http://hdl.handle.net/2117/3523 Sun, 26 May 2013 06:27:28 GMT 2013-05-26T06:27:28Z webmaster.bupc@upc.edu Universitat Politècnica de Catalunya. Servei de Biblioteques i Documentació no http://hdl.handle.net/2117/16654 Title: Crystal structure of a complex of DNA with one AT-hook of HMGA1 Authors: Fonfria Subirós, Elsa; Acosta Reyes, Francisco Javier; Saperas Plana, Núria; Pous, Joan; Subirana Torrent, Juan A.; Campos López, Josefina de Lourdes Abstract: We present here for the first time the crystal structure of an AT-hook domain. We show the structure of an AT-hook of the ubiquitous nuclear protein HMGA1, combined with the oligonucleotide d(CGAATTAATTCG)2, which has two potential AATT interacting groups. Interaction with only one of them is found. The structure presents analogies and significant differences with previous NMR studies: the AT-hook forms hydrogen bonds between main-chain NH groups and thymines in the minor groove, DNA is bent and the minor groove is widened. Fri, 05 Oct 2012 10:27:05 GMT http://hdl.handle.net/2117/16654 2012-10-05T10:27:05Z Fonfria Subirós, Elsa; Acosta Reyes, Francisco Javier; Saperas Plana, Núria; Pous, Joan; Subirana Torrent, Juan A.; Campos López, Josefina de Lourdes no We present here for the first time the crystal structure of an AT-hook domain. We show the structure of an AT-hook of the ubiquitous nuclear protein HMGA1, combined with the oligonucleotide d(CGAATTAATTCG)2, which has two potential AATT interacting groups. Interaction with only one of them is found. The structure presents analogies and significant differences with previous NMR studies: the AT-hook forms hydrogen bonds between main-chain NH groups and thymines in the minor groove, DNA is bent and the minor groove is widened. http://hdl.handle.net/2117/14514 Title: Proteolytic enzymes in detergents: evidence of their presence through activity measurements based on electrophoresis Authors: Saperas Plana, Núria; Fonfria Subirós, Elsa Abstract: This laboratory exercise uses a problem-based approach to expose students to some basic concepts relating to proteins and enzymes. One of the main applications of enzymes at the industrial level is their use in the detergent market. The students examine a detergent sample to ascertain whether proteolytic enzymes are a component and, if so,which colored detergent granules contain them.A4-hour standard exercise is described that can be easily modified to study a number of conditions that affect enzymatic activity. The students also become familiar with polyacrylamide gel electrophoresis as it is used to visualize the products of enzyme activity. Fri, 13 Jan 2012 11:02:11 GMT http://hdl.handle.net/2117/14514 2012-01-13T11:02:11Z Saperas Plana, Núria; Fonfria Subirós, Elsa no This laboratory exercise uses a problem-based approach to expose students to some basic concepts relating to proteins and enzymes. One of the main applications of enzymes at the industrial level is their use in the detergent market. The students examine a detergent sample to ascertain whether proteolytic enzymes are a component and, if so,which colored detergent granules contain them.A4-hour standard exercise is described that can be easily modified to study a number of conditions that affect enzymatic activity. The students also become familiar with polyacrylamide gel electrophoresis as it is used to visualize the products of enzyme activity. http://hdl.handle.net/2117/14369 Title: Uso de la cristalografia de rayos X en el Drug Discovery Authors: Bonin, Irena; Martinell, Marc; Aymami Bofarull, Juan Fri, 30 Dec 2011 08:47:23 GMT http://hdl.handle.net/2117/14369 2011-12-30T08:47:23Z Bonin, Irena; Martinell, Marc; Aymami Bofarull, Juan no http://hdl.handle.net/2117/14368 Title: B2D2- La integración de las técnicas biofísicas en el descubrimiento de fármacos Authors: Aymami Bofarull, Juan; Martinell, Marc Fri, 30 Dec 2011 08:41:20 GMT http://hdl.handle.net/2117/14368 2011-12-30T08:41:20Z Aymami Bofarull, Juan; Martinell, Marc no http://hdl.handle.net/2117/13244 Title: Visualization of sequence and structural features of genomes and chromosome fragments. Application to CpG islands, Alu sequences and whole genomes Authors: Subirana Torrent, Juan A.; Anokian, Ezequiel Abstract: A very simple new program is presented (G-SQUARES). It is useful in order to visualize the composition and basic structural features of whole genomes and selected chromosome regions. The frequency of all dimer and tetramer sequences is reported. Overall structural features are calculated, such as the tendency for alternation. A direct visual comparison among different sequences is easily available. Furthermore, the features which are visualized indicate further studies which should be carried out. Examples are presented on Alu sequences, CpG islands, whole eukaryotic and bacterial genomes. Mon, 19 Sep 2011 13:31:46 GMT http://hdl.handle.net/2117/13244 2011-09-19T13:31:46Z Subirana Torrent, Juan A.; Anokian, Ezequiel no A very simple new program is presented (G-SQUARES). It is useful in order to visualize the composition and basic structural features of whole genomes and selected chromosome regions. The frequency of all dimer and tetramer sequences is reported. Overall structural features are calculated, such as the tendency for alternation. A direct visual comparison among different sequences is easily available. Furthermore, the features which are visualized indicate further studies which should be carried out. Examples are presented on Alu sequences, CpG islands, whole eukaryotic and bacterial genomes. http://hdl.handle.net/2117/13133 Title: DNA coiled coil superstructures in oligonucleotide crystals Authors: Luchi, Daniela de; Urpí Garriga, Lourdes; Subirana Torrent, Juan A.; Campos López, Josefina de Lourdes Abstract: We present the structure of coiled coils found in two oligonucleotide DNA crystals. The sequences d-(ATATATATAT) and d(CGATATATAT) are used. In the first case several coiled coils with different structures are found. In the second case a single structure is present. The results are compared with other coiled coil structures. They might be used in the development of new nanomaterials. Mon, 29 Aug 2011 18:03:32 GMT http://hdl.handle.net/2117/13133 2011-08-29T18:03:32Z Luchi, Daniela de; Urpí Garriga, Lourdes; Subirana Torrent, Juan A.; Campos López, Josefina de Lourdes no We present the structure of coiled coils found in two oligonucleotide DNA crystals. The sequences d-(ATATATATAT) and d(CGATATATAT) are used. In the first case several coiled coils with different structures are found. In the second case a single structure is present. The results are compared with other coiled coil structures. They might be used in the development of new nanomaterials. http://hdl.handle.net/2117/8298 Title: Coiled-coil conformation of a pentamidine-DNA complex Authors: Moreno Chicano, Tadeo; Pous, Joan; Subirana Torrent, Juan A.; Campos López, Josefina de Lourdes Abstract: The coiled-coil structure formed by the complex of the DNA duplex d(ATATATATAT)2 with pentamidine is presented. The duplex was found to have a mixed structure containing Watson-Crick and Hoogsteen base pairs. The drug stabilizes the coiled coil through the formation of cross-links between neighbouring duplexes. The central part of the drug is found in the minor groove as expected, whereas the charged terminal amidine groups protrude and interact with phosphates from neighbouring molecules. The formation of cross-links may be related to the biological effects of pentamidine, which is used as an antiprotozoal agent in trypanosomiasis, leishmaniasis and pneumonias associated with AIDS. The DNA sequence that was used is highly abundant in most eukaryotic genomes. However, very few data are available on DNA sequences which only contain A·T base pairs. Wed, 21 Jul 2010 10:17:45 GMT http://hdl.handle.net/2117/8298 2010-07-21T10:17:45Z Moreno Chicano, Tadeo; Pous, Joan; Subirana Torrent, Juan A.; Campos López, Josefina de Lourdes no The coiled-coil structure formed by the complex of the DNA duplex d(ATATATATAT)2 with pentamidine is presented. The duplex was found to have a mixed structure containing Watson-Crick and Hoogsteen base pairs. The drug stabilizes the coiled coil through the formation of cross-links between neighbouring duplexes. The central part of the drug is found in the minor groove as expected, whereas the charged terminal amidine groups protrude and interact with phosphates from neighbouring molecules. The formation of cross-links may be related to the biological effects of pentamidine, which is used as an antiprotozoal agent in trypanosomiasis, leishmaniasis and pneumonias associated with AIDS. The DNA sequence that was used is highly abundant in most eukaryotic genomes. However, very few data are available on DNA sequences which only contain A·T base pairs.