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Kinetics of DNA hydration

Denisov, Vladimir P. LU ; Carlström, Göran LU orcid ; Venu, Kandadai and Halle, Bertil LU (1997) In Journal of Molecular Biology 268(1). p.118-136
Abstract

The hydration of the d(CGCGAATTCGCG) B-DNA duplex in solution was studied by nuclear magnetic relaxation dispersion (NMRD) of the water nuclei 1H, 2H, and 17O, and by nuclear Overhauser effects (NOEs) in high-resolution two-dimensional 1H NMR spectra. By comparing results from the free duplex with those from its complex with netropsin, water molecules in the 'spine of hydration' in the AATT region of the minor groove could be distinguished from hydration water elsewhere in the duplex. The 2H and 17O relaxation dispersions yield a model-independent residence time of 0.9(±0.1) ns at 4°C for five highly ordered water molecules in the spine. When corrected for frequency... (More)

The hydration of the d(CGCGAATTCGCG) B-DNA duplex in solution was studied by nuclear magnetic relaxation dispersion (NMRD) of the water nuclei 1H, 2H, and 17O, and by nuclear Overhauser effects (NOEs) in high-resolution two-dimensional 1H NMR spectra. By comparing results from the free duplex with those from its complex with netropsin, water molecules in the 'spine of hydration' in the AATT region of the minor groove could be distinguished from hydration water elsewhere in the duplex. The 2H and 17O relaxation dispersions yield a model-independent residence time of 0.9(±0.1) ns at 4°C for five highly ordered water molecules in the spine. When corrected for frequency offset effects, the NOE data yield the same residence time as the NMRD data, giving credence to both methods. At 27°C, the residence time is estimated to 0.2 ns, a factor of 40 shorter than the tumbling time of the duplex. The NMRD data show that all water molecules associated with the duplex, except the five molecules in the spine, have residence times significantly shorter than Ins at 4°C. There is thus no long-lived hydration structure associated with the phosphate backbone. In contrast to 2H and 17O, the 1H relaxation dispersion is dominated by labile DNA protons and therefore provides little information about DNA hydration.

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author
; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
B-DNA hydration, Netropsin, NMR spectroscopy, Oxygen-17 relaxation dispersion, Water residence time
in
Journal of Molecular Biology
volume
268
issue
1
pages
19 pages
publisher
Elsevier
external identifiers
  • scopus:0031585991
  • pmid:9149146
ISSN
0022-2836
DOI
10.1006/jmbi.1996.0862
language
English
LU publication?
yes
id
7920c5f4-4af8-4c00-a7c1-32bac2f5f394
date added to LUP
2019-07-25 21:35:11
date last changed
2024-04-30 18:32:41
@article{7920c5f4-4af8-4c00-a7c1-32bac2f5f394,
  abstract     = {{<p>The hydration of the d(CGCGAATTCGCG) B-DNA duplex in solution was studied by nuclear magnetic relaxation dispersion (NMRD) of the water nuclei <sup>1</sup>H, <sup>2</sup>H, and <sup>17</sup>O, and by nuclear Overhauser effects (NOEs) in high-resolution two-dimensional <sup>1</sup>H NMR spectra. By comparing results from the free duplex with those from its complex with netropsin, water molecules in the 'spine of hydration' in the AATT region of the minor groove could be distinguished from hydration water elsewhere in the duplex. The <sup>2</sup>H and <sup>17</sup>O relaxation dispersions yield a model-independent residence time of 0.9(±0.1) ns at 4°C for five highly ordered water molecules in the spine. When corrected for frequency offset effects, the NOE data yield the same residence time as the NMRD data, giving credence to both methods. At 27°C, the residence time is estimated to 0.2 ns, a factor of 40 shorter than the tumbling time of the duplex. The NMRD data show that all water molecules associated with the duplex, except the five molecules in the spine, have residence times significantly shorter than Ins at 4°C. There is thus no long-lived hydration structure associated with the phosphate backbone. In contrast to <sup>2</sup>H and <sup>17</sup>O, the <sup>1</sup>H relaxation dispersion is dominated by labile DNA protons and therefore provides little information about DNA hydration.</p>}},
  author       = {{Denisov, Vladimir P. and Carlström, Göran and Venu, Kandadai and Halle, Bertil}},
  issn         = {{0022-2836}},
  keywords     = {{B-DNA hydration; Netropsin; NMR spectroscopy; Oxygen-17 relaxation dispersion; Water residence time}},
  language     = {{eng}},
  month        = {{04}},
  number       = {{1}},
  pages        = {{118--136}},
  publisher    = {{Elsevier}},
  series       = {{Journal of Molecular Biology}},
  title        = {{Kinetics of DNA hydration}},
  url          = {{http://dx.doi.org/10.1006/jmbi.1996.0862}},
  doi          = {{10.1006/jmbi.1996.0862}},
  volume       = {{268}},
  year         = {{1997}},
}