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Intramolecular DNA quadruplexes with different arrangements of short and long loops

This paper is available in a repository.
This paper is available in a repository.

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Abstract

We have examined the folding, stability and kinetics of intramolecular quadruplexes formed by DNA sequences containing four G 3 tracts separated by either single T or T 4 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 T 4 , 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 T 4 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 T 4 loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates.