Fitting Solution X-ray Scattering data of DNA structure

Objective

Analyze the of X-ray Solution Scattering Data of a DNA structure.

  • Molecular Dynamics simulation of the DNA structure was perfomed in the explicit solvent to generate the conformational ensembles.
  • In the first set out of the 1020 structures 11 structures fit with the experimental data (upto q=0.6) with chi square less than 1.00. The best fitting with a chi square of 0.576 is shown below.
  • In the second set out of 1020 fitted structures only 1 structure is having chi square value less than 1.00. The best fitting with a chi square of 0.984 is shown below.
  • In the third set all the structures had chi square value above 1.00. The best fitting with a chi square of 1.309 is shown below.
  • Notably the snapshot corresponding to 103ps is observed to have chi square lowest in all the three cases q<0.6, q<0.8 and q<1.0 in crysol fitting.

Inference

  • The study shows that an all atom MD can be used for structure analysis for fitting solution scattering data.
  • Based on the low chi square value from the fitting we could get an idea of cluster of structures corresponding to the experimental data.
  • Since the solution scattering data represents the sum of all average fluctuations of the molecule, an ensemble approach similar to that of solution NMR can be hypothesized.