Sequence dependence and direct measurement of crossover isomer distribution in model Holliday junctions using NMR spectroscopy
(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.
(Less)
- author
- Carlström, Göran LU and Chazin, Walter J.
- publishing date
- 1996-03-19
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Biochemistry
- volume
- 35
- issue
- 11
- pages
- 11 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- pmid:8639504
- scopus:0029880329
- 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
- date last changed
- 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}}, }