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Title: Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.

Abstract

Magnesium ions play important roles in the structure and function of nucleic acids. Whereas the tertiary folding of RNA often requires magnesium ions binding to tight places where phosphates are clustered, the molecular basis of the interactions of magnesium ions with RNA helical regions is less well understood. We have refined the crystal structures of four decamer oligonucleotides, d(ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with bound hexahydrated magnesium ions at high resolution. The structures reveal that A-form nucleic acid has characteristic [Mg(H2O)6]2+ binding modes. One mode has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of guanine bases via hydrogen bonds. Our crystallographic observations are consistent with the recent NMR observations that in solution [Co(NH3)6]3+, a model ion of [Mg(H2O)6]2+, binds in an identical manner. The other mode involves the binding of the ion to phosphates, bridging across the outer mouth of the narrow major groove. These [Mg(H2O)6]2+ ions are found at the most negative electrostatic potential regions of A-form duplexes. We propose that these two binding modes are important in the global charge neutralization, and therefore stability, of A-form duplexes.

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Institutes of Health (NIH); National Science Foundation (NSF); USDOE Office of Science (SC)
OSTI Identifier:
949607
Report Number(s):
ANL/BIO/JA-42482
Journal ID: ISSN 0305-1048; NARHAD; TRN: US201012%%391
DOE Contract Number:
DE-AC02-06CH11357
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nucleic Acids Res.; Journal Volume: 28; Journal Issue: 8 ; 2000
Country of Publication:
United States
Language:
ENGLISH
Subject:
08 HYDROGEN; 36 MATERIALS SCIENCE; CRYSTAL STRUCTURE; ELECTROSTATICS; GUANINE; HYDROGEN; MAGNESIUM IONS; NUCLEIC ACIDS; OLIGONUCLEOTIDES; PHOSPHATES; RESOLUTION; RNA; STABILITY

Citation Formats

Robinson, H., Gao, Y.-G., Sanishvili, R., Joachimiak, A., Wang, A. H.-J., Univ. of Illinois, and Northwestern Univ. Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.. United States: N. p., 2000. Web. doi:10.1093/nar/28.8.1760.
Robinson, H., Gao, Y.-G., Sanishvili, R., Joachimiak, A., Wang, A. H.-J., Univ. of Illinois, & Northwestern Univ. Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.. United States. doi:10.1093/nar/28.8.1760.
Robinson, H., Gao, Y.-G., Sanishvili, R., Joachimiak, A., Wang, A. H.-J., Univ. of Illinois, and Northwestern Univ. Sat . "Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.". United States. doi:10.1093/nar/28.8.1760.
@article{osti_949607,
title = {Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.},
author = {Robinson, H. and Gao, Y.-G. and Sanishvili, R. and Joachimiak, A. and Wang, A. H.-J. and Univ. of Illinois and Northwestern Univ.},
abstractNote = {Magnesium ions play important roles in the structure and function of nucleic acids. Whereas the tertiary folding of RNA often requires magnesium ions binding to tight places where phosphates are clustered, the molecular basis of the interactions of magnesium ions with RNA helical regions is less well understood. We have refined the crystal structures of four decamer oligonucleotides, d(ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with bound hexahydrated magnesium ions at high resolution. The structures reveal that A-form nucleic acid has characteristic [Mg(H2O)6]2+ binding modes. One mode has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of guanine bases via hydrogen bonds. Our crystallographic observations are consistent with the recent NMR observations that in solution [Co(NH3)6]3+, a model ion of [Mg(H2O)6]2+, binds in an identical manner. The other mode involves the binding of the ion to phosphates, bridging across the outer mouth of the narrow major groove. These [Mg(H2O)6]2+ ions are found at the most negative electrostatic potential regions of A-form duplexes. We propose that these two binding modes are important in the global charge neutralization, and therefore stability, of A-form duplexes.},
doi = {10.1093/nar/28.8.1760},
journal = {Nucleic Acids Res.},
number = 8 ; 2000,
volume = 28,
place = {United States},
year = {Sat Jan 01 00:00:00 EST 2000},
month = {Sat Jan 01 00:00:00 EST 2000}
}