Base pairs association constants

One can write acid-base equilibrium constants for the species in the inner compact layer and ion pair association constants for the outer compact layer. In these constants, the concentration or activity of an ion is related to that in the bulk by a term e p(-erp/kT), where yp is the potential appropriate to the layer [25]. The charge density in both layers is given by the algebraic sum of the ions present per unit area, which is related to the number of ions removed from solution by, for example, a pH titration. If the capacity of the layers can be estimated, one has a relationship between the charge density and potential and thence to the experimentally measurable zeta potential [26]. 

Pranata J, Wierschkem SG, Jorgensen WL. OPLS potential functions for nucleotide bases— relative association constants of hydrogen-bonded base-pairs in chloroform. J Am Chem Soc 1990 113 2810-2819. 

The addition of polar molecules to electrolyte solutions effects a much larger change in conductance if low dielectric solvents are employed In a series of papers Gilkerson et a/. studied the ion-molecule interaction of tertiary and quarternary ammonium cations with Lewis bases in low dielectric solvents, like o-dichlorobenzene, chlorobenzene or 1,2-dichloroethane. The change of the ion-pair association constant with concentration of an additive L was attributed to the formation of 1 1 cation-molecule complexes ... 

Association Phenomena According to the theoretical model of spheres in a dielectric continuum the ions are represented as rigid, charged spheres that do not interact with solvent, which is considered to be a medium without any kind of structure. The only interaction is that which occurs between the ions, and the formation of ion pairs is controlled only by electrostatic forces. On these bases, the association constant may be expressed by the Fuoss equation (29) ... 

OPLS Potential Functions for Nucleotide Bases—Relative Association Constants of Hydrogen-Bonded Base Pairs in Chloroform. 

Pranata. J. Wierschke. S.G. Jorgensen. W.L. OPES potential functions for nucleotide bases — Relative association constants of hydrogen-bonded base-pairs in chlorofonn. J. Am. Chem. Soc. 1991. 113 (8). 2810-2819. 

The DNA base pairs guanine (G), cytosine (C), adenine (A) and thymine (T). The uracil-2,6-diaminopyridine pair can also form three hydrogen bonds but has a much lower association constant than G-C. 

Significantly, it has been shown that coordination of nucleobases can enhance base pairing interactions (115). These findings confirm previous theoretical calculations (116). The association constant for Watson-Crick interactions between 9-EtG and 1-MeC was 6.9 M 1, determined... 

Metal-modified base pairs have been reported some time ago for identical (119), complementary (120), and non-complementary bases (59,121-126). These may assemble into a type I quartet through dimerization, as seen for trassociation constant of 59.1 M 1 in d6-DMSO (123). Rather unusual is the involvement of the aromatic C-H5 proton in the hydrogen bond-... 

Table 7 Association and dissociation rate constants for the binding of 22 to d(GCG-Y-GCG) complementary base paired oligonucleotides at 25 °C...

An interesting question then arises as to why the dynamics of proton transfer for the benzophenone-i V, /V-dimethylaniline contact radical IP falls within the nonadiabatic regime while that for the napthol photoacids-carboxylic base pairs in water falls in the adiabatic regime given that both systems are intermolecular. For the benzophenone-A, A-dimethylaniline contact radical IP, the presumed structure of the complex is that of a 7t-stacked system that constrains the distance between the two heavy atoms involved in the proton transfer, C and O, to a distance of 3.3A (Scheme 2.10) [20]. Conversely, for the napthol photoacids-carboxylic base pairs no such constraints are imposed so that there can be close approach of the two heavy atoms. The distance associated with the crossover between nonadiabatic and adiabatic proton transfer has yet to be clearly defined and will be system specific. However, from model calculations, distances in excess of 2.5 A appear to lead to the realm of nonadiabatic proton transfer. Thus, a factor determining whether a bimolecular proton-transfer process falls within the adiabatic or nonadiabatic regimes lies in the rate expression Eq. (6) where 4>(R), the distribution function for molecular species with distance, and k(R), the rate constant as a function of distance, determine the mode of transfer. 

If for simplicity at least v base pairs must be open to form an intermolecular base pair, and that bond itself has v base pairs (V is 3-4 at room temperature from studies of oligonucleotides) then the intermolecular association constant is Ky = s. Assuming equal probability of occurrence of all four bases at any point of the sequence, the probability that any given open end will find its complement is (1/4). ... 

In double-stranded DNA, electron abstraction from the guanine radical cation can be associated with an extremely fast shift of the N1 proton to its Watson-Crick partner cytosine (Scheme 2a) [9]. The equilibrium constant for the protonation of C (pfCa=4.3) with the concomitant deprotonation of G estimated from the pK values of the free nucleosides, is about 2.5 [49]. Within these constraints, the guanine radical should retain some radical cation character [82] and the complete deprotonation of G would require a base pair opening event occurring on a millisecond timescale [74]. An alternative mechanism of G deprotonation is the release of the N2 proton (Scheme 2b). This mechanism was experimentally established for 1-methyl-guanosine conductometric results showed that in neutral solutions, the radical cation of this nucleoside rapidly deprotonates with the formation of the neutral radical [48]. Although the exact mechanism of the G deprotonation in double-stranded DNA requires further clarification, electron abstraction... 

Both associated and nonassociated electrolytes exist in sea water, the latter (typified by the alkali metal ions U+, Na-, K+, Rb+, and Cs-) predominantly as solvated free cations. The major anions. Cl and Br, exist as free anions, whereas as much as 20% of the F in sea water may be associated as the ion-pair MgF+. and 103 may be a more important species of I than I-. Based on dissociation constants and individual ion activity coefficients the distribution of the major cations in sea water as sulfate, bicarbonate, or carbonate ion-pairs has been evaluated at specified conditions by Garrels and Thompson (19621. 

At a quantitative level, near criticality the FL theory overestimates dissociation largely, and WS theory deviates even more. The same is true for all versions of the PMSA. In WS theory the high ionicity is a consequence of the increase of the dielectric constant induced by dipolar pairs. The direct DD contribution of the free energy favors pair formation [221]. One can expect that an account for neutral (2,2) quadruples, as predicted by the MC studies, will improve the performance of DH-based theories, because the coupled mass action equilibria reduce dissociation. Moreover, quadrupolar ionic clusters yield no direct contribution to the dielectric constant, so that the increase of and the diminution of the association constant becomes less pronounced than estimated from the WS approach. Such an effect is suggested from dielectric constant data for electrolyte solutions at low T [138, 139], but these arguments may be subject to debate [215]. We note that according to all evidence from theory and MC simulations, charged triple ions [260], often assumed to explain conductance minima, do not seem to play a major role in the ion distribution. 

Data from spectrophotometric titrations may also be used to determine the association constant (K) between the dye and DNA [25]. The data from spectrophotometric titrations, i.e. absorbance data (A0bs) at a fixed wavelength, are used to determine the concentration of bound dye (Cb), the concentration of uncomplexed dye (c), and the number of bound dye molecules per base pair (r) according to Eqs... 

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