Competition with Duplexes

This duplex-quadruplex competition is of special interest in the case of gene promoters. As discussed in the chapter by L. Hurley, guanine rich sequences are present in the promoter region of key oncogenes, and one can observe an induction of duplex to G-quadruplex transition in the presence of a quadruplex ligand and/or KCl.  

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One of the challenges in the recognition and binding of G-quadruplexes is the competition with duplex (double-stranded) DNA. While it was reported that cationic tetra(A-methylpyridiniumyl) porphyrin, 23 Mn, could target quadruplex DNA, there was no discrimination, since it was also found to bind duplex DNA well. In 2007, Dixon et al. reported a pentacationic manganese(III)... 

Fig. 3.9. Diagram showing the principle of the nick-translation sequencing procedure. For the purpose of illustration the single unique product generated from one nicked molecule is shown. With a heterogeneous set of nicked duplexes nick-translation will proceed from each gap until terminated by the incorporation of a dideoxynucleotide. Since the corresponding deoxynucleotide is also incorporated in competition with the dideoxynucleotide, the eifect of non-random cleavage with DNAase I is minimized.

Use of CRA is competitive with inhibition in deep, high-pressure wells, particularly in those locations where inhibitor supply may be a space and logistic problem. CRA includes stainless steels (austenitic, ferritic, martensitic, and duplex), nickel-based alloys, cobalt-based alloys, and titanium alloys. Economics is a major factor in alloy selection. The 13 Cr tubing has often been used in gas wells for low H2S wells. Tubing materials selection for a deep well could involve price increments between alloys of 1 to 3 million. High-strength CRA is used to minimize costs. SMYS values of 150 ksi (1000 MPa) are common. The CRA is often cold-worked to achieve the required yield strength. 

The experimentally measured water binding energies of nucleotides provide an important set of data required, for instance, to work out the energetics of DNA duplex formation. The Watson-Crick base pair interaction, in solution, is in constant competition with hydration of the individual bases. Thus, the duplex stability depends on the base-base interaction energy relative to the base-water and water-water interaction. Knowing all of the energetic contributions to a complex system such as solvated... 

The experiments summarized in Table 3.1 are done under conditions in which the applied force increases with time. The most-probable mpture force (F ), which is taken from a distribution of measured values, reflects the competition between force loading and bond mpture and, with the exception of the CD inclusion compounds, mpture force increases with loading rate (Evans and Ritchie 1997). The data emphasize that the mechanical strength of the interactions do not necessarily reflect the thermodynamic strength, or association constant, of the interaction. This point is made by comparison of the DNA duplexes (i eq... 

With adequately tailored short Z-form DNA duplexes, H-transfer occurs by intrastrand P-H2 -abstraction [reaction (44) Kawai and Saito 1999 Kawai et al. 2000a], while competitive HI - and a-H2 -abstractions occurs in B-form DNA (Sugiyama et al. 1990,1993, 1996). Predominant Hl -abstraction is observed in a DNA-RNA hybrid (Sugiyama et al. 1997). 

Figure 18.1 Competitive association between Mg2+ (A) and 20 (mM) Na+ (O) with a 24 bp DNA duplex. Depleted anions are shown by (V) and the net charge is given by ( ). Solid lines are fitted to the Hill equation (Eq. (18.3)), while dotted lines are predictions from the nonlinear Poisson—Boltzman model. Reprinted from Bai ft al. (2007).

Luminescence titrations further demonstrate that the ruthenated duplex behaves as a 15 mer bearing one intercalator (76). As free [Ru(phen)2(dppz)]2+ is added to a solution of unmetallated 15 mer duplex, the luminescence increases linearly until the emission reaches saturation at about three equivalents of ruthenium(II) per duplex, consistent with competitive binding of [Ru(phen)2(dppz)]2+ to the 15-mer duplex and an average binding site size of a little more than four base pairs. When the analogous experiment is conducted with the ruthenated duplex, saturation of luminescence occurs after almost two equivalents of [Ru(phen)2(dppz)]2+ are added. This comparison indicates that the covalently bound ruthenium(II) complex is not displaced by additional intercalators. 

Phosphorothioates interact with nucleases and DMA polymerases. These compounds are slovdy metabolized by both endo- and exonucleases and inhibit these enzymes (160, 171). The inhibition of these enzymes appears to be competitive and this may account for seme early data suggesting that phosphorothioates are almost infinitely stable to nucleases. In these studies, the oligonucleotide-to-enzyme ratio was very high and thus the enzyme was inhibited. Phosphorothioates also bind to RNase H when in an RNA-DNA duplex... 

Figure 4.33. Competitive binding of DNAs to 45 A Cd(II)-rich CdS nanoparticles, as followed by the intensity of nanoparticle photoluminescence. (Top trace) The addition of duplex DNA (or buffer, although not labeled) results in a quench subsequent addition of equimolar (CCG)7 quenches more, and (CGG)7 quenches yet more. (Bottom trace) If the competition experiment is performed with (CGG)7 first, no changes are observed with equipmolar (CCG)7 or duplex DNA. These data reconfirm the order of binding constants calculated from emission titration data, (CGG)7 > (CCG)7 duplex DNA. [From Fig. 5 of Ref. 252, with permission.]...

The availability of chemically well defined octamers (A and C) as sDNA substitutes provi s a kinetic tool for the determination of the effects of enzyme inhibitors on the DNA binding site of the enzyme. The 6-amino derivative of 1,2-benzoypyrone, (6-aminocoumarin), competitively inhibits at the octamer duplex A or C sites with an apparent Ki of 28 jiM. Without the inhibition at a fixed NAD+ concentration, a Michaelis-Menten relationship exists between Vinit and the concentration of the octamers (lowest curve in Fig. 3) with an apparent binding constant of 1 jiM. The results shown in Fig. 3 identify a novel site of inhibitors, structurally unrelated to NAD" (12), which act at the DNA binding site of the enzyme. 

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