NMR studies of guanine-rich DNA oligonucleotides: Structures and cation
dynamics
Primož Šket and Janez Plavec
Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana,
Slovenia
DNA molecules can adopt besides the well-known B-type double helix several higher-order
structures, including G-quadruplex structures. G-quadruplexes are stable structures adopted
by DNA guanine-rich sequences that can be found in telomeres, immunoglobulin switch
regions, gene promoter regions and have also been implicated in association with human
diseases, as therapeutic targets in drug design and in potential technical applications as
nanomolecular devices. In the past years G-quadruplex DNA structures are a subject of great
interest since their formation has been suggested to play a role in variety of important
biological processes as well as due to their potential therapeutic applications. The main
building blocks of G-quadruplex structures are stacks of square-planar arrays of G-quartets,
consisting of four guanines that are linked together by eight hydrogen bonds. The major
requirement for the formation of such structures is the presence of cations. Development of
small molecules that can bind and help in formation and stabilization of G-quadruplex
structures has been the focus of search for anti-cancer and anti-viral drugs. By the use of
NMR spectroscopy we have shown that the folding topologies of G-quadruplex structures
critically depend on the sequence details as well as nature of cations present in solution. Small
change in G-rich sequence can cause a dramatic change in topology of G-quadruplex
structures. d(G3T4G4) sequence folds into dimeric fold-back G-quadruplex structure, which
consists of three G-quartet planes, two overhanging guanine residues and diagonal as well as
edge-type loops in the presence of K+, 15NH4+ or Na+ ions. Furthermore, NMR experiments
confirm existence of a mixed mono-K+-mono-15NH4+ form that represents intermediate in the
conversion of di-15NH4+ into di-K+ form of d(G3T4G4)2 G-quadruplex. Recently, 15N-labeled
ammonium ion has been utilized as a non-metallic substitute in combination with 2D NMR
spectroscopy to localize cations inside the interior of G-quadruplex structures as well as
provide insight into kinetics of their movement. Using this approach we have analyzed cation
movement inside a number of G-quadruplex systems of different stoichiometries. Our
findings so far give insight into how structural details of G-quadruplexes play a role in
controlling cation transport and their kinetics along the central axis as well as into bulk
solution.
1. Crnugelj, M.; Sket, P.; Plavec, J., J. Am. Chem. Soc. 2003, 125, 7866-7871.
2. Sket, P.; Crnugelj, M.; Kozminski, W.; Plavec, J., Org. Biomol. Chem. 2004, 2, 19701973.
3. Sket, P.; Crnugelj, M.; Plavec, J., Bioorg. Med. Chem. 2004, 12, 5735-5744.
4. Sket, P.; Crnugelj, M.; Plavec, J., Nucleic Acids Res. 2005, 33, 3691-3697.
5. Sket, P.; Plavec, J., J. Am. Chem. Soc. 2007, 129, 8794-8800.
6. Podbevsek, P.; Hud, N. V.; Plavec, J., Nucleic Acids Res. 2007, 35, 2554-2563.
7. Podbevsek, P.; Sket, P.; Plavec, J., J. Am. Chem. Soc. 2008, 130, 14287-14293.