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Intramolecular DNA quadruplexes with different arrangements of short and long loops.

Rachwal PA, Findlow IS, Werner JM, Brown T, Fox KR - Nucleic Acids Res. (2007)

Bottom Line: The stability increases with the number of single T loops, though the arrangement of different length loops has little effect.In the presence of sodium ions, the sequences with two and three single T loops also adopt a parallel folded structure.Kinetic studies on the complexes with one or two T4 loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.

ABSTRACT
We have examined the folding, stability and kinetics of intramolecular quadruplexes formed by DNA sequences containing four G3 tracts separated by either single T or T4 loops. All these sequences fold to form intramolecular quadruplexes and 1D-NMR spectra suggest that they each adopt unique structures (with the exception of the sequence with all three loops containing T4, which is polymorphic). The stability increases with the number of single T loops, though the arrangement of different length loops has little effect. In the presence of potassium ions, the oligonucleotides that contain at least one single T loop exhibit similar CD spectra, which are indicative of a parallel topology. In contrast, when all three loops are substituted with T4 the CD spectrum is typical of an antiparallel arrangement. In the presence of sodium ions, the sequences with two and three single T loops also adopt a parallel folded structure. Kinetic studies on the complexes with one or two T4 loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates.

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CD spectra of the fluorescently-labelled quadruplex-forming oligonucleotides in the presence of 10 mM lithium phosphate pH 7.4 containing 200 mM KCl (a) or 200 mM NaCl (b). G3T, black; G3T-T4-T, red; G3T4-T-T, blue; G3T4-T-T4, pink; G3T4-T4-T, green; G3T4, cyan. The inset to the upper panel shows the CD spectrum of G3T4 in the presence of different concentrations of KCl: black 1 mM; red, 5 mM; green 20 mM; blue 50 mM; pink, 200 mM.
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Figure 1: CD spectra of the fluorescently-labelled quadruplex-forming oligonucleotides in the presence of 10 mM lithium phosphate pH 7.4 containing 200 mM KCl (a) or 200 mM NaCl (b). G3T, black; G3T-T4-T, red; G3T4-T-T, blue; G3T4-T-T4, pink; G3T4-T4-T, green; G3T4, cyan. The inset to the upper panel shows the CD spectrum of G3T4 in the presence of different concentrations of KCl: black 1 mM; red, 5 mM; green 20 mM; blue 50 mM; pink, 200 mM.

Mentions: Intramolecular quadruplexes can adopt a variety of different topologies in which the strands run in different orientations with lateral, edgewise or diagonal loops. Circular dichroism has frequently been used to indicate whether these fold in a parallel or antiparallel configuration (43,53,54). Parallel quadruplexes, in which the glycosidic bonds are all anti, display a positive CD signal around 265 nm, with a negative peak at 240 nm. In contrast, antiparallel topologies, with both syn and anti bonds, exhibit a positive signal at around 295 nm, with a negative signal or shoulder around 260 nm. CD spectra for these oligonucleotides, in the presence of sodium or potassium ions, are shown in Figure 1 [other studies with related sequences have shown that the fluorophores do not affect the CD spectra (55)].Figure 1.


Intramolecular DNA quadruplexes with different arrangements of short and long loops.

Rachwal PA, Findlow IS, Werner JM, Brown T, Fox KR - Nucleic Acids Res. (2007)

CD spectra of the fluorescently-labelled quadruplex-forming oligonucleotides in the presence of 10 mM lithium phosphate pH 7.4 containing 200 mM KCl (a) or 200 mM NaCl (b). G3T, black; G3T-T4-T, red; G3T4-T-T, blue; G3T4-T-T4, pink; G3T4-T4-T, green; G3T4, cyan. The inset to the upper panel shows the CD spectrum of G3T4 in the presence of different concentrations of KCl: black 1 mM; red, 5 mM; green 20 mM; blue 50 mM; pink, 200 mM.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1919480&req=5

Figure 1: CD spectra of the fluorescently-labelled quadruplex-forming oligonucleotides in the presence of 10 mM lithium phosphate pH 7.4 containing 200 mM KCl (a) or 200 mM NaCl (b). G3T, black; G3T-T4-T, red; G3T4-T-T, blue; G3T4-T-T4, pink; G3T4-T4-T, green; G3T4, cyan. The inset to the upper panel shows the CD spectrum of G3T4 in the presence of different concentrations of KCl: black 1 mM; red, 5 mM; green 20 mM; blue 50 mM; pink, 200 mM.
Mentions: Intramolecular quadruplexes can adopt a variety of different topologies in which the strands run in different orientations with lateral, edgewise or diagonal loops. Circular dichroism has frequently been used to indicate whether these fold in a parallel or antiparallel configuration (43,53,54). Parallel quadruplexes, in which the glycosidic bonds are all anti, display a positive CD signal around 265 nm, with a negative peak at 240 nm. In contrast, antiparallel topologies, with both syn and anti bonds, exhibit a positive signal at around 295 nm, with a negative signal or shoulder around 260 nm. CD spectra for these oligonucleotides, in the presence of sodium or potassium ions, are shown in Figure 1 [other studies with related sequences have shown that the fluorophores do not affect the CD spectra (55)].Figure 1.

Bottom Line: The stability increases with the number of single T loops, though the arrangement of different length loops has little effect.In the presence of sodium ions, the sequences with two and three single T loops also adopt a parallel folded structure.Kinetic studies on the complexes with one or two T4 loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.

ABSTRACT
We have examined the folding, stability and kinetics of intramolecular quadruplexes formed by DNA sequences containing four G3 tracts separated by either single T or T4 loops. All these sequences fold to form intramolecular quadruplexes and 1D-NMR spectra suggest that they each adopt unique structures (with the exception of the sequence with all three loops containing T4, which is polymorphic). The stability increases with the number of single T loops, though the arrangement of different length loops has little effect. In the presence of potassium ions, the oligonucleotides that contain at least one single T loop exhibit similar CD spectra, which are indicative of a parallel topology. In contrast, when all three loops are substituted with T4 the CD spectrum is typical of an antiparallel arrangement. In the presence of sodium ions, the sequences with two and three single T loops also adopt a parallel folded structure. Kinetic studies on the complexes with one or two T4 loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates.

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