Abstract
The human telomere sequence (TTAGGG)4 folds into an unusual conformation possessing three G-tetrads linked by TTA loops. The first loop is a propeller loop while the second and third loops are transverse loops. Using Circular Dichroism (CD) spectroscopy, we have investigated the effect of sequence context on the structures and stabilities of intramolecular G-quadruplexes related to the human telomere sequence by considering all permutations of T and A within the loops. The results indicate that changing only one base in any one loop can have a dramatic effect on the conformation of the quadruplex as well as its melting temperature, Tm. Thus, each sequence studied has a unique CD spectrum and Tm. In general, variants with a modified second loop are the most stable while the wild type sequence is the least stable. The observed difference in CD spectra and melting temperature are discussed in terms of base stacking within the loop and stacking of the loop bases with adjacent G-tetrads.
Highlights
Our research group has been investigating the structure and stability of unusual DNA conformations for many years
Whether we are looking at B - Z junctions [1], DNA hairpins [2,3] or DNA quadruplexes [4], one observation always presents itself—DNA conformation is regulated by sequence and environment
In consideration of the unfolding of the K+ form of the quadruplex formed from (TTAGGG)4, the human telomere sequence, we have previously demonstrated that the unfolding proceeds via a three state mechanism and is reversible [14]
Summary
Our research group has been investigating the structure and stability of unusual DNA conformations for many years. For a DNA oligomer such as (XXXYYY)z, where X is A, C and/or T, Y is G or T and z = 1, 2, 4 or more, the conformation of any secondary structure formed is highly dependent on the identities of X and Y, the number of repeats z and the conditions under which the DNA is prepared (temperature, pH, counterions present and their concentrations, etc.). At 95 ̊C in either Na+ or K+, (TTAGGG) exists as a single stranded structure Upon cooling, it can form an intramolecular quadruplex whose conformation depends upon whether the counterion is Na+ or K+ [5,6,7,8]. Cooling an equimolar mixture of (TTAGGG) and (CCCTAA) from 95 ̊C to 25 ̊C, in either Na+ or K+, will result in the formation of a normal Watson-Crick double helical conformation
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