Quadruplex stability

Apart from telomeres, G-quadruplexes are also present in the upstream promoter regions of certain oncogenes. G-quadruplex targeted molecules may interact at these sites as well. In fact, the cationic prophyrin, TMPyP4 and the core modified expanded prophyrin analogue 5,10,15,20-[tetra(N-methyl-3-pyridyl)]-26,28-diselenasapphyrin chloride (Se2SAP) have been found to cause repression of transcriptional activation of c-MYC in cells by G-quadruplex stabilization (Seenisamy et al, 2005). 

Ambrus A, Chen D, Dai J, Jones RA, Yang D (2005) Solution structure of the biologically relevant G-quadruplex element in the human c-MYC promoter. Implications for G-quadruplex stabilization. Biochemistry 44 2048-2058... 

Table 2 Ionic radii of quadruplex stabilizing cations...

The rapid identification of folded motifs against unfolded single stranded DNA states can quickly performed under strict native conditions. Additional analysis of possible structures present in the bands requires careful consideration, particularly in respect of the speed (voltage) of the run and stability of the quadruplex motif. Quadruplex stability can be sensitive to temperature and bufiering conditions used during the experiment. Additional analysis on the observed bands is required to determine the folded forms present. Visualization of the DNA can be carried out by radioactive labeling or EtBr staining or other dyes. 

The previous paragraph addressed the impact of quartets on G-quadruplex stability. What about the other bases present in the sequence Do they... 

Some cations may actively disrupt quadruplexes stabilization of quadruplex structure by is specifically counteracted by low concentrations of Mn ", Co " or When the quadruplex and monovalent cation concen-... 

The more complicated G-quadruplex stabilizing properties of divalent cations may result from the ability for some divalent cations e.g., Mg ) to only screen electrostatic repulsions between the backbones of a G-quadruplex that coordinates other cations, whereas other divalent cations e.g., Sr ) can stabilize a G-quadruplex both by screening backbone repulsions and by coordination with G-quartets. Qualitatively different behavior may be seen with monovalent cations, as the ability for monovalent cations to screen backbone repulsions is significantly less than that of divalent cations, and monovalent cation stabilization of G-quartets may be less sensitive to G-quadruplex topology and nucleotide sequence. 

Figure 10 G-quadruplex stabilization by telomestatin impairs the binding of GFP-POTl to its normal telomere sites and induces cytoplasmic foci of POTl in EcR293 cells...

Dameria RR, Knickelbein KE, Kepchia D, Jackson A, Armitage BA, Eckert KA, Opresko PL. Telomeric repeat mutagenicity in human somatic cells is modulated by repeat orientation and G-quadruplex stability. DNA Repair. 2010 9 1119-29. 

Many other small molecules are reported to staek with G-quadruplexes and have recently been reviewed in detail. Similarly, metal complexes with planar ligands also like to bind to G-quaduplexes via end-stacking. " A typical example is Mn porphyrin complexes, whieh exhibited both high affinity and excellent selectivity for G-quadruplexes. This is possibly contributed by the metal ions, which are necessary for G-quadruplex stabilization. 

Thermodynamic and kinetic data snggest that quadruplex stability depends on a nnmber of factors, including the type of structure adopted by the DNA strand (or strands), strand sequence, the size of intervening loops, base and phosphate modifications, pH and the presence of cations [19]. Small molecules may stabilize quadraplex DNA (or facihtate DNA folding into quadruplex structures) due to shifting the competitive equilibrium between the single-stranded or Watson-Crick duplex and quadruplex DNA towards the latter form [19,20]. Inhibition activity of G4 ligands depends mainly on the stability of their complexes with telomeric DNA quadruplexes. 

G-quadruplex DNA is found in the telomeric region of chromosomes as well as in the promoter region of several oncogenes. Studies suggest that stabilization of G-quadruplex structures in the telomeres indirectly inhibits telomerase, and enzyme present in >85% of human tumors but not in most normal cells, leading to cell cycle arrest, senescence, and apoptosis. We report here the synthesis, biophysical evaluation of G-quadruplex stabilization and selectivity, and cytotoxicity data for a series of 24-membered macrocyclic polyoxazoles that possess exquisite selectivity for stabilizing G-quadruplex DNA. The effect of various side chains, R and R, on selective G-quadruplex stabilization will be discussed. 

A similar topic was examined by Ida (Ida and Wu 2008). In this study, molecular dynamics was employed exploring G-quadruplex stabilized by Na and Rb cations, which were found to be tightly bound to a quadruplex structure. Moreover, in d(G(4)T(4)G(4) sequences the Na ions are found to be located in the diagonal T-4 loop region of the G-quadruplex, which is formed by two strands of d(G4T4G4) sequence. The authors proposed that the loop Na ion is located above the terminal G-quartet, coordinating to four guanine 06 atoms from the terminal G-quartet and one 02 atom from a loop thymine base and one water molecule. The Na coordination was also supported by quantum chemical calculations on Na chemical shifts. 

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