Authors
Valenti, A., Mattossovich, R., Merlo, R., Schifino, G., Sandomenico, A., Widersten, M., Calio, A., Peters, J., Pastore, A., Parracino, A.
Abstract
DNA topology is a key regulator of chromatin structure and transcription, yet its direct role in transcription factor recognition remains unclear. Here, we investigate how distinct DNA topological states modulate binding of the Saccharomyces cerevisiae bZIP transcription factor GCN4 using topologically defined plasmids. By combining, complementary biochemical approaches, including BioLayer Interferometry applied here for the first time to topology-dependent protein/DNA interactions, we show that DNA supercoiling directly reshapes GCN4/DNA recognition. Positively supercoiled DNA forms more stable and persistent complexes, whereas negatively supercoiled DNA retains greater conformational heterogeneity. To interpret these effects, we performed multiscale molecular simulations. Coarse-grained simulations of plasmids recapitulate the global topology-dependent trends observed experimentally, while matched minicircle models reproduce the same behaviour at the local scale. In strong agreement with experimental data, simulations reveal that DNA topology modulates the conformational ensemble of the GCN4 basic region. Overall, positively supercoiled DNA promotes a more ordered binding mode and localized protein distribution, whereas negatively supercoiled DNA supports increased structural plasticity. These findings identify DNA topology as an active determinant of transcription factor recognition and provide a multiscale framework linking global DNA mechanics to local protein/DNA interactions.
Preprint server:
bioRxiv
The authors list and abstract were imported from bioRxiv on 08 May 2026.
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