Screening of potential pseudo att sites of Streptomyces phage ΦC31 integrase in the human genome.

AIM: ΦC31 integrase mediates site-specific recombination between two short sequences, attP and attB, in phage and bacterial genomes, which is a promising tool in gene regulation-based therapy since the zinc finger structure is probably the DNA recognizing domain that can further be engineered. The aim of this study was to screen potential pseudo att sites of ΦC31 integrase in the human genome, and evaluate the risks of its application in human gene therapy. METHODS: TFBS (transcription factor binding sites) were found on the basis of reported pseudo att sites using multiple motif-finding tools, including AlignACE, BioProspector, Consensus, MEME, and Weeder. The human genome with the proposed motif was scanned to find the potential pseudo att sites of ΦC31 integrase. RESULTS: The possible recognition motif of ΦC31 integrase was identified, which was composed of two co-occurrence conserved elements that were reverse complement to each other flanking the core sequence TTG. In the human genome, a total of 27924 potential pseudo att sites of ΦC31 integrase were found, which were distributed in each human chromosome with high-risk specificity values in the chromosomes 16, 17, and 19. When the risks of the sites were evaluate more rigorously, 53 hits were discovered, and some of them were just the vital functional genes or regulatory regions, such as ACYP2, AKR1B1, DUSP4, etc. CONCLUSION: The results provide clues for more comprehensive evaluation of the risks of using ΦC31 integrase in human gene therapy and for drug discovery.

Supramolecular structures constructed by 3-(2-amino-6-chloropyrimidin-4-yl)-1,1-dimethylprop-2-yn-1-ol monohydrate and 3-[2-amino-6-(3-hydroxy-3,3-dimethylprop-1-yn-1-yl)pyrimidin-4-yl]-1,1-dimethylprop-2-yn-1-ol.

The molecule of 3-(2-amino-6-chloropyrimidin-4-yl)-1,1-dimethylprop-2-yn-1-ol monohydrate, C(9)H(10)ClN(3)O·H(2)O, (I), shows a very polarized molecular-electronic structure, while the polarization is slight for 3-[2-amino-6-(3-hydroxy-3,3-dimethylprop-1-yn-1-yl)pyrimidin-4-yl]-1,1-dimethylprop-2-yn-1-ol, C(14)H(17)N(3)O(2), (II). In the supramolecular structure of (I), a combination of hard N-H···N hydrogen bonds and soft C-H···N hydrogen bonds creates a molecular column. Aromatic π-π stackings between the pyrimidine rings stabilize the column with perpendicular and centroid-centroid distances of 3.283 (3) and 3.588 (1) Å, respectively. Short Cl···Cl contacts further link neighbouring molecular columns, creating a hydrophilic tube in which water molecules are fixed by various hydrogen bonds. In the packing of (II), a one-dimensional molecular chain is formed through several contacts involving hard N-H···O(N) and O-H···O(N) and soft C-H···O hydrogen bonds. Interchain O-H···O hydrogen bonds link the chains giving a two-dimensional stepped network. It is anticipated that study of the influence of hydrogen bonding on the patterns of base pairing and molecular packing in aminopyrimidine structures will shed significant light on nucleic acid structures as well as their functions.

5,17-Dibromo-26,28-dihy-droxy-25,27-diprop-oxy-2,8,14,20-tetra-thia-calix[4]arene.

In the title compound, C(30)H(26)Br(2)O(4)S(4), the thia-calix[4]arene unit adopts a pinched cone conformation, with one of the ether-substituted rings bent towards the calix cavity and the two phenolic rings bent outwards. The phenyl rings make dihedral angles of 27.12 (9), 36.71 (10), 75.04 (8), and 76.01 (7)° with the virtual plane defined by the four bridging S atoms. The two opposite ether-substituted rings are almost parallel to each other, with an inter-planar anagle of 2.99 (12)°, while the two phenolic rings are nearly perpendicular to each other, making a dihedral angle of 74.52 (11)° and a Br⋯Br distance of 13.17 (2) Å. Two intra-molecular O-H⋯O hydrogen bonds between the OH groups and the same ether O atom stabilize the cone conformation. In the crystal, two different chains of mol-ecules, one with alternating and the other with tail-to-tail orientations, are formed by inter-molecular offset-face-to-face π-π stacking inter-actions with distances of 3.606 (3) to 4.488 (4) Šbetween the centroids of the aromatic rings.

8-(2,2,2-Trifluoro-ethoxy)quinolinium perchlorate-8-(2,2,2-trifluoro-ethoxy)quinoline (1/1).

The title compound, C(11)H(9)F(3)NO(+)·ClO(4) (-)·C(11)H(8)F(3)NO or [(C(11)H(8)F(3)NO)H(C(11)H(8)F(3)NO)]ClO(4), contains two 8-(2,2,2-trifluoro-eth--oxy)quinoline molecules, one of which combines a proton from perchloric acid to form the corresponding quinolinium cation. The quinolinium and quinoline rings form a cationic unit via an inter-molecular N-H⋯N hydrogen bond. The heterocyclic units are almost perpendicular to each other [inter-planar angle 86.97 (6)°]. In the crystal, each perchlorate anion bridges two adjacent cationic units and creates a chain by a combination of C-H⋯O hydrogen bonds. Two inversion-related chains associate into a mol-ecular column by π-π stacking inter-actions between the quinolinium rings. The perpendicular and centroid-centroid distances between adjacent quinolinium rings are 3.501 (3) and 3.634 (9) Å, respectively. The molecular column is linked to its neighbors, creating a two-dimensional network via the weak π-π stacking between the quinoline rings [perpendicular and centroid-centroid separations 3.340 (4) and 4.408 (4) Å, respectively]. Finally, a three-dimensional framework is formed by a combination of intermolecular C-F⋯π contacts. One -CF(3) group is disordered over two positions of equal occupancy.

Molecular interaction in binary surfactant mixtures containing alkyl polyglycoside.

Surface tensions were measured for several binary mixtures of a multidegree polymerized alkyl polyglycoside, C12G1.46' with different types of surfactants in 0.1 M NaCl at 25 degrees C. Based on regular solution theory, using a dimensional crystal model and a phase separation model, the molecule exchange energy in mixed monolayer formation (epsilon) and mixed micellization (epsilon(m)) were determined. Surfactants used in the mixtures with C12G1.46 in this study are C12E3S (trioxyethylenated dodecyl sulfonate), C12TAC (dodecyl trimethylammonium chloride), BE-6 (hexaoxyethylenated trisiloxane surfactant), and TMN-6 (hexaoxyethylenated-2,6,8-trimethylnonanol). The mixtures show exchange energy in mixed monolayer formation (epsilon) and mixed micellization (epsilon(m)) ranging from -660 to -1410 J/mol, indicating a decrease in surface energy upon mixing. The decreases in surface energy are in the order C12G1.46/C12E3S > C12G1.46/C12TAC, C12G1.46/C12TAC > C12G2/C12TAC and C12G1.46/BE-6 > C12G1.46/TMN-6. The ability of the mixed monolayer formation relative to the mixed micelle formation of the same binary mixture, measured by the (epsilon-epsilon(m)) values, is in the order C12G1.46/BE-6 > C12G1.46/TMN-6 > C12G1.46/C12E3S-->0 > C12G1.46/C12TAC.

On the alignment space.

Sequences with generalized errors which are called mutations in bioinformatics and generalized error-correcting codes are studied in this paper. In the areas of bioinformatics, computer science and information theory, sequences with generalized errors are discussed respectively for different aims. Firstly, we give the definitions of alignment distance and Levenshtein distance by expansion sequences and discuss their properties and relations. Then the modular structure theory is introduced for strictly describe the expansion sequences. We show that the expansion modular structures of sequences form a Boolean algebra. As applications of the modular structure theory, we give a new and more strict proof of triangle inequality for alignment distance. At last, the definition and construction of generalized error-correcting codes are studied, and some optimal codes with small length are listed.