ArticleMethods in enzymology2015
Hydrodynamic Models of G-Quadruplex Structures.
Article in Methods in enzymology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Rational Polyligand Design for G-Quadruplex Multimer Stabilization.Journal of chemical information and modeling · 2026Article
- Polymeric Properties of Telomeric G-Quadruplex Multimers: Effects of Chemically Inert Crowders.Biomacromolecules · 2025Article
- Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering.Nucleic acids research · 2025Article
- Early Events in G-quadruplex Folding Captured by Time-Resolved Small-Angle X-Ray Scattering.bioRxiv : the preprint server for biology · 2024Article
- Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc, k-Ras and c-Kit promoter sequences.Nucleic acids research · 2022Article
- The solution structures of higher-order human telomere G-quadruplex multimers.Nucleic acids research · 2021Article
- The hTERT core promoter forms three parallel G-quadruplexes.Nucleic acids research · 2020Article
- Human POT1 unfolds G-quadruplexes by conformational selection.Nucleic acids research · 2020Article
- Probing RNA-Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Random Formation of G-Quadruplexes in the Full-Length Human Telomere Overhangs Leads to a Kinetic Folding Pattern with Targetable Vacant G-Tracts.Biochemistry · 2018Article
- G-Quadruplex Secondary Structure Obtained from Circular Dichroism Spectroscopy.Angewandte Chemie (International ed. in English) · 2018Article
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4 authors.
Funding
Abstract
G-quadruplexes are noncannonical four-stranded DNA or RNA structures formed by guanine-rich repeating sequences. Guanine nucleotides can hydrogen bond to form a planar tetrad structure. Such tetrads can stack to form quadruplexes of various molecularities with a variety of types of single-stranded loops joining the tetrads. High-resolution structures may be obtained by X-ray crystallography or NMR spectroscopy for quadruplexes formed by short (≈25 nt) sequences but these methods have yet to succeed in characterizing higher order quadruplex structures formed by longer sequences. An integrated computational and experimental approach was implemented in our laboratory to obtain structural models for higher order quadruplexes that might form in longer telomeric or promoter sequences. In our approach, atomic-level models are built using folding principles gleaned from available high-resolution structures and then optimized by molecular dynamics. The program HYDROPRO is then used to construct bead models of these structures to predict experimentally testable hydrodynamic properties. Models are validated by comparison of these properties with measured experimental values obtained by analytical ultracentrifugation or other biophysical tools. This chapter describes our approach and practical procedures.
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