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Impact of a Snap-Back Loop on Stability and Ligand Binding to a Parallel G-Quadruplex.
- Source :
-
The journal of physical chemistry. B [J Phys Chem B] 2020 Apr 09; Vol. 124 (14), pp. 2778-2787. Date of Electronic Publication: 2020 Mar 25. - Publication Year :
- 2020
-
Abstract
- Various genomic DNA sequences including a MYC promoter sequence are amenable to the formation of a G-quadruplex featuring a snap-back loop with the incorporation of a 3'-terminal guanine into the quadruplex core. To evaluate relative stabilities and ligand binding in more detail, optical, microcalorimetric, and NMR structural studies were performed on both a minimal mutant sequence Pu22T that exclusively folds into a snap-back loop quadruplex and a parallel MYC quadruplex proposed to be the most relevant fold of the MYC promoter in a cellular environment. Similar thermal stabilities for Pu22T and MYC suggest the coexistence of both quadruplexes when derived from a sequence able to fold into both topologies. Isothermal titration calorimetry indicates a mostly identical enthalpy-driven strong binding of an indoloquinoline ligand but with a reduced number of high-affinity binding sites in Pu22T in line with a novel modified FRET competitive melting assay. Corroborated by fluorescence titrations using 2-aminopurine as a fluorescent probe, NMR chemical shift footprints show binding of the ligand at the Pu22T 5'-outer tetrad with the formation of a binding pocket. On the other hand, steric restrictions due to the snap-back loop severely restrict ligand stacking on the 3'-outer tetrad of Pu22T .
- Subjects :
- Calorimetry
DNA
Ligands
Thermodynamics
G-Quadruplexes
Subjects
Details
- Language :
- English
- ISSN :
- 1520-5207
- Volume :
- 124
- Issue :
- 14
- Database :
- MEDLINE
- Journal :
- The journal of physical chemistry. B
- Publication Type :
- Academic Journal
- Accession number :
- 32182431
- Full Text :
- https://doi.org/10.1021/acs.jpcb.0c00700