G-tetrads

Fig. 4 Schematic representation of parallel A and antiparallel B quadruplex form of DNA with the chemical structure of a G-tetrad C...

Although Na+ and Li+ have been found stable in the center of G tetrad, the results of high level of theoretical studies indicate that K+ can only be stable when it is outside the tetrad plane, which explains the fact that potassium cations are usually located between the successive G tetrads. The interaction between a cation and G tetrad around the central area also changes the H-bonding pattern in the G tetrad. In the cation-G tetrad complex, bifurcated H-bonding pattern is replaced by the normal Hoogsteen H-bonding pattern [32]. 

J. Gu et al., A new insight into the structure and stability of hoogsteen hydrogen bonded g-tetrad an ab initio SCF study. Chem. Phys. Lett. 311, 209-214 (1999)... 

J. Gu, J. Leszczynski, A remarkable alteration in the bonding pattern An HF and DFT study of the interactions between the metal cations and the hoogsteen hydrogen-bonded G-tetrad. J. Phys. Chem. A 104, 6308-6313 (2000)... 

Figure 4 G-tetrad and G-quadruplexes. (A) Four guanine residues forming a planar structure G-tetrad through Hoogsteen hydrogen bonding. (B) A parallel G-quadruplex model. (C ) An intermolecular antiparallel G-quadruplex model. (D) An intramolecular basket G-quadruplex model. Each parallelogram in (B), (C), and (/>) represents a G-tetrad.

The chromosomes of eukaryotes are linear, and replication of the free ends of these linear DNA molecules presents particular problems. The sequencing of the ends of chromosomes revealed that they consist of telomeres, hundreds of tandem repeats of a hexanucleotide sequence, which in all vertebrates is d(TTAGGG). These G-rich telomeric sequences can fold into a G-quadruplex, a DNA secondary structure consisting of stacked G-tetrad planes, or G-quartets (Figure 9.18), connected by a network of Hoogsteen hydrogen bonds the cavity in the centre... 

Figure 35 Some G tetrads formed by (a) dG and (b) 9 deaza-2 -dG. (c) The 7-deaza-2 -deoxyxanthosine-AT triad in the R RY motif...

The smallest unimolecular G-quadruplex belongs to the family d(G2NnG2NnG2NnG2), and forms two stacked G-tetrads. The solution structure of such a G-quadruplex in which the first loops are diagonal has been solved. ° A similar structure of a guanosine- and adenosine-rich sequence, but which forms a dimeric structure with two G-tetrads has also been solved by NMR. ° In determining the solution structure of a DNA 3-way junction, van Buuren et... 

An additional constraint for the folding topologies for bimolecular and inter-molecular quadruplexes relates to the number (length) of the linking nucleotides. Short linker lengths, two or less, will prevent diagonal loops from forming due to the distance to be spanned across G tetrad. However, the short... 

Telomeric repeats from other organisms are also prone to quadruplex polymorphism. The Tetrahymena TG4T2G4T telomeric sequence, for example, may adopt several conformations. This sequence forms two novel G-quadruplex structures in Na -containing solution. In the first structure (head-to-head), the two loops are at one end of the G-tetrad core in the second structure (head-to-tail), the two loops are located on opposite ends of the G-tetrad core. In contrast to the human telomere sequence, the proportions of the two forms are similar for a wide range of temperatures their unfolding rates are also similar, with an activation enthalpy of 37 kcal mol . The (G4T4) sequence may also interconvert between parallel and antiparallel structures. 

---