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- Saenz-Mendez, Patricia, et al.
(författare)
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Theoretical prediction of binding modes and hot sequences for allopsoralen-DNA interaction
- 2007
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Ingår i: Chemical Physics Letters. - Amsterdam : Elsevier. - 0009-2614 .- 1873-4448. ; 450:1-3, s. 127-131
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Tidskriftsartikel (refereegranskat)abstract
- Molecular docking studies of two duplex DNA sequences as target fragments and allopsoralen as ligand were performed. The calculated interaction energies showed that the ligand can be docked into the minor groove as well as become intercalated. However, unlike psoralen, allopsoralen preferred binding mode for non-poly-TA sequences is minor groove binding. Calculated energies for intercalation between different base pairs suggest that the predicted sequence selectivity for allopsoralen is analogous to that observed for psoralen. Intercalation is favored in 5'-TpA sites in poly-TA sequences.
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| 3. |
- Saenz-Mendez, Patricia, et al.
(författare)
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Theoretical study of sequence selectivity and preferred binding mode of psoralen with DNA
- 2007
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Ingår i: Research Letters in Physical Chemistry. - : Hindawi Limited. - 1687-6873 .- 1687-6881. ; , s. Article number 60623-
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Tidskriftsartikel (refereegranskat)abstract
- Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand.We found that both binding modes are possible, explaining the low efficiency for monoadduct formation from intercalated ligands. A comparison between the interaction energy for intercalation between different base pairs suggests that the observed sequence selectivity is due to favorable intercalation in 5'-TpA in (AT)n sequences.
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| 7. |
- Markljung, Ellen, et al.
(författare)
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ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth
- 2009
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 7:12, s. e1000256-
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Tidskriftsartikel (refereegranskat)abstract
- A single nucleotide substitution in intron 3 of IGF2 in pigs abrogates a binding site for a repressor and leads to a 3-fold up-regulation of IGF2 in skeletal muscle. The mutation has major effects on muscle growth, size of the heart, and fat deposition. Here, we have identified the repressor and find that the protein, named ZBED6, is previously unknown, specific for placental mammals, and derived from an exapted DNA transposon. Silencing of Zbed6 in mouse C2C12 myoblasts affected Igf2 expression, cell proliferation, wound healing, and myotube formation. Chromatin immunoprecipitation (ChIP) sequencing using C2C12 cells identified about 2,500 ZBED6 binding sites in the genome, and the deduced consensus motif gave a perfect match with the established binding site in Igf2. Genes associated with ZBED6 binding sites showed a highly significant enrichment for certain Gene Ontology classifications, including development and transcriptional regulation. The phenotypic effects in mutant pigs and ZBED6-silenced C2C12 myoblasts, the extreme sequence conservation, its nucleolar localization, the broad tissue distribution, and the many target genes with essential biological functions suggest that ZBED6 is an important transcription factor in placental mammals, affecting development, cell proliferation, and growth.
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| 8. |
- Saenz Mendez, Patricia, et al.
(författare)
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Theoretical study of the structure of neutral, radical and anionic monoperoxo carbonic acid
- 2009
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Ingår i: Journal of Molecular Structure. - : Elsevier. - 0166-1280. ; 913:1-3, s. 131-138
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Tidskriftsartikel (refereegranskat)abstract
- Bicarbonate ion reacts with aqueous hydrogen peroxide, yielding monoperoxocarbonate (HCO4-, PCA-). This species is a better oxidizing agent than hydrogen peroxide itself and has been shown to lead to double bond epoxidation of alkenes under mild conditions. The structure of this anion as well as that of the parent monoperoxocarbonic acid (H2CO4, HPCA) are not known experimentally. The structures of the neutral, anionic and radical species derived from H2CO4 are reported in this paper employing DFT and MP2 methods, both in gas phase and simulating the bulk water solvent using the PCM method. Several conformers are found, of which the most stable one in gas phase has a planar, hydrogen-bonded structure similar to the one observed for peroxyformic acid (PFA). However, optimization of this structure in the bulk solvent leads to a non-planar conformation with a gauche disposition of the bonds in the COOH group. It is furthermore shown that the barriers separating the conformers are much smaller in solution, thus allowing easy interconversion.
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