Tetramolecular Quadruplexes

Nevertheless, one should note that it is not straightforward to compare the stability of structures with different molecularities. For example, the comparison of equilibrium association constants for unimolecular, bi- or tetramolecular quadruplexes is meaningless, as these constants are not expressed in the same units (unit-less, M and respectively). Similarly, a comparison of the AG° might be deceptive. For example, if one compares an intramolecular structure with a bimolecular one (self-complementary) which have the same Tm = 60°C at 1 pM strand concentration, one will determine a hG°(Tm) of 0 and —9.2 kcal moN respectively. Does this mean that the intermolecular complex is more stable Clearly not One faces a similar problem when comparing association rate constants (kon), which are expressed in s ... 

Figure 3 Tetramolecular quadruplex dissociation, (a) Example of an irreversible melting curve (TG4T) in 0.11 M Na recorded at 245 nm with a temperature gradient of 0.2°C min Directions of temperature changes are indicated by arrows. The small difference observed at high temperature between the heating and cooling profiles results from a partial evaporation of the sample, (b) Arrhenius representation of the dissociation rate (In (k ff) shown on the left Y-scale) and lifetime (right Y-scale) of the TG4T (DNA) and IIG4U (RNA) quadruplexes in 0.11 M Na" (ref 27)...

Impact of ion nature on association rate and thermal stability, (a) Association rate constants (ko ) for the TG4T tetramolecular quadruplex in the presence of 0.11 MNa K or NHf (logscale), (b) Apparent melting temperature (Tjp, in °C) for the TG4T tetramolecular quadruplex in the presence of 0.11 M Na, or NH4. As shown in this figure, although ammonium leads to slower quadruplex formation than sodium, the NH4 tetramolecular quadruplex has a higher thermal stability than the same quadruplex in Na ... 

Table 1 Kinetic parameters for tetramolecular quadruplexes (a) Effect of G tract length...

The simplest quadruplex-based higher order structure is a double-quadruplex, in which two tetramolecular quadruplexes associate to form an octaplex. One may distinguish two types of dimers (a) those based on simple stacking of terminal quartets and (b) those involving interlocked base quartets. 

The thermodynamic, kinetic and structural data presented above give some indications about the folding pathway required to form G-quadruplexes. In terms of folding intermediates, the best-studied systems concern tetramolecular quadruplexes. Several experimental and theoretical studies provide clues on the possible ways to a fully formed quadruplex. 

Figure 7 ESI-MS studies of tetramolecular quadruplexes. The TG5T oligonucleotide was incubated in 0.15 M pH 7.0 ammonium acetate buffer for various amounts of time, then analysed by electrospray mass spectrometry (negative mode). From the initial peak corresponding to the TG5T single-strand (SS), one can see the gradual conversion to a quadruplex (G4), as well as the presence of dimeric (Di) and trimeric (Tri) species...

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