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Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths

DOI: 10.1093/nar/gkaa439 DOI Help

Authors: Yashu Zhang (Huazhong Agricultural University) , Kamel El Omari (Diamond Light Source) , Ramona Duman (Diamond Light Source) , Sisi Liu (Huazhong Agricultural University) , Shozeb Haider (University College London) , Armin Wagner (Diamond Light Source) , Gary N. Parkinson (University of London) , Dengguo Wei (Huazhong Agricultural University)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Nucleic Acids Research , VOL 45

State: Published (Approved)
Published: May 2020
Diamond Proposal Number(s): 12305

Open Access Open Access

Abstract: Obtaining phase information remains a formidable challenge for nucleic acid structure determination. The introduction of an X-ray synchrotron beamline designed to be tunable to long wavelengths at Diamond Light Source has opened the possibility to native de novo structure determinations by the use of intrinsic scattering elements. This provides opportunities to overcome the limitations of introducing modifying nucleotides, often required to derive phasing information. In this paper, we build on established methods to generate new tools for nucleic acid structure determinations. We report on the use of (i) native intrinsic potassium single-wavelength anomalous dispersion methods (K-SAD), (ii) use of anomalous scattering elements integral to the crystallization buffer (extrinsic cobalt and intrinsic potassium ions), (iii) extrinsic bromine and intrinsic phosphorus SAD to solve complex nucleic acid structures. Using the reported methods we solved the structures of (i) Pseudorabies virus (PRV) RNA G-quadruplex and ligand complex, (ii) PRV DNA G-quadruplex, and (iii) an i-motif of human telomeric sequence. Our results highlight the utility of using intrinsic scattering as a pathway to solve and determine non-canonical nucleic acid motifs and reveal the variability of topology, influence of ligand binding, and glycosidic angle rearrangements seen between RNA and DNA G-quadruplexes of the same sequence.

Subject Areas: Biology and Bio-materials


Instruments: I02-Macromolecular Crystallography , I23-Long wavelength MX

Documents:
gkaa439.pdf

Discipline Tags:

Structural biology Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX) Long Wavelength Crystallography