Novel numerical and graphical representation of DNA sequences and proteins.

We have introduced novel numerical and graphical representations of DNA, which offer a simple and unique characterization of DNA sequences. The numerical representation of a DNA sequence is given as a sequence of real numbers derived from a unique graphical representation of the standard genetic code. There is no loss of information on the primary structure of a DNA sequence associated with this numerical representation. The novel representations are illustrated with the coding sequences of the first exon of beta-globin gene of half a dozen species in addition to human. The method can be extended to proteins as is exemplified by humanin, a 24-aa peptide that has recently been identified as a specific inhibitor of neuronal cell death induced by familial Alzheimer's disease mutant genes.

Palladium(II) complexes of dialkyl alpha-Anilinobenzylphosphonates. Synthesis, characterization, and cytostatic activity.

The new palladium (II) halide complexes with diethyl and dibutyl esters of (alpha-anilino-N-benzyl) phosphonic acid and diethyl and dibutyl esters of [alpha-(4-benzeneazoanilino)-N-benzyl] phosphonic acid have been prepared and studied. All organophosphorus ligands form dihalide complexes, trans-Pd(L)2X2(X = Cl or Br), with monodentate N-bonded ligand through the anilinobenzyl nitrogen in (alpha-anilino-N-benzyl) phosphonate complexes and through the azo nitrogen in [alpha-(4-benzeneazoanilino)-N-benzyl] phosphonate complexes, respectively, without participation of the phosphoryl group. Azobenzene containing ligands by ortho-metallation also form binuclear organo-palladium complexes, [Pd(L-H)Cl]2, with the metal-metal chloro bridge. The complexes have been identified and characterized by elemental analysis, infrared and 1H NMR, as well as by magnetic and conductometric measurements. All were tested in vitro for their cytostatic activity against KB and L1210 tumor cell lines. The results show that these complexes inhibit the multiplication of these tumor cells, but only the dichloro adduct of diethyl [alpha-(4-benzeneazoanilino)-N-benzyl] phosphonate was found to have activity comparable to that of the antitumor drug cisplatin.

On the choice of optimal methodology for calculation of (13)C and (1)H NMR isotropic chemical shifts in cagelike systems. Case studies of adamantane, 2-adamantanone, and 2,4-methano-2,4-dehydroadamantane.

The (13)C and (1)H isotropic chemical shift values computed at HF, BLYP, B3LYP, and MPW1PW91/6-311+G(2d,p) levels of theory, for the BLYP and B3LYP/6-31G(d,p) optimized geometries of adamantane, 2-adamantanone, and 2,4-methano-2,4-dehydroadamantane ([3.1.1] propellane) are reported and compared with the experimental data. Except for the "inverted" carbon atoms and some of their nearest neighbors, the HF values are superior over the DFT ones, when the isotropic shifts with respect to TMS are in question. However, in case of the relative shifts computed with respect to the most deshielded center within the molecule, the DFT methods yield significantly better agreement with the experimental data than the HF method, the hybrid DFT methods being superior over "pure" DFT ones. The most probable reason for these findings may be the cancellation of errors arising from the inappropriate description of the paramagnetic contributions to the overall shielding tensor within the Kohn-Sham approach when an internal standard (within a molecule) is chosen, instead of an external one. Almost excellent linear correlation was found between the calculated and experimental relative shift values, which is significantly superior at DFT levels than at HF level, further proving the more systematical nature of errors in predicting the second-order magnetic response properties at DFT levels of theory. Among all DFT methods employed, the MPW1PW91 showed the best performance, in line with the significantly improved long-range behavior of this functional, as compared to the B3LYP one.

Quantitative determination of magnetization exchange rate constants from a series of two-dimensional exchange NMR spectra

A method for quantitative determination of magnetization exchange rate constants (cross-relaxation and chemical exchange) from a series of two-dimensional exchange spectra is presented. The method, the least error matrix analysis (LEMA), combines a series of full matrix calculations at different mixing times in a least-squares manner. LEMA embodies the principal advantages of full-relaxation matrix analysis (FMA) and initial rate buildup (BU) analysis. Like FMA, it takes into account all the relations among the spectral matrix elements and in analogy to BU makes use of their time evolution. By means of calculations, simulations, and experiments, we have shown that LEMA provides the dynamic matrix from a given set of experimental data with errors that are smaller than in either FMA or BU calculations.