25-30 August 2019
Henry Ford Building
Europe/Berlin timezone

High-resolution structure of a modified G-quadruplex: implications for conformational preferences of 2’-F-riboguanosine and V-loop flanking residues

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Harnack House and Henry Ford Building

Harnack House and Henry Ford Building

Board: 165
Poster Posters


Linn Haase (Universität Greifswald)


Among the various alternative DNA structures, G-quadruplexes exhibit a remarkable variety of topologies. In this study, two adjacent guanosine residues adopting syn glycosidic bond conformations in a G-quadruplex of (3+1)-hybrid type were substituted by anti-favoring 2’-F-riboguanosine nucleosides (FrG). Residue-specific 15N labeling along with 2D NOE, 1H-13C HSQC and HMBC spectra allowed for the complete resonance assignment of the FrG-modified sequence. Strikingly, it adopts an unusual quadruplex fold with G1 as part of the central tetrad and a zero-nucleotide V-shaped loop connecting the two FrG residues. While some identical or similar topologies with V-loops have been reported in the past years, it is remarkable that this particular modification provokes a fold with one of the incorporated FrG residues forced into the unfavoured syn conformation.
In an attempt to better understand the driving force for this rearrangement, conformations of the two FrG residues flanking the V-loop were analyzed in detail based on 2D NOE and DQF-COSY spectra as well as on F2’-H3’ and F2’-H1’ heteronuclear scalar couplings extracted from selectively 1H-decoupled 19F spectra. In contrast to S-puckered unmodified residues, both FrGs adopt a sugar pucker in the favoured north domain. The C3’-endo pucker of the FrG residue at the 3’-end of the V-loop seems essential for the following sharp turn of the phosphate backbone, as seen in the high-resolution structure calculated from NOE-derived distance restraints. The NMR-structure also demonstrates, that even the syn glycosidic torsion angle of the FrG residue at the V-loop 5’-end is compatible with an N-type sugar pucker. Apparently, the preference of FrG analogs for a C3’-endo conformation outweighs its propensity for an anti glycosidic torsion angle, allowing for the unexpected refolding to the V-loop topology. Finally, stabilization of this fold by north-favouring FrG residues points to a general importance of the C3’-endo conformation for V-loop formation.

Primary authors

Linn Haase (Universität Greifswald) Klaus Weisz (Universität Greifswald)

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