form an oil-in-water (o/w) phase emulsion. Due to the binding preferences of BMVC-12C-Br emulsion to some specific DNA structures, the large emulsion (∼2 µm) bound DNA was separated from the small free DNA in the filtrate by a 0.22 µm pore size MCE membrane. This method is able to isolate the non-parallel G-quadruplexes from the parallel G-quadruplexes and the linear duplexes from both G-quadruplexes. In addition, this method allows us not only to determine the absence of the parallel G-quadruplexes of d(T(2)AG(3))(4) and the presence of the parallel G-quadruplexes of d(T(2)AG(3))(2) in K(+) solution, but also to verify structural conversion from antiparallel to parallel G-quadruplexes of d[AG(3)(T(2)AG(3))(3)] in K(+) solution under molecular PEG condition. Moreover, this emulsion can separate the non-parallel G-quadruplexes of d(G(3)CGCG(3)AGGAAG(5)CG(3)) monomer from the parallel G-quadruplexes of its dimer in K(+) solution. Together with NMR spectra, one can simplify the spectra for both the free DNA and the bound DNA to establish a spectrum-structure correlation for further structural analysis.
authors.affiliation: Department of Chemistry, National Taiwan University, Taipei, Taiwan.
authors.forename: Yu-Lin
authors.initials: YL
authors.lastname: Tsai
authors.forename: Zi-Fu
authors.initials: ZF
authors.lastname: Wang
authors.forename: Wei-Wen
authors.initials: WW
authors.lastname: Chen
authors.forename: Ta-Chau
authors.initials: TC
authors.lastname: Chang
mesh_terms: D002227:Carbazoles / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000302:isolation & purification*; D004655:Emulsions; D005374:Filtration / Q000379:methods*; D005453:Fluorescence; D005456:Fluorescent Dyes / Q000737:chemistry*; D054856:G-Quadruplexes; D006842:Hydrocarbons, Brominated / Q000737:chemistry*; D008856:Microscopy, Fluorescence; D011188:Potassium / Q000737:chemistry; D011726:Pyridinium Compounds / Q000737:chemistry*
chemical_list: C568400:3,6-bis(1-methyl-4-vinylpyridium)-9-(12'-bromodecyl)carbazole diiodide; D002227:Carbazoles; D004655:Emulsions; D005456:Fluorescent Dyes; D006842:Hydrocarbons, Brominated; D011726:Pyridinium Compounds; D004247:DNA; D011188:Potassium