The sequence TC5 (TCCCCC) adopts a tetrameric i-motif structure upon the association of four molecules at acidic pH. Researchers from the IQFR-CSIC and McGill have found that T(araF-C)5 forms an alternative conformation.

The i-motif structure can be described as the intercalation of hemiprotonated cytosine:cytosine (C:C+) base pairs from two parallel duplexes running in opposite orientations. The sequence TC5 (5’-TCCCCC-3’) adopts such structure upon the association of four molecules, which is promoted at acidic pH. In this work, researchers from the IQFR-CSIC and McGill University have found that when the cytosine residues of TC5 are substituted by 2’F-arabinocytosine (araF-C), the sequence is able to form an alternative conformation. Using 1H- and 19F-NMR spectroscopy it was possible to determine the high-resolution structure of this alternative conformer and to find that it is an unprecedented i-motif formed by two tightly turned T(araF-C)5 strands, associated head-to-head, and stabilized by C:C+ and T:T homo-base pairs. While the formation of the tetrameric i-motif also occurs for T(araF-C)5, the existence of interactions involving the fluorine at 2’ position provokes the formation of faster forming species, which behave as off-pathway folding intermediates. Quantum mechanics-based calculations carried out by researchers at the Institute for Research in Biomedicine (IRB) and high-resolution NMR data allowed to unveil interactions that explain the stabilization of the structure. These results expand the scope of potential applications of i-motif in nanotechnology and emphasize the possibility that alternative i-motif conformations may fold in vivo through factors such as protein binding or molecular crowding effects. This work has been published in the journal Communications Chemistry: R. El-Khoury, V. Macaluso, C. Hennecker, A. K. Mittermaier, M. Orozco, C. González, M. Garavís*, M. J. Damha*. “i-Motif folding intermediates with zero-nucleotide loops are trapped by 2′-fluoroarabinocytidine via F···H and O···H hydrogen bonds”. Commun. Chem. https://doi.org/10.1038/s42004-023-00831-7