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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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Mobility of the quadruplex-forming oligonucleotides on a 14% polyacrylamide gel supplemented with 20 mM KCl.
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Figure 2: Mobility of the quadruplex-forming oligonucleotides on a 14% polyacrylamide gel supplemented with 20 mM KCl.

Mentions: We further compared the global structures of these sequences by examining their mobilities in polyacrylamide gels that had been supplemented with 20 mM KCl (Figure 2). Each of the sequences ran as a single band, with the exception of G3T4 which is smeared, possibly because this sequence is less stable under these conditions (Tm ∼ 40°C, see below). G3T has the greatest mobility, as expected as it has the lowest molecular weight. Surprisingly we find that G3T4-T-T has a lower mobility than G3T-T4-T and similarly G3T4-T-T4 is slower than G3T4-T4-T. It appears that the presence of a single T in the central loop reduces the mobility. This will be considered in the Discussion.Figure 2.


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)

Mobility of the quadruplex-forming oligonucleotides on a 14% polyacrylamide gel supplemented with 20 mM KCl.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Mobility of the quadruplex-forming oligonucleotides on a 14% polyacrylamide gel supplemented with 20 mM KCl.
Mentions: We further compared the global structures of these sequences by examining their mobilities in polyacrylamide gels that had been supplemented with 20 mM KCl (Figure 2). Each of the sequences ran as a single band, with the exception of G3T4 which is smeared, possibly because this sequence is less stable under these conditions (Tm ∼ 40°C, see below). G3T has the greatest mobility, as expected as it has the lowest molecular weight. Surprisingly we find that G3T4-T-T has a lower mobility than G3T-T4-T and similarly G3T4-T-T4 is slower than G3T4-T4-T. It appears that the presence of a single T in the central loop reduces the mobility. This will be considered in the Discussion.Figure 2.

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.

Show MeSH