Synchrotron radiation circular dichroism of various G‐quadruplex structures

Abstract

Here we report synchrotron radiation circular dichroism spectra of various G-quadruplexes from 179 to 350 nm, and a number of bands in the vacuum ultraviolet (VUV) are reported for the first time. For a tetramolecular parallel structure, the strongest band in the spectrum is a negative band in the VUV at 182 nm; for a bimolecular antiparallel structure with diagonal loops, a new strong positive band is found at 190 nm; for a bimolecular parallel structure with edgewise loops, a strong positive band at 189 nm is observed; and for a self-folded chair-type structure, the strongest band in the spectrum is a positive band at 187 nm. For the tetramolecular parallel structure, the CD signals at all wavelengths are dominated by contributions from quartets of G bases, and the signal strength is approximately proportional to the number of quartets. Our experiments on well-characterized G-quadruplex structures lead us to question past attributions of CD signals to helix handedness and G quartet polarity. Although differences can be observed in the VUV region for the various quadruplex types, there do not appear to be clear-cut spectral features that can be used to identify specific topological features. It is suggested that this is because a dominant positive band in the VUV seen near 190 nm in all quadruplex structures is due to intrastrand guanine-guanine base stacking. However, our spectra can serve as reference spectra for the G-quadruplex structures investigated and, not least, to benchmark theoretical calculations and empirical models.

Amino‐Acid‐Derived Naphthalenediimides as Versatile G‐Quadruplex Binders

“…The CD spectra of the native G‐quadruplexes did not vary considerably compared with the spectra of NDI–G‐quadruplex assemblies (albeit a small shift of 1–2 nm, particularly for c‐kit1 sequence) and are in good agreement with the CD spectra reported in the literature for the same sequences . This indicates that the ligand has only a small influence on the far‐UV peaks that are associated with the quadruplex structures …”

“…[53] This indicates that the ligand has only as mall influence on the far-UV peaks that are associatedw ith the quadruplex structures. [53,55]…”

Photo-induced electron detachment of protein polyanions in the VUV range

“…3 However, the development of vacuum ultraviolet (VUV) circular dichroism spectrometers, in combination with high-flux and tunable VUV photon sources provided by synchrotron radiation facility, have allowed direct study on biomolecules. [4][5][6][7][8][9][10] Excitation of peptides and proteins arises from π −π *, n−π * excitations, as well as transitions originating from n and π molecular orbitals leading to excitaiton of Rydberg states and to electron ejection into the ionization continuum. 3,11 In the condensed phase such as in vivo, photo damages, in particular oxidation of proteins, is also relayed by initial photon excitation of solvent or other surrounding molecules followed, for example, by charge or radical transfer to the protein.…”

On the formation of the double helix between adenine single strands at acidic pH from synchrotron radiation circular dichroism experiments

“…It should be mentioned that SRCD is a very useful technique to characterize electronic couplings between bases in small DNA segments and to elucidate how the base-base interactions correlate with 4 geometry. [23][24][25] It benefits from high photon fluxes even at low wavelengths, which makes it possible to record spectra in the vacuum ultraviolet (VUV) region (below 200 nm) with high signal-to-noise ratios [26][27][28] as well as providing access to a low wavelength region which often exhibits the largest CD bands 29,30 .…”