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A minimal i-motif stabilized by minor groove G:T:G:T tetrads.

Escaja N, Viladoms J, Garavís M, Villasante A, Pedroso E, González C - Nucleic Acids Res. (2012)

Bottom Line: The repetitive DNA sequences found at telomeres and centromeres play a crucial role in the structure and function of eukaryotic chromosomes.This finding is particularly relevant since these oligonucleotide sequences do not contain contiguous cytosines.Importantly, these structures resemble the loop moiety adopted by an 11-nucleotide fragment of the conserved centromeric protein B (CENP-B) box motif, which is the binding site for the CENP-B.

View Article: PubMed Central - PubMed

Affiliation: Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain.

ABSTRACT
The repetitive DNA sequences found at telomeres and centromeres play a crucial role in the structure and function of eukaryotic chromosomes. This role may be related to the tendency observed in many repetitive DNAs to adopt non-canonical structures. Although there is an increasing recognition of the importance of DNA quadruplexes in chromosome biology, the co-existence of different quadruplex-forming elements in the same DNA structure is still a matter of debate. Here we report the structural study of the oligonucleotide d(TCGTTTCGT) and its cyclic analog d. Both sequences form dimeric quadruplex structures consisting of a minimal i-motif capped, at both ends, by a slipped minor groove-aligned G:T:G:T tetrad. These mini i-motifs, which do not exhibit the characteristic CD spectra of other i-motif structures, can be observed at neutral pH, although they are more stable under acidic conditions. This finding is particularly relevant since these oligonucleotide sequences do not contain contiguous cytosines. Importantly, these structures resemble the loop moiety adopted by an 11-nucleotide fragment of the conserved centromeric protein B (CENP-B) box motif, which is the binding site for the CENP-B.

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Dimeric structures of d<pTCGTTTCGTT>. Cytosines are shown in green, guanines in blue, thymines involved in GT base pairs in red and unpaired thymines in magenta. Backbone is shown in black. Hydrogen bonds are indicated in yellow. (A) Ensemble of the 10 calculated structures. (B and C) Two views of the overall structure. (D and E) Details of the stacking interaction between C:C+ base pairs, with G:T:G:T minor groove tetrads and capping thymines.
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gks911-F6: Dimeric structures of d<pTCGTTTCGTT>. Cytosines are shown in green, guanines in blue, thymines involved in GT base pairs in red and unpaired thymines in magenta. Backbone is shown in black. Hydrogen bonds are indicated in yellow. (A) Ensemble of the 10 calculated structures. (B and C) Two views of the overall structure. (D and E) Details of the stacking interaction between C:C+ base pairs, with G:T:G:T minor groove tetrads and capping thymines.

Mentions: The resulting structure is a dimer consisting of two molecules of d<pTCGTTTCGTT> arranged in an antiparallel way (see schematic representation in Figure 5, left). As reflected by the number of signals in the NMR spectra, the dimer is symmetric. The two decamers associate with each other by forming two intercalated hemi-protonated C:C+ base pairs (C2-C12 and C7-C17), sandwiched by four intermolecular G:T base pairs. The base-paired cytidine residues are magnetically equivalent and the characteristic H1′-H1′ contact between their sugars cannot be observed. These two residues stack onto each other through their 5′ side, interacting with the neighboring G:T base pairs through their 3′ side. This kind of interaction explains the lack of amino proton-H2′/H2″ contacts, observed in larger i-motifs in which interaction between C:C+ base pairs occurs through their 3′ and 5′ sides alternatively. The G:T base pairs form two G:T:G:T tetrads (G3:T16:G13:T6 and G8:T11:G18:T1) by aligning their minor groove sides. In addition to the four hydrogen bonds of the G:T base pairs, each tetrad is stabilized by two additional intermolecular H-bonds between one of the guanine amino protons and the N3 of the opposite guanine (Figure 5, right). Like other minor groove tetrads (40–43), the two base pairs are not in the same plane (Figure 6), but have a mutual inclination, in this case of around 20°. All glycosidic angles for the guanosines and thymidines involved in the tetrads are anti, with values ranging from around −100° for guanosines to −120° to −130° for thymidines. Glycosidic angles for the cytidine residues range from −90° to −110°. All residues adopt predominantly a C2′-endo sugar conformation (S-type). Although intercalated cytidine residues in larger i-motif structures usually adopt a C3′-endo sugar conformation, in this case the sugar conformation is probably affected by its proximity to the loop region and the stacked guanine residues.Figure 6.


A minimal i-motif stabilized by minor groove G:T:G:T tetrads.

Escaja N, Viladoms J, Garavís M, Villasante A, Pedroso E, González C - Nucleic Acids Res. (2012)

Dimeric structures of d<pTCGTTTCGTT>. Cytosines are shown in green, guanines in blue, thymines involved in GT base pairs in red and unpaired thymines in magenta. Backbone is shown in black. Hydrogen bonds are indicated in yellow. (A) Ensemble of the 10 calculated structures. (B and C) Two views of the overall structure. (D and E) Details of the stacking interaction between C:C+ base pairs, with G:T:G:T minor groove tetrads and capping thymines.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3526289&req=5

gks911-F6: Dimeric structures of d<pTCGTTTCGTT>. Cytosines are shown in green, guanines in blue, thymines involved in GT base pairs in red and unpaired thymines in magenta. Backbone is shown in black. Hydrogen bonds are indicated in yellow. (A) Ensemble of the 10 calculated structures. (B and C) Two views of the overall structure. (D and E) Details of the stacking interaction between C:C+ base pairs, with G:T:G:T minor groove tetrads and capping thymines.
Mentions: The resulting structure is a dimer consisting of two molecules of d<pTCGTTTCGTT> arranged in an antiparallel way (see schematic representation in Figure 5, left). As reflected by the number of signals in the NMR spectra, the dimer is symmetric. The two decamers associate with each other by forming two intercalated hemi-protonated C:C+ base pairs (C2-C12 and C7-C17), sandwiched by four intermolecular G:T base pairs. The base-paired cytidine residues are magnetically equivalent and the characteristic H1′-H1′ contact between their sugars cannot be observed. These two residues stack onto each other through their 5′ side, interacting with the neighboring G:T base pairs through their 3′ side. This kind of interaction explains the lack of amino proton-H2′/H2″ contacts, observed in larger i-motifs in which interaction between C:C+ base pairs occurs through their 3′ and 5′ sides alternatively. The G:T base pairs form two G:T:G:T tetrads (G3:T16:G13:T6 and G8:T11:G18:T1) by aligning their minor groove sides. In addition to the four hydrogen bonds of the G:T base pairs, each tetrad is stabilized by two additional intermolecular H-bonds between one of the guanine amino protons and the N3 of the opposite guanine (Figure 5, right). Like other minor groove tetrads (40–43), the two base pairs are not in the same plane (Figure 6), but have a mutual inclination, in this case of around 20°. All glycosidic angles for the guanosines and thymidines involved in the tetrads are anti, with values ranging from around −100° for guanosines to −120° to −130° for thymidines. Glycosidic angles for the cytidine residues range from −90° to −110°. All residues adopt predominantly a C2′-endo sugar conformation (S-type). Although intercalated cytidine residues in larger i-motif structures usually adopt a C3′-endo sugar conformation, in this case the sugar conformation is probably affected by its proximity to the loop region and the stacked guanine residues.Figure 6.

Bottom Line: The repetitive DNA sequences found at telomeres and centromeres play a crucial role in the structure and function of eukaryotic chromosomes.This finding is particularly relevant since these oligonucleotide sequences do not contain contiguous cytosines.Importantly, these structures resemble the loop moiety adopted by an 11-nucleotide fragment of the conserved centromeric protein B (CENP-B) box motif, which is the binding site for the CENP-B.

View Article: PubMed Central - PubMed

Affiliation: Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain.

ABSTRACT
The repetitive DNA sequences found at telomeres and centromeres play a crucial role in the structure and function of eukaryotic chromosomes. This role may be related to the tendency observed in many repetitive DNAs to adopt non-canonical structures. Although there is an increasing recognition of the importance of DNA quadruplexes in chromosome biology, the co-existence of different quadruplex-forming elements in the same DNA structure is still a matter of debate. Here we report the structural study of the oligonucleotide d(TCGTTTCGT) and its cyclic analog d. Both sequences form dimeric quadruplex structures consisting of a minimal i-motif capped, at both ends, by a slipped minor groove-aligned G:T:G:T tetrad. These mini i-motifs, which do not exhibit the characteristic CD spectra of other i-motif structures, can be observed at neutral pH, although they are more stable under acidic conditions. This finding is particularly relevant since these oligonucleotide sequences do not contain contiguous cytosines. Importantly, these structures resemble the loop moiety adopted by an 11-nucleotide fragment of the conserved centromeric protein B (CENP-B) box motif, which is the binding site for the CENP-B.

Show MeSH
Related in: MedlinePlus