Biomedical subjects
Publications and source records attributed to B Pullman.
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A theoretical study of the hydration of the B-form of DNA has been carried out using empirical potential energy functions. In the first stage the hydration scheme of a model compound representing the B-DNA has been determined and the results have been shown to agree to a large extent with those of refined ab initio SCF computations. In the second stage, the stabilization energy due to the presence of water in the first hydration shell was computed by considering the hydrated helix as a supermolecule. The computations indicate appreciable stabilization. The different components contributing to the overall stabilization are determined and analysed.
The variation of the proton chemical shifts due to the formation intermolecular hydrogen bonds is computed for a number of complexes which can be formed between the bases of the nucleic acids. The shifts expected for the isolated base pairs, in particular for the G-N1 H, T(or U)-N3H protons and the protons of the amino groups of A, G c, when combined with previous computations on the shifts to be expected upon base stacking, may enable a refined analysis of the high resolution NMR spectra of self complementary polynucleotides or tRNAs. Two examples are presented of a direct computation of proton shits associated with helix-coil transitions, helpful for deducing the helical structure in solution.
Computations are performed on the proton chemical shifts due to hydrogen bonding between the purine and pyrimidine bases of the nucleic acids and water molecules of their first hydration shell. The water molecules should produce measurable shifts essentially for protons of the bases located close to the site of interaction. For the imino protons of the bases G-N1H and U-N3H participating in hydrogen bonding, the calculated delta delta is larger for the interaction of a base with a complementary base than for its interaction with water. Base pairing will thus produce a downfield shift in water but the measured delta delta due to pairing in this solvent will be smaller than in an inert solvent. Also, the chemical shift difference between G-N1H and U-N3H in water will be larger if the molecules are engaged in pairs than if they are not.
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Intermolecular nuclear shielding values for protons, due to the ring-current effect, are computed for a plane parallel to and 3.4 A above the phenoxazone ring of actinomycin, ethidium, proflavin and quinacrine.
An extension of our previous correlation (C.R. Acad. Sci. Paris, Ser. D (1973) 277, 2257; Biochim. Biophys. Acta (1974) 340, 299) between the geometry of the phosphate group and the conformation of phosphodiesters established by PCILO computations, shows that the probability of gauche-trans or trans-gauche conformations should become appreciable for low values (100-101) of the 33'-P-O5', angle and may even become predominant when the C-O-P angles have also a low value (congruent to 117 degrees). The results agree satisfactorily with available X-ray crystallographic data.
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Quantum-mechanical computations performed by the ab initio self-consistent field molecular orbital method have been used for the determination of the principal hydration sites of acetylcholine in its gauche et trans conformations. The hydration destabilizes the gauche form with respect to the trans one by about 2 kcal/mole. Taking into account, however, that the gauche form is 3 kcal/mole intrinsically more stable, this form still remains the most stable one of acetylcholine in solution.
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