6D54

Low Temperature joint X-ray/neutron structure of DNA oligonucleotide d(GTGGCCAC)2 with 2'-SeCH3 modification on Cyt5

Summary for 6D54

• Entry DOI: 10.2210/pdb6d54/pdb
• Related: 6D4L
• Descriptor: DNA (5'-D(*GP*TP*GP*GP*(CSL)P*CP*AP*C)-3'), MAGNESIUM ION (3 entities in total)
• Functional Keywords: dna, oligonucleotide, selenium modification
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 2569.20

Authors

Kovalevsky, A.,Huang, Z.,Vandavasi, V.G. (deposition date: 2018-04-19, release date: 2018-10-17, Last modification date: 2023-10-04)

Primary citation

Vandavasi, V.G.,Blakeley, M.P.,Keen, D.A.,Hu, L.R.,Huang, Z.,Kovalevsky, A.
Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA.
Structure, 26:1645-, 2018

PubMed Abstract: 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-complementary A-DNA oligonucleotide d[GTGG(C)CAC] containing 2'-SeCH modification on Cyt5 (C) at pH 5.6. We directly observed protonation of a backbone phosphate oxygen of Ade7 at room temperature. The proton is replaced with hydrated Mg upon cooling the crystal to 100 K, indicating that metal binding is favored at low temperature, whereas proton binding is dominant at room temperature.

PubMed: 30244969
DOI: 10.1016/j.str.2018.08.001

Experimental method

NEUTRON DIFFRACTION (1.9 Å)
X-RAY DIFFRACTION (1.65 Å)