Observation of a Dynamic G-Tetrad Flip in Intramolecular G-Quadruplexes

Abstract

A MYC sequence forming an intramolecular G-quadruplex with a parallel topology was modified by the incorporation of 8-bromoguanosine (G) analogues in one of its outer G-tetrads. The propensity of the G analogues to adopt a syn glycosidic torsion angle results in an exceptional monomolecular quadruplex conformation featuring a complete flip of one tetrad while keeping a parallel orientation of all G-tracts as shown by circular dichroism and nuclear magnetic resonance spectroscopic studies. When substituting three of the four G-tetrad residues withG analogues, two coexisting quadruplex conformational isomers with an all-syn and all-anti outer G-quartet are approximately equally populated in solution. A dynamic interconversion of the two quadruplexes with an exchange rate (k) of 0.2 s is demonstrated through the observation of exchange crosspeaks in rotating frame Overhauser effect spectroscopy and nuclear Overhauser effect spectroscopy experiments at 50 °C. The kinetic properties suggest disruption of the corresponding outer G-tetrad but not of the whole quadruplex core during the tetrad flip. Conformational syn-anti isomers with homopolar and heteropolar stacking interactions are nearly isoenergetic with a transition enthalpy of 18.2 kJ/mol in favor of the all-syn isomer.

Development of Green/Red-Absorbing Chromophores Based on a Coumarin Scaffold That Are Useful as Caging Groups

“…By comparison of the photophysical data ( Figure 4 and Table 2) of the three caged derivatives (25)(26)(27) with those of the corresponding model compounds (4, 6 and 7, respectively; see Figure 2 and Table 1), the same tendency was found: the absorption maxima shifted to increasingly longer wavelengths upon incorporation of one, two or three nitro substituents at the ortho and para positions of the phenyl ring conjugated at the 2-position of the coumarin moiety. However, replacement of the methyl group at position 4 by benzoyloxymethyl caused a slight blue-shift in the absorption maximum of the dinitro-(558 nm in 6 vs 551 nm in 26) and the trinitro-(607 nm in 7 vs 596 nm in 27) coumarin derivatives.…”

“…Exchange rate (k ex ) was estimated by plotting the intensity ratio for exchange cross-peaks and the corresponding diagonal peaks in NOESY spectra as a function of the mixing time. 25 Electrospray ionization mass spectra (ESI-MS) were recorded on an instrument equipped with single quadrupole detector coupled to an HPLC, and high-resolution…”

“…for 10 and 12; 0.82 mmol, 2 mol equiv. for 13) were dissolved in anhydrous ACN (20 mL) (25,26) or in a 1:1 mixture of anhydrous DCM/ACN (20 mL) (27) under an Ar atmosphere and protected from light.…”

“…to give the desired coumarin derivative (25)(26)(27). Ndiethylamino)coumarin (25) 154.5, 150.8, 145.2, 140.5, 139.8, 133.6, 129.8, 129.2, 128.7, 127.2, 124.8, 123.9, 119.4, 111.4, 109.4, 107.3, 97.1, 84.7, 62.3, 44.7, 12.5 9, 163.0, 154.1, 151.1, 147.6, 145.4, 142.8, 133.6, 131.9, 129.8, 129.1, 128.7, 126.7, 124.9, 120.9, 118.7, 109.8, 109.4, 107.1, 97.2, 79.4, 62.1, 45.0, 12. (2,4,6-trinitrophenyl)methylene) Ndiethylamino)coumarin (27) 154.0, 151.2, 149.9, 145.4, 144.2, 133.7, 129.9, 129.0, 128.7, 127.4, 125.1, 123.2, 115.9, 110.2, 108.3, 107.2, 97.0, 73.4, 61.9, 45.0, 12.4 methylene)coumarin (28).…”

“…Ndiethylamino)coumarin (25) 154.5, 150.8, 145.2, 140.5, 139.8, 133.6, 129.8, 129.2, 128.7, 127.2, 124.8, 123.9, 119.4, 111.4, 109.4, 107.3, 97.1, 84.7, 62.3, 44.7, 12.5 9, 163.0, 154.1, 151.1, 147.6, 145.4, 142.8, 133.6, 131.9, 129.8, 129.1, 128.7, 126.7, 124.9, 120.9, 118.7, 109.8, 109.4, 107.1, 97.2, 79.4, 62.1, 45.0, 12. (2,4,6-trinitrophenyl)methylene) Ndiethylamino)coumarin (27) 154.0, 151.2, 149.9, 145.4, 144.2, 133.7, 129.9, 129.0, 128.7, 127.4, 125.1, 123.2, 115.9, 110.2, 108.3, 107.2, 97.0, 73.4, 61.9, 45.0, 12.4 methylene)coumarin (28). After evaporation under reduced pressure, the crude product was purified by column 7, 160.5, 152.9, 148.8, 144.8, 143.2, 138.1, 131.6, 127.9, 127.6, 126.8, 126.7, 125.2, 123.0, 122.0, 117.7, 107.5, 107.2, 104.9, 95.3, 82.4, 66.3, 42.8, 19.0, 10.6 in which the superscript "s" stands for standard samples, Abs is the absorbance at the excitation wavelength (λ Ex ), A is the integrated area of the corresponding emission spectrum, and n is the refractive index of the solvent used.…”