Sequence-dependent thermodynamics

Double-crossover molecules have been used extensively to characterize the properties of Holliday junctions. The strong torsional coupling between their crossover points has been exploited to construct symmetric immobile junctions (S. Zhang et al. 1993), junctions in which one of the crossovers is flanked by homology, but is nevertheless unable to branch migrate. Symmetric immobile junctions have been used to characterize crossover isomerization thermodynamics (S. Zhang and Seeman 1994) and, more recently, the sequence dependence of the branch point stability (W. Sun et al., 1998). Double crossover molecules have also been employed to establish the cleavage patterns of endonuclease VII, an enzyme that resolves branched junctions (Fu et al. 1994 a). 

D. Mathews, J. Sabina, M. Zucker, and H. Turner. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J. Mol. Biol, 288 911-940, 1999. 

The DNA lesion 8,5 -cyclo-2 -dG, formed by attack of hydroxyl radicals, contains damage to both base and sugar, and is therefore repaired by nucleotide excision repair enzymes, and is involved in diseases with defective nucleotide excision repair. A mass spectroscopic assay has been developed for the quantitation of the lesion after enzymatic separation of the 5 (R) and 5 (S) isomers. The thermodynamic stability of ODNs containing the oxidative lesion, 2-hydroxy-dA has been examined. It was shown that when the lesion was in the middle of a DNA duplex it behaved as a universal base, in that there was no dilference in Tm when opposite any of the canonical bases. On the other hand, when it was near the termini, there was a preference for base pairing with thymidine, but it also formed base pairs with other nucleotides which was sequence dependent. The extent of oxoprenylation by malondialdehyde or adenine propenal has been investigated in DNA, see (139). ssDNA was found to be more sensitive to oxoprenylation, and supercoiled-DNA more susceptible than linearised plasmid DNA. A variety of intercalators were used, some of which inhibit oxoprenylation, e.g. netropsin, whilst others, like ethidium bromide, caused enhanced oxoprenylation. 

AUawi HT, SantaLucia J Jr. Nearest-neighbor thermodynamics of internal A.C mismatches in DNA sequence dependence and pH effects. Biochemistry 1998 37 9435-44. 

Probe-target hybridization Hybridization buffer composition, temperature control, sequence-dependent kinetics and thermodynamics, washing process Strict control of temperature and buffer composition, replicate samples, careful washing, positive controls... 

We first consider why base sequence effects can affect the thermodynamic stabilities of double-stranded DNA. The neighboring base-base stacking energies have been analyzed in detail (e.g., see [116, 117]). These interactions are base sequence dependent because of potential steric clashes and electrostatic effects between the... 

The temperature dependence of NMR spectra and comparison of that sequence with thermodynamics for other sequences, however, revealed that it actually melts through a hairpin intermediate (31). 

A recent nanosecond range MD simulation on the DNA duplex d(CGCGAATTCGCG)2, based on the AMBER 4.1 force-field and the PME method, confirmed independently the stability of B-form duplexes under these simulation conditions. The authors observed an intrusion of a Na counterion in the DNA minor groove at an ApT step termed subsequently the ApT pocket . They concluded that such ion intrusion in DNA minor grooves may influence thermodynamical and structural DNA properties in a sequence-dependent manner. The dynamical properties as well as the hydration of the B-form d(CCAACGTTGG)2 decamer, shown to be stable in the nanosecond range, were investigated by Cheatham et al. ... 

The preference has both thermodynamic and structural reasons. Initially the sequence dependence of the hairpin-loop thermodynamic stability was attributed... 

A sequence of successive configurations from a Monte Carlo simulation constitutes a trajectory in phase space with HyperChem, this trajectory may be saved and played back in the same way as a dynamics trajectory. With appropriate choices of setup parameters, the Monte Carlo method may achieve equilibration more rapidly than molecular dynamics. For some systems, then, Monte Carlo provides a more direct route to equilibrium structural and thermodynamic properties. However, these calculations can be quite long, depending upon the system studied. 

The first, and to this writing still only case of a ketone a-cleavage-recombi-nation sequence in the steroid field was reported by Butenandt, who found that 17-ketones epimerize at C-13. Ultraviolet irradiation of either stereoisomer produces an equilibrium mixture in which the thermodynamically more favored 13a-compound cf. (15)] with cw-fusion of rings C and D predominates at room temperature. As ultraviolet absorption energies and intensities of the two isomeric ketones are practically identical, the equilibrium composition depends largely on the rate of the competing recombination process from (14). For further examples of the photoisomerization at C-13 of 17-ketosteroids, see ref. 8, 12, 15 and 43. 

The oxidizing power of the halate ions in aqueous solution, as measured by their standard reduction potentials (p. 854), decreases in the sequence bromate > chlorate > iodate but the rates of reaction follow the sequence iodate > bromate > chlorate. In addition, both the thermodynamic oxidizing power and the rate of reaction depend markedly on the hydrogen-ion concentration of the solution, being substantially greater in acid than in alkaline conditions (p, 855). 

---