Accessibility statement

 

New computational tools for analysing DNA simulations 

We have developed SerraNA, which is a program that calculates global elastic constants (persistence length, torsion and stretch modulus) from modelling ensembles [1]. The algorithm was originally designed to understand how elastic constants emerge from atomic fluctuations [2] and it was used to test the emerging properties of amber bsc1 force-field for DNA simulations [3].

WrLINE and SerraLINE softwares have been developed for comparing atomistic resolution data with lower-resolution experimental measurements like AFM, to facilitate comparisons between the two. Both programs were used for mirroring MD simulations and AFM images on supercoiled DNA minicircles [4] . WrLINE allow us to obtain a DNA molecular centre-line, filtering out all the local irregularities [5], and SerraLINE measures angles between different points of the WrLINE’s molecular contour [4].

  1. V Velasco-Berrelleza, M Burmann, JW Shepherd, MC Leake, R Golestanian, A Noy (2020). “SerraNA: a program to determine nucleic acids elasticity from simulation data” Phys Chem Chem Phys, 22, 19254-19266 https://doi.org/10.1039/D0CP02713H
  2. A Noy, R Golestanian (2012) Length dependence of DNA mechanical properties Phys Rev Lett, 109, 228101. DOI:10.1103/PhysRevLett.109.228101.
  3. II Ivan, PD Dans, A Noy, A Perez, I Faustino, A Hopsital, J Walther, P Andrio, R Goni, A Balaceanu, G Portella, F Battistini, JL Gelpi, I Gomez-Pinto, C Gonzalez, M Vendruscolo, CA Laughton, SA Harris, D Case and M Orozco (2016). Parmbsc1: a refined force-field for DNA simulations Nature Methods, 13, 55. DOI:10.1038/nmeth.3658
  4. ALB Pyne, A Noy, K Main, V Velasco-Berrelleza, MM Piperakis, LA Mitchenall, FM Cugliandolo, JG Beton, CEM Stevenson, BW Hoogenboom, AD Bates, A Maxwell, SA Harris (2021). “Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides” Nature Communications, 12, 1053 https://www.nature.com/articles/s41467-021-21243-y
  5. T Sutthibutpong, SA Harris, A Noy (2015). Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA. J Chem Theor Comput, 11, 2768. DOI:10.1021/acs.jctc.5b00035