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Formation of an interlocked quadruplex dimer by d(GGGT)
Yamuna Krishnan-Ghosh1, Dongsheng Liu, Shankar Balasubramanian
1Contribution from the University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
Journal of the American Chemical Society
|September 2, 2004
Summary
The tetranucleotide d(GGGT) self-assembles into parallel quadruplex dimers. Two distinct species, a tetramer and an octamer, were identified, revealing novel structural arrangements including a slipped quadruplex dimer with a unique GTGT tetrad.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- DNA sequences can self-assemble into complex structures.
- G-quadruplexes are non-canonical DNA structures with diverse biological roles.
- The d(GGGT) sequence is known to form quadruplex structures.
Purpose of the Study:
- To investigate the self-assembly of the tetranucleotide d(GGGT).
- To characterize the structures of the resulting quadruplex species.
- To elucidate the mechanism of quadruplex dimer formation.
Main Methods:
- UV-melting studies to identify distinct species and their thermal stability.
- Circular dichroism (CD) spectroscopy to determine quadruplex topology.
- Negative ion nano-electrospray ionization mass spectrometry (nano-ESI-MS) to determine complex stoichiometry.
- High-resolution (1)H Nuclear Magnetic Resonance (NMR) spectroscopy to resolve atomic-level structure.
Main Results:
- Two distinct quadruplex species, Q(l) (tetramer, d(GGGT)(4)) and Q(h) (octamer, d(GGGT)(8)), were identified.
- Both species exhibited CD spectra characteristic of parallel quadruplexes.
- High-resolution NMR confirmed d(GGGT)(4) as a C(4)-symmetric parallel tetramolecular quadruplex.
- The d(GGGT)(8) structure involves the dimerization of a "slipped" parallel quadruplex, forming an additional G-tetrad and a novel GTGT tetrad at the 3' ends.
Conclusions:
- The d(GGGT) sequence forms stable parallel quadruplexes and their dimers.
- A novel "slipped" quadruplex dimer architecture was discovered, involving intermolecular G-tetrad formation.
- The study reveals new insights into G-quadruplex structural diversity and self-assembly mechanisms.
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