The NMR structure of [Xd(C2)]4 investigated by molecular dynamics simulations
(2003) In Magnetic Resonance in Chemistry 41(1). p.18-25- Abstract
- The i-motif tetrameric structure is built up from two parallel duplexes intercalated in a head-to-tail orientation, and held together by hemiprotonated cytosine pairs. Two topologies exist for the i-motif structure, one with outermost 3' extremities and the other with outermost 5' extremities, called the 3'E and 5'E topology, respectively. Since the comparison of sugar and phosphate group interactions between the two topologies is independent of the length of the intercalation motif, the relative stability of the 3'E and 5'E topologies therefore should not depend on this length. Nevertheless, it has been shown that the 3'E topology of the [d(C2)]4 is much more stable than the 5'E topology, and that the former is the only species observed... (More)
- The i-motif tetrameric structure is built up from two parallel duplexes intercalated in a head-to-tail orientation, and held together by hemiprotonated cytosine pairs. Two topologies exist for the i-motif structure, one with outermost 3' extremities and the other with outermost 5' extremities, called the 3'E and 5'E topology, respectively. Since the comparison of sugar and phosphate group interactions between the two topologies is independent of the length of the intercalation motif, the relative stability of the 3'E and 5'E topologies therefore should not depend on this length. Nevertheless, it has been shown that the 3'E topology of the [d(C2)]4 is much more stable than the 5'E topology, and that the former is the only species observed in solution. In order to understand the reason for this atypical behavior, the NMR structure of the [Xd(C2)]4 was determined and analyzed by molecular dynamics simulations. In the NMR structure, the width of the narrow groove is slightly smaller than in previously determined i-motif structures, which supports the importance of phosphodiester backbone interactions in the structure stability. The simulations show that the stacking of cytosines, essential for the i-motif stability, is produced by a similar and non-negative twisting of the phosphodiester backbones. The twisting is induced by an interaction between the backbones; the [Xd(C2)]4 in 5'E topology, exhibiting very limited interaction between the phosphodiester backbones, is thus unstable. Copyright (C) 2002 John Wiley Sons, Ltd. (Less)
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https://lup.lub.lu.se/record/319751
- author
- Malliavin, TE ; Snoussi, Karim LU and Leroy, JL
- organization
- publishing date
- 2003
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- molecular dynamics, cytidine, protonated, proton exchange, i-motif, [Xd(C2)]4, NMR, DNA structure
- in
- Magnetic Resonance in Chemistry
- volume
- 41
- issue
- 1
- pages
- 18 - 25
- publisher
- John Wiley & Sons Inc.
- external identifiers
-
- wos:000180422000003
- scopus:0037233465
- ISSN
- 1097-458X
- DOI
- 10.1002/mrc.1109
- language
- English
- LU publication?
- yes
- id
- 087376cb-91c1-440d-ba33-ec3d67903932 (old id 319751)
- date added to LUP
- 2016-04-01 12:16:50
- date last changed
- 2022-02-03 20:01:37
@article{087376cb-91c1-440d-ba33-ec3d67903932, abstract = {{The i-motif tetrameric structure is built up from two parallel duplexes intercalated in a head-to-tail orientation, and held together by hemiprotonated cytosine pairs. Two topologies exist for the i-motif structure, one with outermost 3' extremities and the other with outermost 5' extremities, called the 3'E and 5'E topology, respectively. Since the comparison of sugar and phosphate group interactions between the two topologies is independent of the length of the intercalation motif, the relative stability of the 3'E and 5'E topologies therefore should not depend on this length. Nevertheless, it has been shown that the 3'E topology of the [d(C2)]4 is much more stable than the 5'E topology, and that the former is the only species observed in solution. In order to understand the reason for this atypical behavior, the NMR structure of the [Xd(C2)]4 was determined and analyzed by molecular dynamics simulations. In the NMR structure, the width of the narrow groove is slightly smaller than in previously determined i-motif structures, which supports the importance of phosphodiester backbone interactions in the structure stability. The simulations show that the stacking of cytosines, essential for the i-motif stability, is produced by a similar and non-negative twisting of the phosphodiester backbones. The twisting is induced by an interaction between the backbones; the [Xd(C2)]4 in 5'E topology, exhibiting very limited interaction between the phosphodiester backbones, is thus unstable. Copyright (C) 2002 John Wiley Sons, Ltd.}}, author = {{Malliavin, TE and Snoussi, Karim and Leroy, JL}}, issn = {{1097-458X}}, keywords = {{molecular dynamics; cytidine; protonated; proton exchange; i-motif; [Xd(C2)]4; NMR; DNA structure}}, language = {{eng}}, number = {{1}}, pages = {{18--25}}, publisher = {{John Wiley & Sons Inc.}}, series = {{Magnetic Resonance in Chemistry}}, title = {{The NMR structure of [Xd(C2)]4 investigated by molecular dynamics simulations}}, url = {{http://dx.doi.org/10.1002/mrc.1109}}, doi = {{10.1002/mrc.1109}}, volume = {{41}}, year = {{2003}}, }