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Competitive Na+ and Rb+ binding in the minor groove of DNA

Cesare Marincola, Flaminia; Denisov, Vladimir LU and Halle, Bertil LU (2004) In Journal of the American Chemical Society 126(21). p.6739-6750
Abstract
Sequence-dependent coordination of alkali ions to the nucleotide bases in the minor groove of AT-tract B-DNA has recently been inferred from X-ray crystallography, solution NMR and computer simulations. Here, we present new Na-23 and Rb-87 magnetic relaxation dispersion (MRD) data that demonstrate competitive and long-lived binding of Na+ and Rb+ ions in the minor groove of the B-DNA duplex [d(CGCGAATTCGCG)](2). The Na+/Rb+ selectivity of the minor groove is found to be weak, consistent with local structural flexibility. The ion occupancies derived from the MRD data are substantially higher than previously reported, suggesting that groove-bound ions significantly influence the energetics and structural polymorphism of DNA in vivo. For... (More)
Sequence-dependent coordination of alkali ions to the nucleotide bases in the minor groove of AT-tract B-DNA has recently been inferred from X-ray crystallography, solution NMR and computer simulations. Here, we present new Na-23 and Rb-87 magnetic relaxation dispersion (MRD) data that demonstrate competitive and long-lived binding of Na+ and Rb+ ions in the minor groove of the B-DNA duplex [d(CGCGAATTCGCG)](2). The Na+/Rb+ selectivity of the minor groove is found to be weak, consistent with local structural flexibility. The ion occupancies derived from the MRD data are substantially higher than previously reported, suggesting that groove-bound ions significantly influence the energetics and structural polymorphism of DNA in vivo. For example, in the presence of 0.20 M Na+ and 0.56 M Rb+ at 4 degreesC, the ApT site in the minor groove is occupied by a Rb+ ion, a Na+ ion, or a water molecule 40, 10, and 50% of the time, respectively. In the absence of Rb+, the Na+ occupancy increases to 50%. At 4 degreesC, the mean residence time of groove-bound ions is 0.2 +/- 0.1 mus for Rb+ and 10 ns to 100 mus for Na+. A shorter correlation time of 2 ns is attributed to counterions bridging cross-strand phosphate groups. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of the American Chemical Society
volume
126
issue
21
pages
6739 - 6750
publisher
The American Chemical Society
external identifiers
  • pmid:15161302
  • wos:000221671400054
  • scopus:2542583798
ISSN
1520-5126
DOI
10.1021/ja049930z
language
English
LU publication?
yes
id
2f2c067c-6e4d-4379-865a-0fbfa1cba0e9 (old id 141090)
date added to LUP
2007-06-29 13:28:14
date last changed
2017-07-23 04:34:17
@article{2f2c067c-6e4d-4379-865a-0fbfa1cba0e9,
  abstract     = {Sequence-dependent coordination of alkali ions to the nucleotide bases in the minor groove of AT-tract B-DNA has recently been inferred from X-ray crystallography, solution NMR and computer simulations. Here, we present new Na-23 and Rb-87 magnetic relaxation dispersion (MRD) data that demonstrate competitive and long-lived binding of Na+ and Rb+ ions in the minor groove of the B-DNA duplex [d(CGCGAATTCGCG)](2). The Na+/Rb+ selectivity of the minor groove is found to be weak, consistent with local structural flexibility. The ion occupancies derived from the MRD data are substantially higher than previously reported, suggesting that groove-bound ions significantly influence the energetics and structural polymorphism of DNA in vivo. For example, in the presence of 0.20 M Na+ and 0.56 M Rb+ at 4 degreesC, the ApT site in the minor groove is occupied by a Rb+ ion, a Na+ ion, or a water molecule 40, 10, and 50% of the time, respectively. In the absence of Rb+, the Na+ occupancy increases to 50%. At 4 degreesC, the mean residence time of groove-bound ions is 0.2 +/- 0.1 mus for Rb+ and 10 ns to 100 mus for Na+. A shorter correlation time of 2 ns is attributed to counterions bridging cross-strand phosphate groups.},
  author       = {Cesare Marincola, Flaminia and Denisov, Vladimir and Halle, Bertil},
  issn         = {1520-5126},
  language     = {eng},
  number       = {21},
  pages        = {6739--6750},
  publisher    = {The American Chemical Society},
  series       = {Journal of the American Chemical Society},
  title        = {Competitive Na+ and Rb+ binding in the minor groove of DNA},
  url          = {http://dx.doi.org/10.1021/ja049930z},
  volume       = {126},
  year         = {2004},
}