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• W3147496087 endingPage "2261" @default.
• W3147496087 startingPage "2249" @default.
• W3147496087 abstract "Nucleic acid-ion interactions are fundamentally important to the physical, energetic, and conformational properties of DNA and RNA. These interactions help fold and stabilize highly ordered secondary and tertiary structures, such as G-quadruplexes (GQs), which are functionally relevant in telomeres, replication initiation sites, and promoter sequences. The c-kit proto-oncogene encodes for a receptor tyrosine kinase and is linked to gastrointestinal stromal tumors, mast cell disease, and leukemia. This gene contains three unique GQ-forming sequences that have proposed antagonistic effects on gene expression. The dominant GQ, denoted c-kit1, has been shown to decrease expression of c-kit transcripts, making the c-kit1 GQ a promising drug target. Toward disease intervention, more information is needed regarding its conformational dynamics and ion binding properties. Therefore, we performed molecular dynamics simulations of the c-kit1 GQ with K+, Na+, Li+, and mixed salt solutions using the Drude-2017 polarizable force field. We evaluated GQ structure, ion sampling, core energetics, ion dehydration and binding, and ion competition and found that each analysis supported the known GQ-ion specificity trend (K+ > Na+ > Li+). We also found that K+ ions coordinate in the tetrad core antiprismatically, whereas Na+ and Li+ align coplanar to guanine tetrads, partially because of their attraction to surrounding water. Further, we showed that K+ occupancy is higher around the c-kit1 GQ and its nucleobases than Na+ and Li+, which tend to interact with backbone and sugar moieties. Finally, we showed that K+ binding to the c-kit1 GQ is faster and more frequent than Na+ and Li+. Such descriptions of GQ-ion dynamics suggest the rate of dehydration as the dominant factor for preference of K+ by DNA GQs and provide insight into noncanonical nucleic acids for which little experimental data exist." @default.
• W3147496087 created "2021-04-13" @default.
• W3147496087 creator A5025714037 @default.
• W3147496087 creator A5055696559 @default.
• W3147496087 date "2021-06-01" @default.
• W3147496087 modified "2023-10-16" @default.
• W3147496087 title "Cation competition and recruitment around the c-kit1 G-quadruplex using polarizable simulations" @default.
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• W3147496087 doi "https://doi.org/10.1016/j.bpj.2021.03.022" @default.
• W3147496087 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8390831" @default.
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• W3147496087 hasPublicationYear "2021" @default.
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