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Biochem Biophys Rep
2015 Oct 03;5:439-447. doi: 10.1016/j.bbrep.2015.09.022.
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Complicated behavior of G-quadruplexes and evaluating G-quadruplexes' ligands in various systems mimicking cellular circumstance.
Wang SK
,
Su HF
,
Gu YC
,
Lin SL
,
Tan JH
,
Huang ZS
,
Ou TM
.
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Environments surrounding G-rich sequences remarkably affect the conformations of these structures. A proper evaluation system mimicking the crowded environment in a cell with macromolecules should be developed to perform structural and functional studies on G-quadruplexes. In this study, the topology and stability of a G-quadruplex formed by human telomeric repeat sequences were investigated in a macromolecule-crowded environment created by polyethylene glycol 200 (PEG200), tumor cell extract, and Xenopus laevis egg extract. The interactions between small molecules and telomeric G-quadruplexes were also evaluated in the different systems. The results suggested that the actual behavior of G-quadruplex structures in cells extract is quite different from that in the PEG crowding system, and proteins or other factors in extracts might play a very important role in G-quadruplex structures.
Fig. 1. Structures of the G-quadruplex ligands used in this paper, the cationic porphyrin TMPyP4, the quindoline derivatives SYUIQ-05 and SYUIQ-FM05, and the isaindigotone derivative ISD-05.
Fig. 4. The FRET melting curves of HTG-21 G-quadruplex in ionic buffer (A), dialysis buffer (B), cell-free system (C), control system (D), and Xenopus laevis egg extracts (E), with or without 0.2 μM or 0.4 μM TMPyP4, SYUIQ-05, SYUIQ-FM05, and ISD-05.
Fig. 6. Effects of different compounds on the polymerase stop assay with HTG21 and its corresponding mutant sequence HTG21-mu in the cell free system, Xenopus laevis egg extract, and dialysis buffer mentioned before. All of the compounds were at 2.5 μM. Data represented means of six independent experiments with standard error.
Fig. 2. (A), CD spectra of 5 μM HTG21 oligomer in non-ionic buffer (10 mM TrisâHCl buffer, pH 7.4), ionic buffer [10 mM TrisâHCl buffer (pH 7.4) containing 110 mM KCl], dialysis buffer, control system (dialysis buffer with 40% PEG), Xenopus laevis egg extract, and cell-free system (dialysis buffer with cell extract). (B), The FRET melting curves of HTG21G-quadruplex in ionic buffer, dialysis buffer, cell-free system, X. laevis egg extract, and control system.
Fig. 3. Effects of different systems on the polymerase stop assay with HTG21 and its corresponding mutant sequence HTG21-mu in a normal PCR reaction buffer, the cell free system, Xenopus laevis egg extract, dialysis buffer, dialysis buffer A, and control system mentioned before. Data represented means of six independent experiments with standard error.
Fig. 5. Fitted curves obtained by MST measurements of 5â-FAM-labeled HTG-21 with ligands diluted 1:2 from 20 μM for 14 times.
Fig. 7. Gel electrophoresis of HTG21 in ionic buffer [10Â mM TrisâHCl buffer (pH 7.4) containing 110Â mM KCl], cell free system, Xenopus laevis egg extract, and control system (the dialysis buffer containing 40% PEG).
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