Combined neutron and X-ray diffraction studies of DNA in crystals and solutions

Leal, Ricardo M. F.; Callow, Shirley; Callow, Philip; Blakeley, Matthew P.; Cardin, C.J.; Denny, William A.; Teixeira, Susana; Mitchell, Edward P.; Forsyth, V. Trevor

doi:10.1107/s0907444910017713

Cited by 9 publications

(8 citation statements)

References 24 publications

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“…We did not observe H/D exchange of C8-H proton on any of the three guanine nucleobases in 1_RT or 1_LT , although significant exchange of this proton with D in Gua was previously documented in the neutron structure of hexameric Z-DNA (Chatake et al, 2005). In addition, unlike in the previous neutron structure of the decameric A-DNA (Leal et al, 2010), we did not observe protonation of N7 in guanine or N3 in adenine nucleobases in our current XN structures.…”

Section: Resultscontrasting

confidence: 99%

Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA

et al. 2018

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Summary Nucleic acids can fold into well-defined 3D structures that help determine their function. Knowing precise nucleic acid structures can also be used for the design of nucleic acid-based therapeutics. However, locations of hydrogen atoms, which are key players of nucleic acid function are normally not determined with X-ray crystallography. Accurate determination of hydrogen atom positions can provide indispensable information on protonation states, hydrogen bonding, and water architecture in nucleic acids. Here, we used neutron crystallography in combination with X-ray diffraction to obtain joint X-ray/neutron structures at both room- and cryo-temperatures of a self-complimentary A-DNA oligonucleotide d[GTGG(CSe)CAC]2 containing 2’-SeCH3 modification on Cyt5 (CSe) at pH 5.6. We directly observed protonation of a backbone phosphate oxygen of Ade7 at room temperature. The proton is replaced with hydrated Mg2+ upon cooling the crystal to 100K, indicating that metal binding is favoured at low temperature, whereas proton binding is dominant at room temperature.

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Section: Resultscontrasting

confidence: 99%

Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA

et al. 2018

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“…The analysis will be carried out with the aid of the PHENIX software package (Adams et al, 2009(Adams et al, , 2010 optimized for joint refinements (Afonine et al, 2010) and can be expected to yield detailed information on the molecular structure of TTR, including information relating to amino-acid protonation states and hydration. There is now ample evidence demonstrating that information of this type almost invariably provides new insights into functional aspects of protein structure (Blakeley et al, 2008;Gardberg et al, 2009Gardberg et al, , 2010Howard et al, 2011;Kovalevsky et al, 2010Kovalevsky et al, , 2011Leal et al, 2009Leal et al, , 2010Teixeira et al, 2008Teixeira et al, , 2010Tomanicek et al, 2010Tomanicek et al, , 2011. This analysis will be of importance for an understanding of monomer and dimer interactions and the role that structured water plays in these interactions.…”

Section: Resultsmentioning

confidence: 99%

Preliminary neutron crystallographic study of human transthyretin

et al. 2011

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Preliminary studies of perdeuterated crystals of human transthyretin (TTR) have been carried out using the LADI-III and D19 diffractometers at the Institut Laue-Langevin in Grenoble. The results demonstrate the feasibility of a full crystallographic analysis to a resolution of 2.0 Å using Laue diffraction and also illustrate the potential of using monochromatic instruments such as D19 for higher resolution studies where larger crystals having smaller unit cells are available. This study will yield important information on hydrogen bonding, amino-acid protonation states and hydration in the protein. Such information will be of general interest for an understanding of the factors that stabilize/ destabilize TTR and for the design of ligands that may be used to counter TTR amyloid fibrillogenesis.

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“…Even so, hydrogen atoms are not normally located, though their positions can be determined by neutron diffraction in favourable cases. 83,84 It is often possible to infer hydrogen locations from water structure, since the phosphate backbone does not protonate and is always the lone pair donor. In the structure shown in Figure 15a, the authors report that the decamer was bent by the presence of Ca 2+ ions in addition to Mg 2+ ions.…”

Section: Working With Dna Crystals 41 Metal Ion Diversity In the Crymentioning

confidence: 99%

Interactions Between Metal Ions and DNA

Cardin

2019

Structure and Bonding

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84 years elapsed between the announcements of the Periodic Table and that of the DNA double helix in 1953, and the two have been combined in many ways since then. In this chapter an outline of the fundamentals of DNA structure leads into a range of examples showing how the natural magnesium and potassium ions found in nature can be substituted in a diversity of applications. The dynamic structures found in nature have been studied in the more controlled, but artificial environment of the DNA crystal using examples from sodium to platinum, and also in a range of DNA-binding metal complexes. While nmr is an essential technique for studying nucleic acid structure and conformation, most of our knowledge of metal ion binding has come from X-ray crystallography. These days the structures studied, and therefore also the diversity of metal binding, go beyond the double helix to triplexes, hairpin loops, junctions and quadruplexes, and the chapter describes briefly how these pieces fit into the DNA jigsaw. In a final section, the roles of metal cations in the crystallisation of new DNA structures are discussed, along with an introduction to the versatility of the Periodic Table of absorption edges for nucleic acid structure determination.

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Combined neutron and X-ray diffraction studies of DNA in crystals and solutions

Cited by 9 publications

References 24 publications

Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA

Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA

Preliminary neutron crystallographic study of human transthyretin

Interactions Between Metal Ions and DNA

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