Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label

Xiaojun Zhang, Cui Xia Xu, Rosa Di Felice, Jiri Sponer, Barira Islam, Petr Stadlbauer, Yuan Ding, Lingling Mao, Zong Wan Mao, Peter Z. Qin

Research output: Contribution to journalArticle

9 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)360-372
Number of pages13
JournalBiochemistry
Volume55
Issue number2
DOIs
Publication statusPublished - 18 Dec 2015
Externally publishedYes

Fingerprint

G-Quadruplexes
Conformations
Labels
Nucleotides
Guanine
Electron resonance
Untranslated RNA
DNA
Gene expression
Oligonucleotides
Labeling
Electrons
Molecular dynamics
Nucleic Acid Conformation
Salts
Genes
Crowding
Spectroscopy
Ligands
Molecular Dynamics Simulation

Cite this

Zhang, Xiaojun ; Xu, Cui Xia ; Di Felice, Rosa ; Sponer, Jiri ; Islam, Barira ; Stadlbauer, Petr ; Ding, Yuan ; Mao, Lingling ; Mao, Zong Wan ; Qin, Peter Z. / Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label. In: Biochemistry. 2015 ; Vol. 55, No. 2. pp. 360-372.
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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.",
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Zhang, X, Xu, CX, Di Felice, R, Sponer, J, Islam, B, Stadlbauer, P, Ding, Y, Mao, L, Mao, ZW & Qin, PZ 2015, 'Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label', Biochemistry, vol. 55, no. 2, pp. 360-372. https://doi.org/10.1021/acs.biochem.5b01189

Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label. / Zhang, Xiaojun; Xu, Cui Xia; Di Felice, Rosa; Sponer, Jiri; Islam, Barira; Stadlbauer, Petr; Ding, Yuan; Mao, Lingling; Mao, Zong Wan; Qin, Peter Z.

In: Biochemistry, Vol. 55, No. 2, 18.12.2015, p. 360-372.

Research output: Contribution to journalArticle

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AU - Zhang, Xiaojun

AU - Xu, Cui Xia

AU - Di Felice, Rosa

AU - Sponer, Jiri

AU - Islam, Barira

AU - Stadlbauer, Petr

AU - Ding, Yuan

AU - Mao, Lingling

AU - Mao, Zong Wan

AU - Qin, Peter Z.

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KW - G-Quadruplexes

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