Journal
NUCLEIC ACIDS RESEARCH
Volume 35, Issue 12, Pages 4214-4222Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkm316
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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.
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