title: Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label.
abstract: Guanine-rich oligonucleotides can form a unique G-quadruplex (GQ) structure with stacking units of four guanine bases organized in a plane through Hoogsteen bonding. GQ structures have been detected in vivo and shown to exert their roles in maintaining genome integrity and regulating gene expression. Understanding GQ conformation is important for understanding its inherent biological role and for devising strategies to control and manipulate functions based on targeting GQ. Although a number of biophysical methods have been used to investigate structure and dynamics of GQs, our understanding is far from complete. As such, this work explores the use of the site-directed spin labeling technique, complemented by molecular dynamics simulations, for investigating GQ conformations. A nucleotide-independent nitroxide label (R5), which has been previously applied for probing conformations of noncoding RNA and DNA duplexes, is attached to multiple sites in a 22-nucleotide DNA strand derived from the human telomeric sequence (hTel-22) that is known to form GQ. The R5 labels are shown to minimally impact GQ folding, and inter-R5 distances measured using double electron-electron resonance spectroscopy are shown to adequately distinguish the different topological conformations of hTel-22 and report variations in their occupancies in response to changes of the environment variables such as salt, crowding agent, and small molecule ligand. The work demonstrates that the R5 label is able to probe GQ conformation and establishes the base for using R5 to study more complex sequences, such as those that may potentially form multimeric GQs in long telomeric repeats.
authors.affiliation: Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Zhang
authors.affiliation: School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, China.
authors.forename: Cui-Xia
authors.initials: CX
authors.lastname: Xu
authors.affiliation: Department of Physics and Astronomy, University of Southern California , Los Angeles, California 90089, United States.|Center S3, CNR institute of Nanoscience , Modena, Italy.
authors.forename: Rosa
authors.initials: R
authors.lastname: Di Felice
authors.affiliation: Central European Institute of Technology (CEITEC), Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic.|Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic.
authors.forename: Jiri
authors.initials: J
authors.lastname: Sponer
authors.affiliation: Central European Institute of Technology (CEITEC), Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic.
authors.forename: Barira
authors.initials: B
authors.lastname: Islam
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Stadlbauer
authors.affiliation: Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Ding
authors.affiliation: School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, China.
authors.forename: Lingling
authors.initials: L
authors.lastname: Mao
authors.affiliation: School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, China.
authors.forename: Zong-Wan
authors.initials: ZW
authors.lastname: Mao
authors.affiliation: Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.
authors.forename: Peter Z
authors.initials: PZ
authors.lastname: Qin
mesh_terms: D054856:G-Quadruplexes; D006801:Humans; D009609:Nitrous Oxide / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D009841:Oligonucleotides; D009609:Nitrous Oxide