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

Venu Gopal Vandavasi; Matthew P. Blakeley; David A. Keen; Lillian R. Hu; Zhen Huang; Andrey Kovalevsky

doi:10.1016/j.str.2018.08.001

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

Venu Gopal Vandavasi, Matthew P. Blakeley, David A. Keen, Lillian R. Hu, Zhen Huang, Andrey Kovalevsky

Single Crystal Diffraction

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

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 ^Se )CAC] ₂ containing 2′-SeCH ₃ modification on Cyt5 (C ^Se ) 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 ²⁺ upon cooling the crystal to 100 K, indicating that metal binding is favored at low temperature, whereas proton binding is dominant at room temperature.

Original language	English
Pages (from-to)	1645-1650.e3
Journal	Structure
Volume	26
Issue number	12
DOIs	https://doi.org/10.1016/j.str.2018.08.001
State	Published - Dec 4 2018

Funding

This research at ORNL's High Flux Isotope Reactor (IMAGINE beamline) was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, US Department of Energy (DOE). The authors thank Institut Laue Langevin (beamline LADI-III) for awarded neutron beamtime. Notice: This manuscript has been authored by UT-Battelle under DOE contract no. DE-AC05-00OR22725. This work was supported by the ORNL Laboratory Directed Research and Development grant to A.K. and by NIH ( R01GM095881 and R42ES026935 ) to Z.H.; and the US Department of Energy 's Office of Basic Energy Sciences.

Funders	Funder number
Office of Basic Energy Sciences
Scientific User Facilities Division
US Department of Energy
UT-Battelle
National Institutes of Health	R01GM095881
U.S. Department of Energy
National Institute of Environmental Health Sciences	R42ES026935
Laboratory Directed Research and Development

Keywords

A-form DNA
RNA
hydrogen bonding
metal binding
neutron crystallography
oligonucleotide crystallization
protonation
selenium modification and derivatization

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10.1016/j.str.2018.08.001

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

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 Se )CAC] 2 containing 2′-SeCH 3 modification on Cyt5 (C Se ) 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 2+ upon cooling the crystal to 100 K, indicating that metal binding is favored at low temperature, whereas proton binding is dominant at room temperature.",

keywords = "A-form DNA, RNA, hydrogen bonding, metal binding, neutron crystallography, oligonucleotide crystallization, protonation, selenium modification and derivatization",

author = "Vandavasi, {Venu Gopal} and Blakeley, {Matthew P.} and Keen, {David A.} and Hu, {Lillian R.} and Zhen Huang and Andrey Kovalevsky",

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T1 - Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA

AU - Vandavasi, Venu Gopal

AU - Blakeley, Matthew P.

AU - Keen, David A.

AU - Hu, Lillian R.

AU - Huang, Zhen

AU - Kovalevsky, Andrey

PY - 2018/12/4

Y1 - 2018/12/4

N2 - 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 Se )CAC] 2 containing 2′-SeCH 3 modification on Cyt5 (C Se ) 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 2+ upon cooling the crystal to 100 K, indicating that metal binding is favored at low temperature, whereas proton binding is dominant at room temperature.

AB - 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 Se )CAC] 2 containing 2′-SeCH 3 modification on Cyt5 (C Se ) 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 2+ upon cooling the crystal to 100 K, indicating that metal binding is favored at low temperature, whereas proton binding is dominant at room temperature.

KW - A-form DNA

KW - RNA

KW - hydrogen bonding

KW - metal binding

KW - neutron crystallography

KW - oligonucleotide crystallization

KW - protonation

KW - selenium modification and derivatization

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ER -

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

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