Duplex sequence-dependent stability

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. 

The previously described PNA analogue (19) " pairs with thymidine when in a Hoogsteen strand of a bis-PNA. The conformationally constrained analogue of (19, 20), was evaluated in bis-PNA, but there was no improvement of stability compared to (19). The conformationally constrained PNA monomer (21, X=F) targeted towards DNA, formed stable structures, but was sequence dependent. PNA containing (21, X=H) preferentially forms stable parallel duplexes with DNA rather than antiparallel. PNA containing the peptide ribonucleic acid derivatives (22) are reported, but no additional data is provided. ... 

Stability of a Ni -containing, 2PA-modilied PNA DNA duplex did not depend on the duplex sequence, and (b) the effect of Ni on the duplex stability depended on the ionic strength of the solution (137). In most cases, addition of > 1 equiv of metal ion per pair of adjacent 2PA ligands destabilized the duplex, suggesting that steric and electrostatic repulsion occurs when each of the 2PA ligands binds a metal ion. 

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 thermodynamic stability (melting) of DNA containing an AP is markedly reduced (Gelfand et al. 1998). In a 13-mer DNA duplex, this lesion does not alter the global B-form conformation, but it induces a significant enthalpic destabilization of the duplex the amount of which being strongly dependent on the base sequence. 

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