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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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The intercalation topologies of the i-motif tetramers of C3TC3, C3TC2 and C4TC2. Their NMR spectra have characteristics indicating that as in [C2TC2]41 (2), the tetramers include two intercalated duplexes, one (yellow) with a T•T pair (green) stacked on the 5′-adjacent C•C+ pair and the other (red) whose thymidines are looped out in the i-motif wide grove (blue circle). A black heavy line marks the face of the bases oriented in the 5′-direction. The magnetization transfer detected between the T imino protons of each duplex establishes that concerted opening/closing of the T•T pairs switches the duplex conformations. Full intercalation topology of the tetramers of C3TC3 and C3TC2 prevents association into sms. This implies that the sms building block is a minor tetrameric species formed by a reaction parallel to that leading to the fully intercalated tetramer.
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gks161-F6: The intercalation topologies of the i-motif tetramers of C3TC3, C3TC2 and C4TC2. Their NMR spectra have characteristics indicating that as in [C2TC2]41 (2), the tetramers include two intercalated duplexes, one (yellow) with a T•T pair (green) stacked on the 5′-adjacent C•C+ pair and the other (red) whose thymidines are looped out in the i-motif wide grove (blue circle). A black heavy line marks the face of the bases oriented in the 5′-direction. The magnetization transfer detected between the T imino protons of each duplex establishes that concerted opening/closing of the T•T pairs switches the duplex conformations. Full intercalation topology of the tetramers of C3TC3 and C3TC2 prevents association into sms. This implies that the sms building block is a minor tetrameric species formed by a reaction parallel to that leading to the fully intercalated tetramer.

Mentions: The evolution in opposite directions of the tetramer and sms fractions demonstrates that the sms are not built by association of this tetramer species. The NMR spectra of C4TC2, C3TC2 and C3TC3 recorded during sms built-up present a common characteristic features providing key information about the intercalation topology of the corresponding tetramers. The spectra of C3TC3 are exemplary (Figure 5). They show two thymidine imino proton peaks of comparable intensities (11.2–10.95 ppm) that increase as a function of the time as the tetramer fraction measured by chromatography. These thymidine imino protons were therefore assigned to the tetramer. Magnetization transfer experiments show that selective saturation of either the 11.2 or the 10.95 ppm peak results in saturation of both protons (Figure 5). This demonstrates that the thymidine exchanges within the tetramer between two non-equivalent environments. The inter-conversion rate between the two environments of [C3TC3]4 was determined by measuring the magnetization transferred between the T imino protons as a function of the length of the saturation pulse (14). We find that it is equal to 1 s at 0° and to 50 ms at 20°C. It is noteworthy that the NMR properties of the thymidine imino proton of [C3TC3]4, [C3TC2]4 and [C4TC2]4 are identical to those previously described for the thymidines of [C2TC2]4 (14). This gives a strong argument to assume that these tetramers have an intercalation topology similar to that of [C2TC2]4 (Figure 6) and that thymidine exchange reflects, as in [C2TC2]4, duplexe inter-conversion within the tetramers.Figure 5.


Junctions between i-motif tetramers in supramolecular structures.

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

The intercalation topologies of the i-motif tetramers of C3TC3, C3TC2 and C4TC2. Their NMR spectra have characteristics indicating that as in [C2TC2]41 (2), the tetramers include two intercalated duplexes, one (yellow) with a T•T pair (green) stacked on the 5′-adjacent C•C+ pair and the other (red) whose thymidines are looped out in the i-motif wide grove (blue circle). A black heavy line marks the face of the bases oriented in the 5′-direction. The magnetization transfer detected between the T imino protons of each duplex establishes that concerted opening/closing of the T•T pairs switches the duplex conformations. Full intercalation topology of the tetramers of C3TC3 and C3TC2 prevents association into sms. This implies that the sms building block is a minor tetrameric species formed by a reaction parallel to that leading to the fully intercalated tetramer.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gks161-F6: The intercalation topologies of the i-motif tetramers of C3TC3, C3TC2 and C4TC2. Their NMR spectra have characteristics indicating that as in [C2TC2]41 (2), the tetramers include two intercalated duplexes, one (yellow) with a T•T pair (green) stacked on the 5′-adjacent C•C+ pair and the other (red) whose thymidines are looped out in the i-motif wide grove (blue circle). A black heavy line marks the face of the bases oriented in the 5′-direction. The magnetization transfer detected between the T imino protons of each duplex establishes that concerted opening/closing of the T•T pairs switches the duplex conformations. Full intercalation topology of the tetramers of C3TC3 and C3TC2 prevents association into sms. This implies that the sms building block is a minor tetrameric species formed by a reaction parallel to that leading to the fully intercalated tetramer.
Mentions: The evolution in opposite directions of the tetramer and sms fractions demonstrates that the sms are not built by association of this tetramer species. The NMR spectra of C4TC2, C3TC2 and C3TC3 recorded during sms built-up present a common characteristic features providing key information about the intercalation topology of the corresponding tetramers. The spectra of C3TC3 are exemplary (Figure 5). They show two thymidine imino proton peaks of comparable intensities (11.2–10.95 ppm) that increase as a function of the time as the tetramer fraction measured by chromatography. These thymidine imino protons were therefore assigned to the tetramer. Magnetization transfer experiments show that selective saturation of either the 11.2 or the 10.95 ppm peak results in saturation of both protons (Figure 5). This demonstrates that the thymidine exchanges within the tetramer between two non-equivalent environments. The inter-conversion rate between the two environments of [C3TC3]4 was determined by measuring the magnetization transferred between the T imino protons as a function of the length of the saturation pulse (14). We find that it is equal to 1 s at 0° and to 50 ms at 20°C. It is noteworthy that the NMR properties of the thymidine imino proton of [C3TC3]4, [C3TC2]4 and [C4TC2]4 are identical to those previously described for the thymidines of [C2TC2]4 (14). This gives a strong argument to assume that these tetramers have an intercalation topology similar to that of [C2TC2]4 (Figure 6) and that thymidine exchange reflects, as in [C2TC2]4, duplexe inter-conversion within the tetramers.Figure 5.

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