Interaction of zinc ions with d(CGCAATTGCG) in a 2.9 Å resolution X-ray structure

Montserrat Soler-López; Lucy Malinina; Valentina Tereshko; Valentina Zarytova; Juan A. Subirana

doi:10.1007/s00775-001-0333-z

Interaction of zinc ions with d(CGCAATTGCG) in a 2.9 Å resolution X-ray structure

Montserrat Soler-López, Lucy Malinina, Valentina Tereshko, Valentina Zarytova, Juan A. Subirana

Hormel Institute

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

22 Scopus citations

Abstract

We have synthesized and crystallized in the presence of Zn²⁺ ions the peptidyl-oligonucleotide adduct CH₃CO-(Arg)₄-NH- (CH₂)₆-NH-p-d(CGCAAT-TGCG). This is the first structure obtained from a deoxyoligonucleotide crystallized in the presence of zinc ions. Zn ions are clearly visible in the 2.9 Å resolution map. On the other hand, the peptide tail is not visible in the crystal structure as determined by X-ray diffraction. The terminal bases C1 and G10 are found in extra-helical positions. Their phosphates are ligands of a Zn²⁺ ion, located in a special position of the unit cell. This ion plays an important role in the packing arrangement, since it binds four different DNA molecules. Two other Zn²⁺ ions are also important for DNA packing. They interact specifically with the N7 atoms of the terminal G2 and G10 bases, but not with the internal G8. This result supports the hypothesis that transition metals do not interact with the bases of duplex DNA in the B form.

Original language	English (US)
Pages (from-to)	533-538
Number of pages	6
Journal	Journal of Biological Inorganic Chemistry
Volume	7
Issue number	4-5
DOIs	https://doi.org/10.1007/s00775-001-0333-z
State	Published - 2002

Bibliographical note

Funding Information:
Acknowledgements This work has been s upported in part by the Dirección General de Enseñanza Superior e Investigación Cientí-fica (grant PM98-0135), the Generalitat de Catalunya (grant 1999SGR-00144) and the Training and Mobility of Researchers (Large Scientific Facilities) programme at the European Molecular Biology Laboratory, Hamburg Outstation (ERBFMGECT-980134), and the Russian Foundation of Basic Research (99-04-49224 and 49731). L.M. also acknowledges support from NATO Collaboration Linkage grant LST.CLG.976607.

Keywords

Guanine-ion interactions
Oligonucleotide structure
X-ray diffraction
Zinc

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@article{cb8d9d84b049433e8df9a3468cbeae2c,

title = "Interaction of zinc ions with d(CGCAATTGCG) in a 2.9 {\AA} resolution X-ray structure",

abstract = "We have synthesized and crystallized in the presence of Zn2+ ions the peptidyl-oligonucleotide adduct CH3CO-(Arg)4-NH- (CH2)6-NH-p-d(CGCAAT-TGCG). This is the first structure obtained from a deoxyoligonucleotide crystallized in the presence of zinc ions. Zn ions are clearly visible in the 2.9 {\AA} resolution map. On the other hand, the peptide tail is not visible in the crystal structure as determined by X-ray diffraction. The terminal bases C1 and G10 are found in extra-helical positions. Their phosphates are ligands of a Zn2+ ion, located in a special position of the unit cell. This ion plays an important role in the packing arrangement, since it binds four different DNA molecules. Two other Zn2+ ions are also important for DNA packing. They interact specifically with the N7 atoms of the terminal G2 and G10 bases, but not with the internal G8. This result supports the hypothesis that transition metals do not interact with the bases of duplex DNA in the B form.",

keywords = "Guanine-ion interactions, Oligonucleotide structure, X-ray diffraction, Zinc",

author = "Montserrat Soler-L{\'o}pez and Lucy Malinina and Valentina Tereshko and Valentina Zarytova and Subirana, {Juan A.}",

note = "Funding Information: Acknowledgements This work has been s upported in part by the Direcci{\'o}n General de Ense{\~n}anza Superior e Investigaci{\'o}n Cient{\'i}-fica (grant PM98-0135), the Generalitat de Catalunya (grant 1999SGR-00144) and the Training and Mobility of Researchers (Large Scientific Facilities) programme at the European Molecular Biology Laboratory, Hamburg Outstation (ERBFMGECT-980134), and the Russian Foundation of Basic Research (99-04-49224 and 49731). L.M. also acknowledges support from NATO Collaboration Linkage grant LST.CLG.976607.",

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AU - Soler-López, Montserrat

AU - Malinina, Lucy

AU - Tereshko, Valentina

AU - Zarytova, Valentina

AU - Subirana, Juan A.

N1 - Funding Information: Acknowledgements This work has been s upported in part by the Dirección General de Enseñanza Superior e Investigación Cientí-fica (grant PM98-0135), the Generalitat de Catalunya (grant 1999SGR-00144) and the Training and Mobility of Researchers (Large Scientific Facilities) programme at the European Molecular Biology Laboratory, Hamburg Outstation (ERBFMGECT-980134), and the Russian Foundation of Basic Research (99-04-49224 and 49731). L.M. also acknowledges support from NATO Collaboration Linkage grant LST.CLG.976607.

PY - 2002

Y1 - 2002

N2 - We have synthesized and crystallized in the presence of Zn2+ ions the peptidyl-oligonucleotide adduct CH3CO-(Arg)4-NH- (CH2)6-NH-p-d(CGCAAT-TGCG). This is the first structure obtained from a deoxyoligonucleotide crystallized in the presence of zinc ions. Zn ions are clearly visible in the 2.9 Å resolution map. On the other hand, the peptide tail is not visible in the crystal structure as determined by X-ray diffraction. The terminal bases C1 and G10 are found in extra-helical positions. Their phosphates are ligands of a Zn2+ ion, located in a special position of the unit cell. This ion plays an important role in the packing arrangement, since it binds four different DNA molecules. Two other Zn2+ ions are also important for DNA packing. They interact specifically with the N7 atoms of the terminal G2 and G10 bases, but not with the internal G8. This result supports the hypothesis that transition metals do not interact with the bases of duplex DNA in the B form.

AB - We have synthesized and crystallized in the presence of Zn2+ ions the peptidyl-oligonucleotide adduct CH3CO-(Arg)4-NH- (CH2)6-NH-p-d(CGCAAT-TGCG). This is the first structure obtained from a deoxyoligonucleotide crystallized in the presence of zinc ions. Zn ions are clearly visible in the 2.9 Å resolution map. On the other hand, the peptide tail is not visible in the crystal structure as determined by X-ray diffraction. The terminal bases C1 and G10 are found in extra-helical positions. Their phosphates are ligands of a Zn2+ ion, located in a special position of the unit cell. This ion plays an important role in the packing arrangement, since it binds four different DNA molecules. Two other Zn2+ ions are also important for DNA packing. They interact specifically with the N7 atoms of the terminal G2 and G10 bases, but not with the internal G8. This result supports the hypothesis that transition metals do not interact with the bases of duplex DNA in the B form.

KW - Guanine-ion interactions

KW - Oligonucleotide structure

KW - X-ray diffraction

KW - Zinc

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Interaction of zinc ions with d(CGCAATTGCG) in a 2.9 Å resolution X-ray structure

Abstract

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Keywords

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