Recording and Analyzing Nucleic Acid Distance Distributions with X‐Ray Scattering Interferometry (XSI). Issue 1 (7th June 2018)

• Record Type: Journal Article
• Authors: Zettl, Thomas; Das, Rhiju; Harbury, Pehr A. B.; Herschlag, Daniel; Lipfert, Jan; Mathew, Rebecca S.; Shi, Xuesong
• Editors: Beaucage, Serge L.; Bergstrom, Donald E.; Herdewijn, Piet; Matsuda, Akira
• Is Part Of: Current protocols in nucleic acid chemistry. Volume 73:Issue 1(2018)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2018-06-07
• Subjects: ensemble determination -- energy landscape -- gold nanocrystals -- molecular ruler -- structure determination -- small angle X‐ray scattering -- X‐ray scattering interferometry; Nucleic acids -- Laboratory manuals; Nucleic Acids -- chemical synthesis; Nucleic acids; Laboratory Manuals; Electronic books; Laboratory manuals; 572.8028
• DOI: 10.1002/cpnc.54
• Languages: English
• ISSNs: 1934-9270

Abstract

Abstract: Most structural techniques provide averaged information or information about a single predominant conformational state. However, biological macromolecules typically function through series of conformations. Therefore, a complete understanding of macromolecular structures requires knowledge of the ensembles that represent probabilities on a conformational free energy landscape. Here we describe an emerging approach, X‐ray scattering interferometry (XSI), a method that provides instantaneous distance distributions for molecules in solution. XSI uses gold nanocrystal labels site‐specifically attached to a macromolecule and measures the scattering interference from pairs of heavy metal labels. The recorded signal can directly be transformed into a distance distribution between the two probes. We describe the underlying concepts, present a detailed protocol for preparing samples and recording XSI data, and provide a custom‐written graphical user interface to facilitate XSI data analysis. © 2018 by John Wiley & Sons, Inc.