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The NMR structure of [Xd(C2)]4 investigated by molecular dynamics simulations

Malliavin, TE; Snoussi, Karim LU and Leroy, JL (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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author
organization
publishing date
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
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
2007-09-17 19:31:39
date last changed
2018-05-29 12:24:21
@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},
  keyword      = {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},
  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},
  volume       = {41},
  year         = {2003},
}