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The “sugar” coarse-grained DNA model

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Abstract

More than 20 coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability and provide the possibility of the transition of the DNA double helix from the B-form to the A-form during interactions with biological molecules. We propose a CG representation of the ribose conformational flexibility. We substantiate the choice of the CG sites (six per nucleotide) needed for the ”sugar” GC DNA model, and obtain the potentials of the CG interactions between the sites by the ”bottom-up” approach using the all-atom AMBER force field. We show that the representation of the ribose flexibility requires one non-harmonic and one three-particle potential, the forms of both the potentials being different from the ones generally used. The model also includes (i) explicit representation of ions (in an implicit solvent) and (ii) sequence dependence. With these features, the sugar CG DNA model reproduces (with the same parameters) both the B- and A- stable forms under corresponding conditions and demonstrates both the A to B and the B to A phase transitions.

The proposed coarse-grained DNA model allows to reproduce both the B- and A- DNA forms and the transitions between them under corresponding conditions.

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Acknowledgments

We thank Prof. Alexey Onufriev who obtained an all-atom trajectory of B-DNA in water for us; Prof. Modesto Orozco and Dr. Agnes Noy who kindly granted us the trajectory of A-DNA [62]; and U. Deva Priyakumar who sent us .pdb files of DNA molecule with an opening base [71]. For MD simulations, we used (properly modified) program written by Dr. A.V. Savin [74, 75].

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  1. N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119991, Russia

    N. A. Kovaleva, I. P. Koroleva (Kikot), M. A. Mazo & E. A. Zubova

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  1. N. A. Kovaleva
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  2. I. P. Koroleva (Kikot)
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  3. M. A. Mazo
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  4. E. A. Zubova
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Correspondence to E. A. Zubova.

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The work was supported by the Russian Science Foundation (award 16-13-10302). The simulations were carried out at the Joint Supercomputer Center of Russian Academy of Sciences.

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Kovaleva, N.A., Koroleva (Kikot), I.P., Mazo, M.A. et al. The “sugar” coarse-grained DNA model. J Mol Model 23, 66 (2017). https://doi.org/10.1007/s00894-017-3209-z

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