Affinity labeling of a single guanine bulge

Journal of the American Chemical Society
Kazuhiko NakataniIsao Saito

Abstract

We have developed a conceptually new method for the selective labeling of duplex DNA containing a guanine bulge with a masked form of fluorescent 2-amino-1,8-naphthyridine. A naphthyridine derivative 2 tethering DNA-alkylating epoxide was synthesized from (S)-epichlorohydrin and naphthyridine derivative 1, which selectively binds to the guanine bulge duplex. HPLC analysis of the labeling reaction of bulge duplex d(GTT GTGTTG GA)/d(CAA CA A ACC T) (TGT/A_A) with 2 showed a formation of 2-TGT adduct for the guanine bulge. The reaction proceeded for the guanine bulge and a reduced efficiency for the cytosine bulge, but not at all for adenine and thymine bulges. The site of covalent bond formation in 2-TGT was unambiguously identified at the guanine two bases away from the bulge by the use of MALDI-TOF MS analysis of the oligomer fragments produced by strand scission. The labeling reaction was also observed for the guanine bulge flanking two G-C base pairs (CGC/G_G), producing a 2:1 adduct (2.2-CGC). Upon hydrolysis of 2-TGT and 2.2-CGC with concentrated hydrogen chloride, a release of fluorescent 2-aminonaphthyridine from the adduct was clearly detected, verifying a concept of an affinity labeling of the guanine bulge with a maske...Continue Reading

Citations

Jun 4, 2008·Dalton Transactions : an International Journal of Inorganic Chemistry·Jun-Feng ZhangJian-Hua Chen
Aug 11, 2010·Chemical Communications : Chem Comm·Guangtao Song, Jinsong Ren
Nov 8, 2011·Acta Crystallographica. Section E, Structure Reports Online·Zhen Li
Jul 20, 2007·Chemistry & Biodiversity·Xiao-Cheng WengXiang Zhou
Nov 12, 2013·Dalton Transactions : an International Journal of Inorganic Chemistry·Jian PengHua Liu
Jun 21, 2012·Chemistry : a European Journal·Tadao TakadaKazushige Yamana
May 13, 2014·Analytical Sciences : the International Journal of the Japan Society for Analytical Chemistry·Yingya KanRuqin Yu
Sep 28, 2018·Inorganic Chemistry·Moustafa T Gabr, F Christopher Pigge

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