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Twist-stretch relations in nucleic acids

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Abstract

Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite twist-stretch patterns and stretching properties when overwound under a constant applied load. The key structural features of the A-form RNA and B-form DNA helices are here incorporated in a three-dimensional mesoscopic Hamiltonian model which accounts for the radial, bending and twisting fluctuations of the base pairs. Using path integral techniques which sum over the ensemble of the base pair fluctuations, I compute the average helical repeat of the molecules as a function of the load. The obtained twist-stretch relations and stretching properties, for short A- and B-helical fragments, are consistent with the opposite behaviors observed in kilo-base long molecules.

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Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request.

Notes

  1. This holds if, in the experimental setup, only two ends of the strands are anchored. Instead, the over-stretching transition is shifted to \(\sim 110\) pN when all four ends of the strands are anchored so that the helix is torsionally constrained.

  2. As the long term stability of physiological B-DNA is required in a multitude of applications, dehydration conditions are routinely employed e.g, in methods for digital information storage (Grass et al. 2015). On the other hand, dehydration may structurally transform DNA, unwind the helix and ultimately lead to unwanted denaturation effects (Ghoshdastidar and Senapati 2018).

  3. The presence of a hydroxyl group bound to the 2’ carbon of the ribose ring is the key reason forcing RNA to coil into the A-form (Fohrer et al. 2006)

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  1. School of Science and Technology, University of Camerino, 62032, Camerino, Italy

    Marco Zoli

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Zoli, M. Twist-stretch relations in nucleic acids. Eur Biophys J 52, 641–650 (2023). https://doi.org/10.1007/s00249-023-01669-6

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