SerraNA: a program to determine nucleic acids elasticity from simulation data

The resistance of DNA to stretch, twist and bend is broadly well estimated by experiments and is important for gene regulation and chromosome packing. However, their sequence-dependence and how bulk elastic constants emerge from local fluctuations is less understood. Here, we present SerraNA, which...

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Bibliographic Details
Published in:Physical chemistry chemical physics : PCCP 2020-09, Vol.22 (34), p.19254-19266
Main Authors: Velasco-Berrelleza, Victor, Burman, Matthew, Shepherd, Jack W, Leake, Mark C, Golestanian, Ramin, Noy, Agnes
Format: Article
Language:English
Subjects:
Bends
Chromosomes
Computer simulation
Deoxyribonucleic acid
Dependence
DNA
DNA - chemistry
Elastic properties
Elasticity
Mechanical properties
Molecular Dynamics Simulation
Nucleic Acid Conformation
Nucleic acids
Parameters
Software
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Summary:The resistance of DNA to stretch, twist and bend is broadly well estimated by experiments and is important for gene regulation and chromosome packing. However, their sequence-dependence and how bulk elastic constants emerge from local fluctuations is less understood. Here, we present SerraNA, which is an open software that calculates elastic parameters of double-stranded nucleic acids from dinucleotide length up to the whole molecule using ensembles from numerical simulations. The program reveals that global bendability emerge from local periodic bending angles in phase with the DNA helicoidal shape. We apply SerraNA to the whole set of 136 tetra-bp combinations and we observe a high degree of sequence-dependence with differences over 200% for all elastic parameters. Tetramers with TA and CA base-pair steps are especially flexible, while the ones containing AA and AT tend to be the most rigid. Thus, AT-rich motifs can generate extreme mechanical properties, which are critical for creating strong global bends when phased properly. Our results also indicate base mismatches would make DNA more flexible, while protein binding would make it more rigid. SerraNA is a tool to be applied in the next generation of interdisciplinary investigations to further understand what determines the elasticity of DNA. AT-rich motifs can generate extreme mechanical properties, which are critical for creating strong global bends when phased properly.
ISSN:1463-9076
1463-9084
DOI:10.1039/d0cp02713h