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Sequence dependence and direct measurement of crossover isomer distribution in model Holliday junctions using NMR spectroscopy

Carlström, Göran LU orcid and Chazin, Walter J. (1996) In Biochemistry 35(11). p.3534-3544
Abstract

A 32-base-pair model of the Holliday junction (HJ) intermediate in genetic recombination has been prepared and analyzed in-depth by 2D and 3D 1H NMR spectroscopy. This HJ (J2P1) corresponds to a cyclic permutation of the base pairs at the junction relative to a previously studied HJ [J2; Chen, S.-M., and Chazin, W. J. (1994) Biochemistry 33, 11453-11459], designed to probe the effect of the sequence at the n - 1 position (where n is the residue directly at the branch point) on the stacking geometry. Observation of several interbase nuclear Overhauser effects (NOEs) clearly indicates a strong preference for the isomer opposite that observed for J2, confirming the dependence of stacking isomer preference on the sequence at the... (More)

A 32-base-pair model of the Holliday junction (HJ) intermediate in genetic recombination has been prepared and analyzed in-depth by 2D and 3D 1H NMR spectroscopy. This HJ (J2P1) corresponds to a cyclic permutation of the base pairs at the junction relative to a previously studied HJ [J2; Chen, S.-M., and Chazin, W. J. (1994) Biochemistry 33, 11453-11459], designed to probe the effect of the sequence at the n - 1 position (where n is the residue directly at the branch point) on the stacking geometry. Observation of several interbase nuclear Overhauser effects (NOEs) clearly indicates a strong preference for the isomer opposite that observed for J2, confirming the dependence of stacking isomer preference on the sequence at the junction. As for other model HJs studied, a small equilibrium distribution of the alternate isomer could be identified. A sample of J2P1 was prepared with a single 15N-labeled thymine residue at the branch point. ID 15N-filtered 1H-detected experiments on this sample at low temperature give strong support for the co-existence of the two stacking isomers and provide a much more direct and accurate measure of the crossover isomer distribution. The comparative analysis of our immobile HJs and a model cruciform structure [Pikkemaat, J. A., van den Elst, H., van Boom, J. H., and Altona, C. (1994) Biochemistry 33, 14896-14907] sheds new light on the issue of the relevance of crossover isomer preference in vivo.

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type
Contribution to journal
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published
subject
in
Biochemistry
volume
35
issue
11
pages
11 pages
publisher
The American Chemical Society (ACS)
external identifiers
  • scopus:0029880329
  • pmid:8639504
ISSN
0006-2960
DOI
10.1021/bi952571n
language
English
LU publication?
no
id
830b63d2-6bd0-4365-b1df-e152dae71ec2
date added to LUP
2019-01-16 13:39:01
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2024-02-14 15:10:51
@article{830b63d2-6bd0-4365-b1df-e152dae71ec2,
  abstract     = {{<p>A 32-base-pair model of the Holliday junction (HJ) intermediate in genetic recombination has been prepared and analyzed in-depth by 2D and 3D <sup>1</sup>H NMR spectroscopy. This HJ (J2P1) corresponds to a cyclic permutation of the base pairs at the junction relative to a previously studied HJ [J2; Chen, S.-M., and Chazin, W. J. (1994) Biochemistry 33, 11453-11459], designed to probe the effect of the sequence at the n - 1 position (where n is the residue directly at the branch point) on the stacking geometry. Observation of several interbase nuclear Overhauser effects (NOEs) clearly indicates a strong preference for the isomer opposite that observed for J2, confirming the dependence of stacking isomer preference on the sequence at the junction. As for other model HJs studied, a small equilibrium distribution of the alternate isomer could be identified. A sample of J2P1 was prepared with a single <sup>15</sup>N-labeled thymine residue at the branch point. ID <sup>15</sup>N-filtered <sup>1</sup>H-detected experiments on this sample at low temperature give strong support for the co-existence of the two stacking isomers and provide a much more direct and accurate measure of the crossover isomer distribution. The comparative analysis of our immobile HJs and a model cruciform structure [Pikkemaat, J. A., van den Elst, H., van Boom, J. H., and Altona, C. (1994) Biochemistry 33, 14896-14907] sheds new light on the issue of the relevance of crossover isomer preference in vivo.</p>}},
  author       = {{Carlström, Göran and Chazin, Walter J.}},
  issn         = {{0006-2960}},
  language     = {{eng}},
  month        = {{03}},
  number       = {{11}},
  pages        = {{3534--3544}},
  publisher    = {{The American Chemical Society (ACS)}},
  series       = {{Biochemistry}},
  title        = {{Sequence dependence and direct measurement of crossover isomer distribution in model Holliday junctions using NMR spectroscopy}},
  url          = {{http://dx.doi.org/10.1021/bi952571n}},
  doi          = {{10.1021/bi952571n}},
  volume       = {{35}},
  year         = {{1996}},
}