However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. ![]() G-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. In this review, we summarize recent studies that have investigated the effects of surrounding conditions (e.g., metal cations, pH, and crowding) on G4 conformations and the application of G4s mainly in biosensor fields, and in others. Many studies have been conducted to characterize G4 conformations under various conditions, not only to use G4s in practical applications but also to reveal its function in vivo. G4 conformations are dramatically altered by the surrounding conditions, such as metal cations, pH, and crowding. However, there are some challenges about its practical use due to the difference between practical sample conditions and experimental ones. Furthermore, G4 is a great scaffold of aptamers since many aptamers folded into G4s have also been reported. Asvarious conformations of G4s could form from one sequence depending on varying conditions, many researchers have developed G4-based sensors. ![]() While G4s have some functions in vivo, there are many reports of developed applications that use G4s. In general, metal cations, such as potassium and sodium, stabilize G4s through coordination in the G-quartet. There are three typical topologies of G4: parallel, anti-parallel, and hybrid. G4s play important roles in vivo, such as telomere maintenance, transcription, and DNA replication. G-quadruplex (G4) is a non-canonical structure that is formed in G-rich sequences of nucleic acids. The database is included in the g4dbr package () and can be explored online (). The application handles automatically most of the data processing, and allows generating custom figures and reports. We also built an R-based open-source application to build and consult a database, wherein further sequences can be incorporated in the future. Based on these results, we make a short-list of sequences that adopt the same structure in the MS assay as reported by NMR, and provide recommendations on using them for MS-based assays. In order to establish standardized MS-based screening assays, we studied 28 sequences with documented NMR structures in (usually ∼100 mM) potassium, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM trimethylammonium acetate. Reversibility offers possibilities for its utilization as a conformational switch within different compartments of living cell enabling specific ligand and protein interactions. ![]() The (de)protonation of A20 is the key for pH driven structural transformation of htel1-ΔG23. Populations of TD and KDH+ forms are controlled by pH. Specific stacking interactions amongst two G-quartets flanking base triples and base pairs in TD and KDH+ forms are reflected in 10 K higher thermal stability of KDH+. ![]() NMR, CD, and UV spectroscopy have demonstrated that topology of KDH+ form is distinctive with unique protonated T18⋅A20+⋅G5 base triple and other capping structural elements that provide novel insight into structural polymorphism and heterogeneity of G-quadruplexes in general. A four-repeat human telomere DNA sequence without the 3′-end guanine, d (htel1-ΔG23) has been found to adopt two distinct two G-quartet antiparallel basket-type G-quadruplexes, TD and KDH+ in presence of KCl.
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