title: Formation and recognition of G-quadruplex in promoter of c-myb oncogene by electrospray ionization mass spectrometry.
abstract: In this study, electrospray ionization mass spectrometry (ESI-MS) is used to study the formation of G-quadruplex by d(GGAGGAGGAGGA) which locates at the promoter region of c-myb gene. In addition, a natural small molecule, dehydrocorydaline from a Chinese herb, is found to have the highest binding affinity with the G-quadruplex in nine natural small molecules studied, and the binding selectivity of this natural molecule toward the c-myb G-quadruplex with respect to corresponding duplex DNA is significantly higher than that of the broad-spectrum G-quadruplex-ligand TMPyP4. The result from ESI-MS indicates that the gas-phase kinetic stability of the G-quadruplex can be enhanced by binding of dehydrocorydaline. To further investigate the binding properties of dehydrocorydaline to the G-quadruplex, Autodock3 is used to calculate the docked sites and docked energies of small molecules binding to the G-quadruplex and the result shows that the docked energy of dehydrocorydaline is the biggest in the nine small molecules used, consistent with the result from ESI-MS.
authors.affiliation: Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
authors.forename: Xiaojie
authors.initials: X
authors.lastname: Cui
authors.forename: Gu
authors.initials: G
authors.lastname: Yuan
mesh_terms: D000470:Alkaloids / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D002942:Circular Dichroism; D054856:G-Quadruplexes; D020570:Genes, myb; D006801:Humans; D008024:Ligands; D011166:Porphyrins / Q000737:chemistry / Q000378:metabolism; D011401:Promoter Regions, Genetic; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D013816:Thermodynamics
chemical_list: D000470:Alkaloids; D008024:Ligands; D011166:Porphyrins; C007232:dehydrocorydalin; C021096:tetra(4-N-methylpyridyl)porphine