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Junctions between i-motif tetramers in supramolecular structures.

Guittet E, Renciuk D, Leroy JL - Nucleic Acids Res. (2012)

Bottom Line: The symmetry of i-motif tetramers gives to cytidine-rich oligonucleotides the capacity to associate into supramolecular structures (sms).We show that a stretch of only two cytidines either at the 3'- or 5'-end is long enough to link the tetramers into sms.The analysis of the properties of sms formed by oligonucleotides differing by the length of the oligo-C stretches, the sequence orientation and the nature of the non-C base provides a model of the junction connecting the tetramers in sms.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Chimie et Biologie Structurales, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France.

ABSTRACT
The symmetry of i-motif tetramers gives to cytidine-rich oligonucleotides the capacity to associate into supramolecular structures (sms). In order to determine how the tetramers are linked together in such structures, we have measured by gel filtration chromatography and NMR the formation and dissociation kinetics of sms built by oligonucleotides containing two short C stretches separated by a non-cytidine-base. We show that a stretch of only two cytidines either at the 3'- or 5'-end is long enough to link the tetramers into sms. The analysis of the properties of sms formed by oligonucleotides differing by the length of the oligo-C stretches, the sequence orientation and the nature of the non-C base provides a model of the junction connecting the tetramers in sms.

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Related in: MedlinePlus

GPC-1000 chromatograms at 20°C of a 9 mM C3TC3 solutions and of 3 mM C5TC2 and C5GC3 solutions at equilibrium. The top horizontal scale, drawn according to the column calibration, indicates the elution positions of nucleic acids containing the indicated base numbers. The non-resolved tetramer, dimer and monomer in equilibrium with the sms are eluted in the peaks at 8.2 min. The exclusion and permeation times are indicated by dotted lines.
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gks161-F7: GPC-1000 chromatograms at 20°C of a 9 mM C3TC3 solutions and of 3 mM C5TC2 and C5GC3 solutions at equilibrium. The top horizontal scale, drawn according to the column calibration, indicates the elution positions of nucleic acids containing the indicated base numbers. The non-resolved tetramer, dimer and monomer in equilibrium with the sms are eluted in the peaks at 8.2 min. The exclusion and permeation times are indicated by dotted lines.

Mentions: The size of sms measured at equilibrium by gel filtration chromatography on GPC-1000 column (Figure 7) and by electrophoresis on PA gels (Figure 8) are in fairly good agreement. At the concentration of 1 mM, the equilibrium distributions of the sms of C5TC2 and C3TC3 are centered on molecular weights corresponding to the association of 20 and 15 tetramers respectively. Considering that the distance between sequentially adjacent i-motif C•C+ pairs is 6.3 Å, the lengths of these structures should be ∼70 nm. The sms eluted in the rising edge of the chromatograms are about 10 times larger. The size of sms increases with the sample concentration, as shown with the example of a 9 mM C3TC3 solution whose sms distribution at equilibrium corresponds to the assembly of 170 tetramers (Figure 7). Due to exchange during chromatography, only averaged molecular weight are accessible at 20°C for the sms of C2TCn and C5PurC2 oligonucleotides. In 1–3 mM solutions, the elution times of the sms formed by these oligonucleotides correspond to structures including 5–8 tetramers (Supplementary Figure S2). In a 3 mM solution at equilibrium, the sms of C5AC3 (Figure 7) are about three times larger than those of C5AC2.Figure 7.


Junctions between i-motif tetramers in supramolecular structures.

Guittet E, Renciuk D, Leroy JL - Nucleic Acids Res. (2012)

GPC-1000 chromatograms at 20°C of a 9 mM C3TC3 solutions and of 3 mM C5TC2 and C5GC3 solutions at equilibrium. The top horizontal scale, drawn according to the column calibration, indicates the elution positions of nucleic acids containing the indicated base numbers. The non-resolved tetramer, dimer and monomer in equilibrium with the sms are eluted in the peaks at 8.2 min. The exclusion and permeation times are indicated by dotted lines.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3367196&req=5

gks161-F7: GPC-1000 chromatograms at 20°C of a 9 mM C3TC3 solutions and of 3 mM C5TC2 and C5GC3 solutions at equilibrium. The top horizontal scale, drawn according to the column calibration, indicates the elution positions of nucleic acids containing the indicated base numbers. The non-resolved tetramer, dimer and monomer in equilibrium with the sms are eluted in the peaks at 8.2 min. The exclusion and permeation times are indicated by dotted lines.
Mentions: The size of sms measured at equilibrium by gel filtration chromatography on GPC-1000 column (Figure 7) and by electrophoresis on PA gels (Figure 8) are in fairly good agreement. At the concentration of 1 mM, the equilibrium distributions of the sms of C5TC2 and C3TC3 are centered on molecular weights corresponding to the association of 20 and 15 tetramers respectively. Considering that the distance between sequentially adjacent i-motif C•C+ pairs is 6.3 Å, the lengths of these structures should be ∼70 nm. The sms eluted in the rising edge of the chromatograms are about 10 times larger. The size of sms increases with the sample concentration, as shown with the example of a 9 mM C3TC3 solution whose sms distribution at equilibrium corresponds to the assembly of 170 tetramers (Figure 7). Due to exchange during chromatography, only averaged molecular weight are accessible at 20°C for the sms of C2TCn and C5PurC2 oligonucleotides. In 1–3 mM solutions, the elution times of the sms formed by these oligonucleotides correspond to structures including 5–8 tetramers (Supplementary Figure S2). In a 3 mM solution at equilibrium, the sms of C5AC3 (Figure 7) are about three times larger than those of C5AC2.Figure 7.

Bottom Line: The symmetry of i-motif tetramers gives to cytidine-rich oligonucleotides the capacity to associate into supramolecular structures (sms).We show that a stretch of only two cytidines either at the 3'- or 5'-end is long enough to link the tetramers into sms.The analysis of the properties of sms formed by oligonucleotides differing by the length of the oligo-C stretches, the sequence orientation and the nature of the non-C base provides a model of the junction connecting the tetramers in sms.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Chimie et Biologie Structurales, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France.

ABSTRACT
The symmetry of i-motif tetramers gives to cytidine-rich oligonucleotides the capacity to associate into supramolecular structures (sms). In order to determine how the tetramers are linked together in such structures, we have measured by gel filtration chromatography and NMR the formation and dissociation kinetics of sms built by oligonucleotides containing two short C stretches separated by a non-cytidine-base. We show that a stretch of only two cytidines either at the 3'- or 5'-end is long enough to link the tetramers into sms. The analysis of the properties of sms formed by oligonucleotides differing by the length of the oligo-C stretches, the sequence orientation and the nature of the non-C base provides a model of the junction connecting the tetramers in sms.

Show MeSH
Related in: MedlinePlus