Potential for measurement of the distribution of DNA folds in complex environments using Correlated X-ray Scattering

Abstract

In vivo chromosomal behavior is dictated by the organization of genomic DNA at length scales ranging from nanometers to microns. At these disparate scales, the DNA conformation is influenced by a range of proteins that package, twist and disentangle the DNA double helix, leading to a complex hierarchical structure that remains undetermined. Thus, there is a critical need for methods of structural characterization of DNA that can accommodate complex environmental conditions over biologically relevant length scales. Based on multiscale molecular simulations, we report on the possibility of measuring supercoiling in complex environments using angular correlations of scattered X-rays resulting from X-ray free electron laser (xFEL) experiments. We recently demonstrated the observation of structural detail for solutions of randomly oriented metallic nanoparticles [D. Mendez et al., Philos. Trans. R. Soc. B 360 (2014) 20130315]. Here, we argue, based on simulations, that correlated X-ray scattering (CXS) has the potential for measuring the distribution of DNA folds in complex environments, on the scale of a few persistence lengths.

Recording and Analyzing Nucleic Acid Distance Distributions with X‐Ray Scattering Interferometry (XSI)

“…The application of XSI to nanocrystal-labeled proteins will provide a new window into protein conformational ensembles, especially for folding intermediates and intrinsically disordered proteins (IDPs). Finally, the application of next-generation free electron lasers with very high brilliance could allow measurement of correlated and time resolved distances between multiple sites in a macromolecule, with a time resolution of tens of femtoseconds (Arnlund et al, 2014; Bada et al, 2000; Ball, 2017; Doniach, 2000; Mendez et al, 2014; Mendez et al, 2016; Schenk et al, 2016; SLAC & LCLS, 2010; Smolsky et al, 2007). …”

Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

“…Solution CXS measurements at an XFEL have the potential to reveal the internal structural details of proteins and other biomolecules without the use of crystallization (Saldin, Poon et al, 2010;Saldin et al, 2009;Pande et al, 2014;Schenk et al, 2015), although recovering the intensity correlations from solution diffraction measurements is challenging. In order to use CXS effectively on solution data, it is necessary to develop a robust analysis technique that can effectively extract intensity correlations while minimizing systematic noise on a per-shot basis.…”