title: Structure variations of TBA G-quadruplex induced by 2'-O-methyl nucleotide in K+ and Ca2+ environments.
abstract: Thrombin binding aptamer (TBA), a 15-mer oligonucleotide of d(GGTTGGTGTGGTTGG) sequence, folds into a chair-type antiparallel G-quadruplex in the K(+) environment, and each of two G-tetrads is characterized by a syn-anti-syn-anti glycosidic conformation arrangement. To explore its folding topology and structural stability, 2'-O-methyl nucleotide (OMe) with the C3'-endo sugar pucker conformation and anti glycosidic angle was used to selectively substitute for the guanine residues of G-tetrads of TBA, and these substituted TBAs were characterized using a circular dichroism spectrum, thermally differential spectrum, ultraviolet stability analysis, electrophoresis mobility shift assay, and thermodynamic analysis in K(+) and Ca(2+) environments. Results showed that single substitutions for syn-dG residues destabilized the G-quadruplex structure, while single substitutions for anti-dG residues could preserve the G-quadruplex in the K(+) environment. When one or two G-tetrads were modified with OMe, TBA became unstructured. In contrast, in Ca(2+) environment, the native TBA appeared to be unstructured. When two G-tetrads were substituted with OMe, TBA seemed to become a more stable parallel G-4 structure. Further thermodynamic data suggested that OMe-substitutions were an enthalpy-driven event. The results in this study enrich our understanding about the effects of nucleotide derivatives on the G-quadruplex structure stability in different ionic environments, which will help to design G-quadruplex for biological and medical applications.
authors.affiliation: Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China Department of Chemistry, Shenyang Medical College, Shenyang 110034, China.
authors.forename: Xiaoyang
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Liu
authors.affiliation: Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Yan
authors.affiliation: Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Yuan
authors.affiliation: Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China.
authors.forename: Liwen
authors.initials: L
authors.lastname: An
authors.affiliation: Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China yfguan55@sina.com.
authors.forename: Yifu
authors.initials: Y
authors.lastname: Guan
mesh_terms: D001483:Base Sequence; D002118:Calcium / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D054856:G-Quadruplexes; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry*; D011188:Potassium / Q000378:metabolism*; D014466:Ultraviolet Rays
chemical_list: D009711:Nucleotides; D011188:Potassium; D002118:Calcium
keywords: TBA; ionic environment; nucleotide derivative; structure variation