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Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts

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Abstract

Bending of double-stranded (ds) DNA plays a crucial role in many important biological processes and is relevant for nanotechnological applications. Among all the elements that have been studied in relation to dsDNA bending, A-tracts stand out as one of the most controversial. The “ApA wedge” theory was disproved when a series of linear polynucleotides containing phased 5′-A4T4-3′ or 5′-T4A4-3′ runs were shown to be bent or straight, respectively, and crystallographic evidence revealed that A-tracts are unbent. Furthermore, some of the smallest dsDNA minicircles described to date (~ 100 bp in size) lack A-tracts and are subjected to varying levels of torsional stress. Representative DNA sequences from this experimental background were modeled in atomic detail and their dynamic behavior was simulated over hundreds of nanoseconds using the AMBER force field ParmBSC1. Subsequent analysis of the resulting trajectories allowed us to (i) unambiguously establish the location of the bends in all cases; (ii) identify the structural elements that are directly responsible for the macroscopically detected curvature; and (iii) reveal the importance not only of coherently summing the effects of the bending elements when they are in synchrony with the natural repeat of the helix (i.e. separated by an integral number of helical turns) but also when alternated with a half-integral separation of opposite effects. We conclude that the major determinant of the macroscopically observed bending is the proper grouping and phasing of the positive roll imposed by pyrimidine-purine (YR) steps and the negative or null roll characteristic of RY steps and A-tracts, respectively. This conclusion is in very good agreement with the structural parameters experimentally derived for much smaller DNA molecules either alone or as found in DNA–protein complexes. We expect that this work will pave the way for future studies on drug-induced DNA bending, DNA shape readout by transcription factors, structure of circular extrachromosomal DNA, and custom design of curved DNA origami scaffolds.

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Acknowledgements

A.M. gratefully acknowledges being the recipient of a predoctoral fellowship from the University of Alcalá. We are indebted to Jason Swails for help provided in the AMBER reflector regarding circular DNA molecules, Jürgen Walther for assistance at the MCDNA server, and the anonymous reviewers for helpful suggestions. We thankfully acknowledge the GPU time granted on Minotauro (BCV-2019-2-0016) and the technical support provided by staff at the Barcelona Supercomputing Center.

Funding

Financial support from the Spanish Ministerio de Economía y Competitividad (SAF2015-64629-C2-2-R) and PharmaMar S.A.U. (Colmenar Viejo, Madrid, Spain) is gratefully acknowledged.

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  1. Area of Pharmacology, Department of Biomedical Sciences and “Unidad Asociada IQM-CSIC”, School of Medicine and Health Sciences, University of Alcalá, 28805, Alcalá de Henares, Madrid, Spain

    Alberto Mills & Federico Gago

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Mills, A., Gago, F. Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts. J Comput Aided Mol Des 34, 253–265 (2020). https://doi.org/10.1007/s10822-020-00288-z

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