Bimolecular quadruplex

The folding topologies available to intramolecular quadruplexes are more varied and complex than those available to the intermolecular or bimolecular quadruplexes due to the additional linking nucleotides. Structural examples from X-ray and show just a few of the possible structures... 

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. 

Data on the kinetics of bimolecular quadruplexes are scarce. Attachment of a long single-stranded tail to an oligonucleotide bearing two guanine blocks destabilizes and delays bimolecular quadruplex formation. This property has been used to determine the effect of quadruplex ligands on quadruplex forma-tion " " (see below). The second order rate constant for the formation of the bimolecular structure was estimated to be 3 x 10 M s in the absence of ligand. 

Figure 2 Bimolecular quadruplex analysis, (a) Melting and cooling profiles of the Oxy 1.5 sequence (G4T4G4) in 0.11 M Na with a temperature gradient of 0.2°C min (b) Arrhenius representation of the association (In (K Co) open circles) and dissociation (In (Kg ) filled circles) rates of the bimolecular quadruplex f ormed by G4T4G4...

The relative free energies of Na vs. K" coordination within a G-quadruplex have been determined under equilibrium conditions using H NMR spectroscopy. This study used the G-quadruplex formed by d(G3T4G3), a sequence that forms a bimolecular quadruplex with three G-quartets in the presence of either Na or K" ions. H chemical shifts were followed as a sample of [d(G3T4G3)]2 was converted from its Na" form to its K" form by titration with... 

Krishnan-Ghosh, Y. Whimey, A. M. Balasubramanian, S. Dynamic covalent chemistry of self-templating PNA oligomers Formation of a bimolecular PNA quadruplex. Chem. Commun. 2005, 3068-3070. 

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... 

Figure 1 Summary of the different equilibria involving G-quadruplexes. We wish to emphasize the differences between tetramolecular (panel a), bimolecular (panel b) and intramolecular (panel c) complexes. In the latter case, two possible quadruplex folds are presented a similar situation may occur for bimolecular structures.

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 ... 

In principle, by using an SPR apparatus with a G-rich strand attached to the matrix and different strand concentrations of the complementary oligonucleotide in solution, one can determine the k n and koff values for the intramolecular quadruplex and the bimolecular duplex. One of the major conclusions of these experiments is that both the folded and unfolded forms of the intramo-... 

P. Hazel, G.N. Parkinson and S. Neidle, Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex, J. Am. Chem. Soc., 2006, 128, 5480-5487. 

A. The G-quadruplex formed by d[AGGG(TTAGGG)3] is of particular interest because it represents four units of the human telomere repeat sequence. Details of the crystal structure formed by this sequence in the presence of ions and in the presence of Na ions are discussed below in Section 4.6. The crystal structure of the bimolecular G-quadruplex adopted by the dodecamer sequence d(TAGGGTTAGGGT), also derived from the human telomere repeat sequence, has been determined and similarly contains K" ions coordinated between adjacent G-quartets (PDB ID 1K8P). ... 

In agreement with X-ray crystallographic and NMR spectroscopy studies, molecular dynamics calculations on the bimolecular G-quadruplex [d(G3T4G3)]2 have demonstrated the localization of ions between the neighboring G-quartets and in octahedral coordination by guanine 06 oxy-gens. Two ions were found to be slightly offset from a central location between pairs of adjacent G-quartet planes because of repulsive forces between the ion pairs." We note that solid-state NMR spectroscopy has also been used to locate cations in G-quadruplexes. A recent Na NMR study has confirmed that three Na cations reside inside the bimolecular G-quadruplex... 

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