Antiparallel quadruplexes

Low concentrations of either Na or K facilitate formation of the antiparallel quadruplex, while high cation concentration promotes formation of the parallel... 

A simplified version of the human telomeric motif G3T2AG3 adopts an antiparallel quadruplex conformation, as demonstrated by a positive CD band at 290 nm. Interestingly, this quadruplex is unstable in 150 mM KCl (but not NaCl), as it slowly (within days) isomerizes into a parallel guanine quadruplex. This isomerization is facilitated at higher temperatures. The resulting structure may be similar to the crystal structure determined in potassium for the TAG3T2AG3T sequence." ... 

To study the UAG3T UAG3T quadruplexes kinetics, the authors performed different types of experiments. Addition of an excess of the complementary strand induces a time-dependent formation of the duplex, whose kinetics are related to quadruplex unfolding. A single exponential function perfectly fits the data for each form. At temperature below 40°C, the parallel quadruplex unfolds faster than the antiparallel one. As the antiparallel quadruplex has slightly higher activation energy of dissociation (Eob = +43 kcal moN v.s. +34 kcal mol for the parallel form), kinetic stability is reversed above 40°C. At 37°C, the lifetimes of the two quadruplexes are very close, around 2 h. To study their kinetics of... 

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

Fig. 4. Possible homo-dimers of psPtDNA (A) antiparallel duplex, (B) parallel duplex, (C) quadruplex. Adapted from Ref. (28).

Ca2+aq reacts very rapidly with adp3- and with atp4-(236,710). Rate constants for onward reaction of [M(adp)] and [M(atp)]2, M — Ca2+, Mg24, or Mn2+, with creatine phosphotransferase are similar - 1. 7 x 106, 5.3 x 106, 7.4 x l(r M 4s 1 respectively (at 284 K) for the adp complexes, and indeed are similar to the value of 23 x 106M-1s-1 for the reaction of adp itself with creatine phosphotransferase (711). Kinetic parameters and binding constants have been established for interaction of the antiparallel form of the G-quadruplex d(T4G4T4) with Ca2+aq and for the subsequent Ca2+-promoted antiparallel parallel equilibrium (cf. Section IV.C above) (607). 

Ambrus, A., Chen, D., Dai, J., Biabs, T., Jones, R.A. and Yang, D. (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution, Nucleic Acids Res., 34, 2723-2735. 

Much like the search for protein-binding compounds requires consideration of tertiary structure in addition to peptide sequence, thinking about selective nucleic acid binding solely in the context of primary sequence is often an oversimplification. In the context of DNA recognition, a particularly important example of this is the case of G-quadruplexes. As their name implies, these structures consist of stacked tetrads of guanosine bases, typically ordered around a monovalent cation. One representative structure, a quadruplex derived from human telomeric DNA, is shown in Fig. 5 many variants of this motif formed by either parallel or antiparallel DNA strands have been observed. 

LNA has frequently been used to stabilise duplex structures, but in triplex structures the effect is mixed. Partial substitution of a DNA TFO by LNA increases triplex stability, whilst complete substitution leads to destabilisation. Optimal stabilisation was found with substitution every 2-3 nucleotides of the TFO. The incorporation of LNA into a G-quadruplex structure was shown to alter the orientation of the quadruplex from antiparallel to parallel. ... 

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.

Which Quadruplexes are the Most Stable Intra-, Bi- or Tetramolecular Parallel or Antiparallel ... 

The first indication that several conformations could be observed came from the comparison of the NMR solution and an earlier X-ray structure of the Oxytricha bimolecular quadruplex. The initial X-ray structure contained many of the features found in the solution structure but differed in the orientation of the thymine loops edge-loops were observed by X-ray as compared to diagonal-loops in the NMR structure. However, a recent analysis corrected this earlier crystallographic study and demonstrated that this quadruplex adopts a structure with two strands forming an antiparallel diagonal arrangement, indicating that the native structure is the same in solution and in the crystalline state. 

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. 

The four-repeat human telomeric d[AGGG(TTAGGG)3] sequence was shown to form an intramolecular G-quadruplex in Na solution, in which guanines around each tetrad are syn syn anti anti, loops are successively edgewise-diagonal-edgewise and each G-tract has both a parallel and an antiparallel adjacent strands [Figure lO(a-c)]. By contrast, the crystal structure of the same... 

A.T. Phan and D.J. Patel, Two-repeat human telomeric d(TAG-GGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution Distinct topologies thermodynamic, properties, and folding/unfolding kinetics, J. Am. Chem. Soc., 2003, 125, 15021-15027. 

D. Yang, An intramolecular G-quadruplex structure with mixed parallel/ antiparallel G-strands formed in the human BCL-2 promoter region in solution, J. Am. Chem. Soc., 2006, 128, 1096-1098. 

The reasons for the dramatic difference between the solution-state Na form and the crystal-state form of d[AGGG(TTAGGG)3] are yet to be fully elucidated major changes in structure have previously been noted in CD studies of the transition, although it had not been possible to assign structures to the individual species. On the other hand, several recent studies have demonstrated that an antiparallel G-quadruplex is formed by the human telomere repeat sequence in solution in the presence of both Na and... 

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