1 research outputs found
Tertiary DNA Structure in the Single-Stranded hTERT Promoter Fragment Unfolds and Refolds by Parallel Pathways via Cooperative or Sequential Events
The discovery of G-quadruplexes and other DNA secondary
elements
has increased the structural diversity of DNA well beyond the ubiquitous
double helix. However, it remains to be determined whether tertiary
interactions can take place in a DNA complex that contains more than
one secondary structure. Using a new data analysis strategy that exploits
the hysteresis region between the mechanical unfolding and refolding
traces obtained by a laser-tweezers instrument, we now provide the
first convincing kinetic and thermodynamic evidence that a higher
order interaction takes place between a hairpin and a G-quadruplex
in a single-stranded DNA fragment that is found in the promoter region
of human telomerase. During the hierarchical unfolding or refolding
of the DNA complex, a 15-nucleotide hairpin serves as a common species
among three intermediates. Moreover, either a mutant that prevents
this hairpin formation or the addition of a DNA fragment complementary
to the hairpin destroys the cooperative kinetic events by removing
the tertiary interaction mediated by the hairpin. The coexistence
of the sequential and the cooperative refolding events provides direct
evidence for a unifying kinetic partition mechanism previously observed
only in large proteins and complex RNA structures. Not only does this
result rationalize the current controversial observations for the
long-range interaction in complex single-stranded DNA structures,
but also this unexpected complexity in a promoter element provides
additional justification for the biological function of these structures
in cells