Thermodynamics base-pairing

It can be seen from the figure that the electrostatic repulsive forces between the macrocations are overwhelmed, probably by hydrophobic attractive forces between their hydrophobic side groups. It should be noted that the complimentary base-base pairing is unimportant in the present case. If this is not the case, the mixtures of APVP and TPVP should show the largest hypochromicity. This, however, is not the case. The importance of the hydrophobic interactions between nucleic acid bases has been proposed by Ts o et al.I9 from thermodynamic parameters of various nucleic acid bases or nucleosides in aqueous media. 

In order to determine the influence of the bridge length on the efficiency of the hole transfer between guanines, we studied double strands where the number of (A T)n base pairs between the guanines were varied (Fig. 9). In these experiments the GGG unit acts as a thermodynamic sink for the charge [17]. 

Further experiments focused therefore on [RuCl(en)(r 6-tha)]+ (12) and [RuCl(rj6-p-cym)(en)]+ (22), which represent the two different classes, and their conformational distortion of short oligonucleotide duplexes. Chemical probes demonstrated that the induced distortion extended over at least seven base pairs for [RuCl(rj6-p-cym)(en)]+ (22), whereas the distortion was less extensive for [RuCl(en)(rj6-tha)]+ (12). Isothermal titration calorimetry also showed that the thermodynamic destabilization of the duplex was more pronounced for [RuCl(r 6-p-cym)(en)]+ (22) (89). DNA polymerization was markedly more strongly inhibited by the monofunctional Ru(II) adducts than by monofunctional Pt(II) compounds. The lack of recognition of the DNA monofunctional adducts by HMGB1, an interaction that shields cisplatin-DNA adducts from repair, points to a different mechanism of antitumor activity for the ruthenium-arenes. DNA repair activity by a repair-proficient HeLa cell-free extract (CFE) showed a considerably lower level of damage-induced DNA repair synthesis (about six times) for [RuCl(en)(rj6-tha)] + compared to cisplatin. This enhanced persistence of the adduct is consistent with the higher cytotoxicity of this compound (89). 

Applications in infrared spectroscopy A and B bands, iron-coordinated CO, 232, 186-187 application to allosteric mechanisms, 249, 566 bacteriorhodopsin, 246, 9, 380-381 caged compounds, 246, 6, 520-521 DNA [base pair formation, 246, 506 conformation, 246, 506-507 denaturation thermodynamics, 246, 506 ligand interactions, 246, 6, 507 sample requirements, 246, 506] fatty acyl ester determination in small cell samples, 233,... 

Recall that the secondary-structure model for RNA is a model - and a crude one at that. It neglects pseudo knots and other tertiary interactions, does not take deviations from the additive nearest neighbor energy model into account, and is based on thermodynamic parameters extracted from melting experiments by means of multidimensional fitting procedures. Thus, you cannot expect perfect predictions for each individual sequence. Rather, the accuracy is on the order of 50% of the base pairs for the minimum free energy structure. 

In addition to the base-pairing disruption, this melting also destroys the stacking of bases in fixed orientations relative to one another that is observed in the duplex. Later, we will present an argument based upon thermodynamic measurements of the stabilities of synthetic oligonucleotides (small pieces of synthetic nucleic acids) that the next-nearest neighbor interactions observed in the base stacking sequence are a major contributor to the relative stabilities of duplexes. 

Melt temperature measurements indicated that the thermodynamic stability of the probe molecules can be adjusted using the oligomer matrix to achieve lower Tm values by as much as 5 °C, with retention of selectivity for discrimination of single base pair mismatches [14]. The enhanced temperature sensitivity may ultimately provide for the development of analytical devices of extremely high selectivity. Devices containing immobilized... 

AG a, where AG. c refers to the symmetrical proton transfer between two identical carbon bases and AG aa the symmetrical proton transfer for a catalysing acid-base pair HA/A. The inequality is justified because proton transfers between oxygen and nitrogen bases are much faster than those to and from carbon bases. In the simplified equation (20) changing the catalyst HA or A affects AG only through the thermodynamic term GA. Differentiation of... 

In the lower panel of Fig. 17.3 are melt curves for HPc at 1574 cm-1 (squares) and 1661 cm-1 (circles). The upper panel shows melt curves for tRNAphe at 1620 cm-1 (squares) and 1661 cm-1 (circles). For HPC (lower), these wavenumbers correspond to base stacking (1574 cm-1 ring vibrations) and base pairing (1661 cm-1 G-C pairing). The melt curves (and subsequent thermodynamics) are virtually identical. It will be shown later, however, that the kinetics at the two different wavenumbers are very different. The wavenumbers for the tRNA (upper) correspond to A-U base... 

Thermodynamic and kinetic studies have demonstrated that the alternating purine-pyrimidine polynucleotide poly(dA-dT) folds into smaller duplexes which melt independently of each other in solution (16,17). The NMR spectrum should be considerably simplified since all base pairs are structurally equivalent due to the symmetry of the alternating purine-pyrimidine duplex. 

Spontaneous DNA Damage Hydrolysis of the A-glycosyl bond between deoxyribose and a purine in DNA creates an AP site. An AP site generates a thermodynamic destabilization greater than that created by any DNA mismatched base pair. This effect is not completely understood. Examine the structure of an AP site (see Fig. 8-33b) and describe some chemical consequences of base loss. 

Properties such as thermodynamic values, sequence asymmetry, and polymorphisms that contribute to RNA duplex stability are taken into account by these databases (Pei and Tuschl 2006). In addition, artificial neural networks have been utilized to train algorithms based on the analysis of randomly selected siRNAs (Huesken et al. 2005). These programs siphon significant trends from large sets of RNA sequences whose efficacies are known and validated. Certain base pair (bp) positions have a tendency to possess distinct nucleotides (Figure 9.2). In effective nucleotides, position 1 is preferentially an adenosine (A) or uracil (U), and many strands are enriched with these nucleotides along the first 6 to 7 bps of sequence (Pei and Tuschl 2006). The conserved RISC cleavage site at nucleotide position 10 favors an adenosine, which may be important, while other nucleotides are... 

An important parameter for comparison with theory as well as for understanding many properties would be relative binding energies or stabilities. Unfortunately those are hard to assess in the gas phase. One of the few experiments to report thermodynamic binding energies between base pairs is the work by Yanson et al. in 1979, based on field ionization [25], Relative abundances of nucleobase clusters in supersonic beams are an unreliable measure of relative stability for a two reasons First, supersonic cooling is a non-equilibrium process and thus comparison with thermal populations is tenuous at best. Secondly, ionization probabilities may be a function of cluster composition. The latter is certainly the case for multi photon ionization, as will be discussed in detail below. 

Figure 21-26. Electron binding to the Watson-Crick MAMT base pair solvated by formic acid at the Hoogsteen site (I). In consequence of intermolecular proton transfers the radicals MAH" (III) and MAH"+(IV) are formed and the unpaired electron becomes localized on 9-methyladenine. Both initial electron attachment and two following intermolecular proton transfers are thermodynamically favourable and the accompanying changes of B3LYP electronic energies are given below the arrows in kcal/mol (Figure 7 of ref. [67]. Reprinted with permission. Copyright 2007 American Chemical Society.)...

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