Conformations of nicked and gapped DNA structures by NMR and molecular dynamic simulations in water.

We have analyzed and compared the molecular structures and dynamics of DNA duplexes containing a nick or a gap of one nucleotide where the base in front of the gap is a guanine. The continuous strand has the sequence 5'(CAGAGTCXCTGGCTC) where the residue X is absent for the nick, 14-mer, and where it is a G residue for the gap. Duplexes were formed with the two corresponding 7-mers. Neither of these is phosphorylated adjacent at the nick site, but it is a good model for a single strand break. For the nick structure, the quantitative NMR data show that the global conformation is very close to canonical B-form DNA, but it displays enhanced local flexibility. For the gap structure, we observe only one species in which the extra G is well stacked into the helix. The two half-helices around this residue also show a B-form conformation. As with the nick duplex, the adjacent G imino protons show enhanced exchange with solvent. The gap does not close completely. Using distance constraints, MD calculations show that the nick conformation is very close to a duplex with no lesion but is indeed more flexible in the central part. The gapped structure shows two families of conformations. One is close to B-DNA, the other is significantly kinked at the gap which reduces the size of the cavity. We observe a spine of hydration within the cavities, similar, but of different geometry in the two cases.

Horseradish peroxidase-dependent oxidation of deuteroporphyrin IX into chlorins.

Chlorins are cyclic tetrapyrrole derivatives of great interest for use in photodynamic therapy. We have found that horseradish peroxidase (EC 1.11.1.7) (HRP) can convert deuteroporphyrin IX (Deutero) into chlorins. Some characteristics of this enzymatic transformation were investigated. The formation of chlorins was determined spectrophotometrically by monitoring the change in absorbance in the Q-band region (638 nm). The reaction occurred without addition of H2O2 and had a pH optimum of 7.5. The presence of thiol-containing reductants, with a great preference for reduced glutathione, was required and could not be substituted by adding H2O2. Ascorbic acid acted as a potent inhibitor of the reaction, while other organic acids (citric and benzoic) had little to no inhibitory effect. The requirement for O2 was suggested by the inhibitory effect of sodium hydrosulfite and was confirmed by carrying the assay in nitrogen-saturated solutions. Though the reaction occurred without adding H2O2, low amounts of H2O2 (3-30 microM) were stimulatory to the assay. However, concentrations of 300 microM H2O2 or higher were inhibitory. Similarly, light was not required, but was stimulatory at low levels and inhibitory at high levels. Catalase and deferoxamine were inhibitory, but superoxide dismutase and mannitol had no effects. Kinetic analysis and respiratory studies suggest that HRP may initially react with reduced glutathione in a reaction that does not consume much oxygen. The ensuing steps, probably involving an oxygen free radical and porphyrin radical intermediates, consume a large amount of O2 to oxidize Deutero into chlorin.

Solution structure of two mismatches G.G and I.I in the K-ras gene context by nuclear magnetic resonance and molecular dynamics.

Two mismatches, G.G and I.I, have been incorporated at the central position of 5'd-(GCCACXAGCTC).d(GAGCTXGTGGC) in order to carry out NMR and molecular dynamics studies. These duplexes constitute the sequence 29-39 of the K-ras gene coding for the glycine 12, a hot spot for mutation. The NMR spectra show that the duplexes are not greatly distorted by the introduction of the mismatches and their global conformation is that of a canonical B-form double helix. For the duplex containing the G.G mismatch, we propose for the major species, a type of pairing involving one hydrogen bond between the imino group of one central guanine and the carbonyl group of the opposite guanine. Both bases are in an anti conformation. Two conformations, with the same donor and acceptor pattern can coexist, one is obtained from the other by a 180 degrees rotation about the pseudodyadic axis. Exchange between the two forms is observed by NMR at low temperature. A minor species involving hydrogen bonding between the guanine amino group and the carbonyl group of the guanine on the opposite strand may also exist as shown by the molecular dynamics calculations. For the I.I mismatch we observe the same major species, i.e., hydrogen bonding between an imino proton of one base and the carbonyl group of the base on the opposite strand with both bases in an anti conformation. Exchange between these two conformations is faster than for the G.G mismatch. Further, we observe that the I.I mismatch adopts a minor conformation, in which one or other of the bases is in the syn conformation.