Strand Stoichiometry

A rationalisation for their approach is provided in Huppert and Balasubramanian, who consider four principle parameters of importance. These are (a) the strand stoichiometry, (b) the number of stacked tetrads in the quadruplex core, (c) the presence of mutations or deletions, and (d) the length and composition of loops. Some of these parameters may be resolved by consideration of the structures and previously known results, while others are resolved by experimentation. The following descriptions and commentary are also valid for the approach of Todd and Neidle.  

Quadruplexes can be uni-, bi- or tetramolecular. Since under physiological conditions the strand concentration of DNA is relatively low (order nM), except in rare exceptions such as Stylonychia lemnae macronuclei,interstrand quadruplexes will be strongly disfavoured. Therefore, only sequences that can from intramolecular quadruplexes were considered. 

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Although the final stoichiometry of the solution was 2 1 1 in bases Ag+ BH4, the complexes formed have a maximum of 4 Ag+ or 4 Ag atoms per DNA strand, as demonstrated by electrospray ionization mass spectrometry. This stoichiometry was explained as an end-effect of the short oligonucleotide. Moreover, H NMR indicates that silver interaction with cytosine base is stronger than with other bases. 

Burger RM, Peisach J, Horwitz SB (1982a) Stoichiometry of DNA strand scission and aldehyde formation by bleomycin. J Biol Chem 257 8612-8614... 

Figure 3. Binding of Cu(II) to single-stranded poly(A) and poly(C) in 0.1M NaClOh and 0.01 M sodium cacodylate, pH 6, 25° 0.1°. 6b is fractional saturation of potential binding sites assuming Cu(Il) nucleotide stoichiometry of 1 2.

In 1996, Smith and coworkers published two papers on mass spectrometric studies of protein-DNA complexes.40,41 The first mass spectral analysis of a protein-DNA complex studied the oligonucleotide-binding stoichiometry of the gene V protein. This system was extensively studied in solution, and it is known that, under physiological conditions, the gene V protein forms a dimer which is known to bind single-stranded DNA with high affinity... 

New rhenium(I) biotin complexes containing the extended planar diimine ligands dppz and dppn (17) have been prepared to explore bifunctional biological probes [44], These complexes bind to double-stranded calf thymus DNA by intercalation, as revealed by absorption and emission titrations. HABA assays show that all the complexes bind to avidin with a stoichiometry of 4 1 ([Re] [avidin]). Similar to other rhenium(I) diimine biotin complexes described above, the emission intensities... 

The two main types of infinite chain anions are the pyroxenes, which contain singlestrand chains of composition (SiO ) (Fig. 8-4) and the amphiboles, which contain double-strand, cross-linked chains or bands of composition (SLOif),. Note that the general formula of the anion in a pyroxene is the same as in a silicate with a cyclic anion. Silicates with this general stoichiometry are often called metasilicates, especially in older literature. There is actually neither metasilidc add nor any discrete metasilicate anion. With the exception of the few metasilicates with cyclic anions, such compounds contain infinite chain anions. 

To form double-stranded poly(A)-poly(U), equimolar amounts of the two homopolymers are mixed at a concentration of 0.6-1.5 fiM nucleotide (about 200-500 /iig/ml) in 0.1 A/ NaCl, 0.01 M phosphate pH 7 at room temperature and allowed to anneal for a few hours. Hypochromicity occurs at 260 nm when a double helix is formed and at both 260 and 280 nm when a triple helix is formed. At room temperature and 0.1 Af NaCl, only the stoichiometry determines which helix will form. At high ionic strength (0.7 M NaCl), and at high temperature, even a 1 1 mixture will form a triple helix with time triple-strand formation is also favored by... 

Figure 8 depicts an example of such a process in which a tetrahedrally disposed Cu1 ion is treated with a mixture of a linear ligand strand (17) and a stoichiometric amount of a macrocyclic bidentate ligand (18) whose coordination site lies on the inside of the cycle.24 This assembly is successful despite the fact that the interlaced rotaxane is probably less stable than the competing complex Cu(17)2. This is because the stoichiometry of the reagent mixture forces the formation of Cu( 17) to be accompanied by the formation of Cu(18)2 which is thermodynamically highly unstable. The other obvious competitor, Cu2(17)2+, is less stable than [Cu(17)(18)]+, because four-coordinate Cu1 cannot easily accommodate the two tridentate terminal binding sites on (17). 

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