Research Topics
Species | Ramon EritjaSummaryAffiliation: Agencia Estatal Consejo Superior de investigaciones Cient?ficas Location: Barcelona, Spain URL: http://www.iqac.csic.es/index.php?option=com_ogngrups&view=detall_grup&Itemid=81&cid=47&lang=en Summary: The general aim of the group is the preparation of nucleic acid derivatives that will be used to improve a particular aspect of the applications that use oligonucleotides. Specifically research is directed towards the following topics: 1) Synthesis of modified oligonucleotides to be used in the fabrication of molecular circuits based on DNA, bidimensional DNA aarys, Origami DNA. 2) Synthesis of oligonucleotides that contain 8-aminopurines and the study of the stabilizing properties of DNA/RNA triples helices. 3) Rational synthesis of molecules with affinity for double stranded DNA. Structural studies on G-quadruplex. 4) Synthesis of oligonucleotide-peptide and peptide nucleic acid derivatives. 5) Synthesis of oligonucleotides carrying biologically relevant nucleosides involved in DNA repair, DNA methylation, mutagenesis and so on. Grants: Multifunctional nanotechnology for selective detection and treatment of cancer (MULTIFUN). 2011-2014. EECC project Structiral studies of biomolecules of biomedical and technological interest (MOL2MED) 2011-2013. Spanish Nacional Project Structural study of peptide domains of hepatitis C viral proteins with inhibitory activity against HIV-1 and RNA aptamers with binding properties to PrP protein. 2010-2011. Spanish-Italian bilateral colaborative action. Multi-scale formation of functional nanocrystal-molecule assemblies and architectures (FUNMOL). 2008-2011. EECC project Self-assembled guanosine structures for molecular electronic devices (G4net). 2008-2012. COST Project Design and functionality of non-linear electrochemical nanscale devices (Dynamo). 2007-2009. EE CC project Synthesis and properties of modified oligonucleotides with potential biomedical and structural interest. (OMIBE). 2007-2009. Spanish Nacional Project. Nucleic Acids Chemistry group. 2007-2014. CIBER-BBN Networking Center on Bioengeneering, Biomaterials and Nanomedicine. Spanish National Health Institute Carlos III. Nucleic Acids Chemistry group. 2007-2014. Institute for Research in Biomedicine (IRB Barcelona). Group of synthesis and structure of biomolecules. 2009-2013. Regional Government of Catalonia Publications
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Detail Information
Publications
Synthesis and properties of oligonucleotides carrying cryptolepine derivativesRamon Eritja
Department of Structural Biology, Instituto de Biologia Molecular de Barcelona, C S I C, Jordi Girona 18 26, E 08034 Barcelona
Chem Biodivers 1:289-95. 2004..When cryptolepine is attached to a polypyrimidine oligonucleotide designed to form a parallel triplex, the triplex shows none or weak stabilization...- Effect of north bicyclo[3.1.0]hexane 2'-deoxy-pseudosugars on RNA interference: a novel class of siRNA modificationMontserrat Terrazas
Institute for Research in Biomedicine, CIBER BBN, Spanish Research Council, Barcelona, Spain
Chembiochem 12:1056-65. 2011..The results from these studies suggest that this modification might be valuable for the development of siRNAs for therapeutic applications... - Synthesis of lipid-oligonucleotide conjugates for RNA interference studiesSantiago Grijalvo
Institute for Research in Biomedicine, IQAC CSIC, CIBER BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Edifici Helix, Baldiri Reixac 10, Barcelona, Spain
Chem Biodivers 8:287-99. 2011..All the lipid-siRNA derivatives were compatible with RNA interference machinery if transfected with oligofectamine. In the absence of a transfection agent, some lipid-siRNA derivatives can exert a slight reduction of gene expression... - A direct, efficient method for the preparation of siRNAs containing ribo-like North bicyclo[3.1.0]hexane pseudosugarsMontserrat Terrazas
Institute for Research in Biomedicine IRB Barcelona, Networking Center on Bioengineering, Biomaterials and Nanomedicine CIBER BBN, Barcelona, Spain
Org Lett 13:2888-91. 2011..The resulting North ribo-methanocarba-modified siRNAs are compatible with the intracellular RNAi machinery and can mediate specific degradation of target mRNA... - Stepwise synthesis of RNA conjugates carrying peptide sequences for RNA interference studiesAnna Aviñó
Institute for Research in Biomedicine Barcelona, Edifici Helix, Baldiri Reixac 15, 08028 Barcelona, Spain
Mol Divers 13:287-93. 2009..The siRNA duplex carrying the nuclear localization peptide sequence at the 3'-end of the passenger strand has similar inhibitory properties as those of unmodified or cholesterol-modified RNA duplexes... - Synthesis and hybridization properties of modified oligodeoxynucleotides carrying non-natural basesAnna Aviñó
Institute for Research in Biomedicine, IQAC CSIC, CIBER BBN Networking Center on Bioengineering, Biomaterials and Nanomedicine, Edifici Helix, Baldiri Reixac 15, E 08028 Barcelona
Chem Biodivers 6:117-26. 2009..Magnesium ions were shown to stabilize preferentially the bimolecular duplex form. The results indicate the importance of the modifications and the role of cations in shifting the structural equilibrium... - Targeting the G-quadruplex-forming region near the P1 promoter in the human BCL-2 gene with the cationic porphyrin TMPyP4 and with the complementary C-rich strandMiquel del Toro
Department of Analytical Chemistry, University of Barcelona, Marti i Franques 1 11, E 08028 Barcelona, Spain
Biochimie 91:894-902. 2009..7) M(-1) (at pH 7.1). Finally, the pH-induced formation of quadruplex structures from the Watson-Crick double-helix is characterized... - Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectraJoaquim Jaumot
Department of Analytical Chemistry, Universitat de Barcelona, Diagonal 647, Barcelona E 08028, Spain
Anal Chim Acta 642:117-26. 2009..Moreover, these classification methods also provided the most characteristic wavelengths used in the classification procedures... - DNA (Cytosine-C5) methyltransferase inhibition by oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone (zebularine aglycon) at the enzymatic target siteDana M Van Bemmel
Department of Biochemistry and Molecular Biology, Omaha, NE 68198 5870, USA
Biochem Pharmacol 78:633-41. 2009..The differing stability and reversibility of the covalent bonds may partially account for the observed differences in cytotoxicity between zebularine and 5-azacytidine inhibitors... - Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamerHisao Saneyoshi
Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
Nucleic Acids Res 37:5589-601. 2009..1.0]hexane nucleosides appear to be excellent tools for studying the role of key conformational parameters that are critical for the formation of a stable, antiparallel G-tetrad DNA structures... - Label-free DNA biosensors based on functionalized carbon nanotube field effect transistorsMaria Teresa Martinez
Instituto de Carboquimica, Miguel Luesma, 4 Zaragoza, Spain
Nano Lett 9:530-6. 2009..After hybridization, statistically significant changes were observed in key transistor parameters. Hybridized DNA traps both electrons and holes, possibly caused by the charge-trapping nature of the base pairs... - Experimental measurement of carbohydrate-aromatic stacking in water by using a dangling-ended DNA model systemJuan C Morales
Department of Bioorganic Chemistry, Instituto de Investigaciones Quimicas, CSIC Universidad de Sevilla, Sevilla, Spain
Chemistry 14:7828-35. 2008..The noncovalent forces involved seem to be dispersion forces and nonconventional hydrogen bonds, whereas hydrophobic effects do not seem to drive the interaction... - 8-Amino guanine accelerates tetramolecular G-quadruplex formationJulien Gros
Muséum National d Histoire Naturelle MNHN USM 503, INSERM U565, CRNS UMR 5153, 43 rue Cuvier CP26, F 75231, Paris Cedex 05, France
Chem Commun (Camb) . 2008..We demonstrate here that 8-amino guanine () strongly accelerates quadruplex formation, which makes this nucleobase the most attractive replacement for guanine in the context of tetramolecular parallel quadruplexes... - Study of the interaction between the G-quadruplex-forming thrombin-binding aptamer and the porphyrin 5,10,15,20-tetrakis-(N-methyl-4-pyridyl)-21,23H-porphyrin tetratosylateMiquel del Toro
Department of Analytical Chemistry, Universitat de Barcelona, Barcelona E 08028, Spain
Anal Biochem 379:8-15. 2008..7+/-0.2. Melting and circular dichroism data reflected that the initial G-quadruplex structure of TBA is stabilized in the interaction complex, being slightly distorted by the presence of the ligand... - Solid-phase synthesis of oligomers carrying several chromophore units linked by phosphodiester backbonesAnna Aviñó
Institute for Research in Biomedicine IRB Barcelona, Josep Samitier 1 5, E 08028 Barcelona, Spain
Bioorg Med Chem Lett 18:2306-10. 2008..Specifically, the synthesis of chromophore units having a protected-hydroxyl group and a phosphoramidite function is described, along with a method to link several units using solid-phase phosphite-triester protocols... - Synthesis of oligonucleotide derivatives using ChemMatrix supportsStefania Mazzini
Institute for Research in Biomedicine, Barcelona Science Park, University of Barcelona, Spain
Chem Biodivers 5:209-18. 2008..Moreover, these supports can be used for the preparation of oligonucleotides in anhydrous solvents, followed by hybridization of the complementary sequences in aqueous buffers... - Incorporation of zebularine from its 2'-deoxyribonucleoside triphosphate derivative and activity as a template-coding nucleobaseCasimir L Dowd
Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
Nucleosides Nucleotides Nucleic Acids 27:131-45. 2008..Computer modeling of base-pairing structures supported a better fit of zebularine opposite guanine than adenine. Zebularine acts as a cytosine analog, which supports its activity as an inhibitor of cytosine methyltransferase... - Synthesis of oligonucleotides carrying 5'-5' linkages using copper-catalyzed cycloaddition reactionsMargarita Alvira
Institut de Biologia Molecular de Barcelona CSIC, CIBER BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Josep Samitier 1, E 08028 Barcelona
Chem Biodivers 4:2798-809. 2007..The non-templated chemical ligation of two oligonucleotides via copper-catalyzed [3+2] cycloaddition is described. By solid-phase methodology, oligonucleotides carrying 5'-5' linkages can be obtained in good yields... - Alpha,gamma-peptide nanotube templating of one-dimensional parallel fullerene arrangementsCésar Reiriz
Departamento de Quimica Organica, Universidad de Santiago de Compostela, E 15782 Santiago de Compostela, Spain
J Am Chem Soc 131:11335-7. 2009..The introduction of C(60) into cyclic peptides allows the preparation of supramolecular 1D fullerene arrangements induced by peptide nanotube formation under appropriate conditions... - The use of conformationally rigid nucleoside probes to study the role of sugar pucker and nucleobase orientation in the thrombin binding aptamerHisao Saneyoshi
Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
Nucleic Acids Symp Ser (Oxf) . 2009.... - Branched RNA: A New Architecture for RNA InterferenceAnna Aviñó
Institute for Research in Biomedicine IRB Barcelona, Institute of Advanced Chemistry of Catalonia IQAC CSIC, Networking Centre on Bioengineering, Biomaterials, and Nanomedicine CIBER BBN, Baldiri Reixac 10, 08028 Barcelona, Spain
J Nucleic Acids 2011:586935. 2011..As the method described here is compatible with most RNA modifications described to date, these compounds may be further functionalized to obtain more potent siRNA derivatives and can be attached to suitable delivery systems... - Synthesis and in vitro inhibition properties of siRNA conjugates carrying glucose and galactose with different presentationsAnna Aviñó
Institute for Research in Biomedicine IRB Barcelona, Institute for Advanced Chemistry of Catalonia IQAC CSIC, Networking Centre on Bioengineering, Biomaterials and Nanomedicine CIBER BBN, Baldiri Reixac 10, 08028 Barcelona, Spain
Mol Divers 15:751-7. 2011..These results demonstrate receptor-mediated uptake of siRNA carrying galactose residues, although the efficacy of the process is not enough for efficient RNA interference experiments... - Highly polar carbohydrates stack onto DNA duplexes via CH/? interactionsRicardo Lucas
Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC Universidad de Sevilla, Americo Vespucio, 49, 41092 Sevilla, Spain
J Am Chem Soc 133:1909-16. 2011..These results reveal carbohydrate-DNA base stacking as a potential recognition motif to be used in drug design, supramolecular chemistry, or biobased nanomaterials... - Synthesis and properties of small interfering RNA duplexes carrying 5-ethyluridine residuesMontserrat Terrazas
Institute for Research in Biomedicine IRB Barcelona, Institute for Advanced Chemistry of Catalonia IQAC CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine CIBER BBN, Baldiri i Reixac 10, 08028 Barcelona, Spain
Mol Divers 15:677-86. 2011.... - Chemical equilibria studies using multivariate analysis methodsJoaquim Jaumot
Solution Equilibria and Chemometrics Group Associated Unit UB CSIC, Department of Analytical Chemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Spain
Anal Bioanal Chem 399:1983-97. 2011..If any of these conditions is not fulfilled, a hybrid-modeling approach may be a better option because all the contributions (chemical and unknown) can be modeled and the ambiguities inherent to soft-modeling methods show minor effects... - Development of a Novel Fluorescence Assay Based on the Use of the Thrombin-Binding Aptamer for the Detection of O-Alkylguanine-DNA Alkyltransferase ActivityMaría Tintoré
Institute for Research in Biomedicine IRB Barcelona IQAC CSIC, CIBER BBN Networking Centre on Bioengineering Biomaterials and Nanomedicine, Cluster Building, Baldiri i Reixac 10, 08028 Barcelona, Spain
J Nucleic Acids 2010:. 2010..This new fluorescence resonance energy transfer assay has been designed to detect the conformational change of TBA that is induced by the removal of the O(6)-methyl group... - Synthesis of oligonucleotides carrying amino lipid groups at the 3'-end for RNA interference studiesSantiago Grijalvo
Institute for Research in Biomedicine IRB Barcelona, Networking Center on Bioengineering, Biomaterials and Biomedicine CIBER BBN and Institute for Advanced Chemistry of Catalonia IQAC, Spanish Research Council CSIC, Cluster Building, Baldiri Reixac 10, E 08028 Barcelona, Spain
J Org Chem 75:6806-13. 2010.... - G-quadruplex nucleic acidsRamon Eritja
IRB Barcelona, IQAC CSIC, Jordi Girona 16 26, 08034 Barcelona, Spain
J Nucleic Acids 2010:. 2010 - Structural properties of g,t-parallel duplexesAnna Aviñó
Institute for Research in Biomedicine, IQAC CSIC, CIBER BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Edifici Helix, Baldiri Reixac 15, 08028 Barcelona, Spain
J Nucleic Acids 2010:. 2010..Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex... - Solid-phase synthesis of oligodeoxynucleotides containing N4-[2-(t-butyldisulfanyl)ethyl]-5-methylcytosine moietiesSónia Pérez-Rentero
Institute for Research in Biomedicine Barcelona, CIBER BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Institute for Advanced Chemistry of Catalonia IQAC, CSIC, Baldiri Reixac 10, E 08028 Barcelona, Spain
Molecules 15:5692-707. 2010..The resulting thiolated oligonucleotides are useful intermediates to generate oligonucleotide conjugates carrying molecules of interest at internal positions of a DNA sequence... - Synthesis, cell-surface binding, and cellular uptake of fluorescently labeled glucose-DNA conjugates with different carbohydrate presentationBegoña Ugarte-Uribe
Unidad de Biofisica, Centro Mixto CSIC UPV EHU, Universidad del Pais Vasco, 48080 Bilbao, Spain
Bioconjug Chem 21:1280-7. 2010..Conjugates with tetravalent presentation of glucose did not improve cell uptake... - Modified siRNAs for the study of the PAZ domainAlvaro Somoza
IMDEA Nanociencia, 28049, Madrid, Spain
Chem Commun (Camb) 46:4270-2. 2010..Such modifications contribute positively to the stability of siRNAs in human serum... - Stepwise synthesis of oligonucleotide-peptide conjugates containing guanidinium and lipophilic groups in their 3'-terminiSantiago Grijalvo
Institute for Research in Biomedicine, Networking Center on Bioengineering, Biomaterials and Nanomedicine CIBER BBN, Barcelona, Spain
Bioorg Med Chem Lett 20:2144-7. 2010..Oligonucleotide-phosphorothioate conjugates were evaluated as potential antisense oligonucleotides in the inhibition of the luciferase gene... - pH-Modulated Watson-Crick duplex-quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription initiation sitePavel Bucek
Department of Analytical Chemistry, University of Barcelona, Marti i Franques 1 11, 08028 Barcelona, Spain
Chemistry 15:12663-71. 2009..0 to 6.5, approximately, under the experimental conditions tested in this study. At pH 7.0, the duplex is practically the only species present... - A flexible method for the fabrication of gold nanostructures using oligonucleotide derivativesRamon Eritja
Instituto de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Cientificas, Jordi Girona 18 26, 08034 Barcelona, Spain
Nucleosides Nucleotides Nucleic Acids 26:1605-9. 2007..The simplest structure (80 nm, linear) is formed by 4 oligonucleotides. By changing some of these components changes on length, shape, and recognition system easily can be introduced... - Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivativesElena Cubero
, , Universitat de Barcelona, , Barcelona 08028, Spain
J Am Chem Soc 124:3133-42. 2002..The large stabilization of the parallel-stranded helix upon 8-amino substitution agrees with a Hoogsteen pairing, confirming MD, NMR, and CD data, and suggests new methods to obtain DNA triplexes for antigene and antisense purposes... - Toward an ICPMS-linked DNA assay based on gold nanoparticles immunoconnected through peptide sequencesArben Merkoçi
Grup de Sensors i Biosensors, Departament de Quimica, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
Anal Chem 77:6500-3. 2005..2 pmol. The method may have significant potential as an important ICPMS-based nonradioactive DNA detection method for the simultaneous determination of various sequences by labeling different kinds of inorganic nanoparticles... - A straightforward synthesis of 5'-peptide oligonucleotide conjugates using N(alpha)-Fmoc-protected amino acidsSandra M Ocampo
Institut de Biologia Molecular de Barcelona, CSIC, Jordi Girona 18-26, E-08034 Barcelona, Spain
Org Lett 7:4349-52. 2005..The method uses commercially available reagents and is successful with most natural amino acids. The simplicity of the method may encourage researchers to prepare new oligonucleotide-peptide conjugates with novel properties... - Additional binding sites for anionic phospholipids and calcium ions in the crystal structures of complexes of the C2 domain of protein kinase calphaWendy F Ochoa
Instituto de Biologia Molecular de Barcelona CSIC, Jordi Girona Salgado 18 26, E 08034 Barcelona, Spain
J Mol Biol 320:277-91. 2002..Implications for PKCalpha activity of these structural results, in particular at the level of the binding affinity of the C2 domain to membranes, are discussed... - Effect of base stacking on the relative thermodynamic stability of oligonucleotide complexes: a spectroscopic studyDierdre Murphy
Nanotechnology Group, NMRC, Lee Maltings, Prospect Row, Cork, Ireland
J Biomol Struct Dyn 22:195-204. 2004..9 kcal/mol. The influence of a mispaired base in these systems is shown to destabilize a nick complex by 3.1 kcal/mol and a gap complex by 2.8 kcal/mol, respectively... - Inhibition of HhaI DNA (Cytosine-C5) methyltransferase by oligodeoxyribonucleotides containing 5-aza-2'-deoxycytidine: examination of the intertwined roles of co-factor, target, transition state structure and enzyme conformationAdam S Brank
Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198-4525, USA
J Mol Biol 323:53-67. 2002..HhaI that prevents DNA and co-factor release and (2) that methylation of ZCyt in DNA is not required for inhibition of M.HhaI... - Monitoring denaturation behaviour and comparative stability of DNA triple helices using oligonucleotide-gold nanoparticle conjugatesDeirdre Murphy
Nanotechnology Group, NMRC, Lee Maltings, Cork, Ireland
Nucleic Acids Res 32:e65. 2004.... - Potent inhibition of HhaI DNA methylase by the aglycon of 2-(1H)-pyrimidinone riboside (zebularine) at the GCGC recognition domainVictor E Marquez
Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Maryland 21702, USA
Ann N Y Acad Sci 1002:154-64. 2003..The drugs responsible for these effects-zebularine and 5-azacytidine/2'-deoxy-5-azacytidine-are contrasted in terms of chemical stability and possible metabolic activation by a brief structure-activity analysis... - Convenient synthesis of 8-amino-2'-deoxyadenosineMiriam Frieden
Instituto de Biologia Molecular de Barcelona, C.S.I.C. Jordi Girona, Barcelona, Spain
Nucleosides Nucleotides Nucleic Acids 22:193-202. 2003..The use of this reaction for the preparation of 8-aminoadenine derivatives needed for the preparation of oligonucleotides carrying 8-aminoadenine is discussed... - Peptide-PNA conjugates: targeted transport of antisense therapeutics into tumorsWalter Mier
, Radiologische Klinik, Abteilung Nuklearmedizin, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
Angew Chem Int Ed Engl 42:1968-71. 2003 - Iodouracil-mediated photocrosslinking of DNA to EcoRII restriction endonuclease in catalytic conditionsOlga V Babkina
Department of Chemistry and Belozersky Institute of Physical and Chemical Biology, Moscow State University, Moscow 119992, Russia
Photochem Photobiol Sci 1:636-40. 2002..Photocrosslinking of EcoRII to the IdU-containing DNA duplex occurred in a pre-reactive complex formed in the presence of Ca2+ ions. Photocrosslinking yields as a function of time and UV-laser light intensity were studied... - DNA duplexes containing photoactive derivatives of 2'-deoxyuridine as photocrosslinking probes for EcoRII DNA methyltransferase-substrate interactionElizaveta V Koudan
Department of Chemistry, Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Russia
J Biomol Struct Dyn 20:421-8. 2002..Amino acid residues from this region may take part both in substrate recognition and stabilization of the extrahelical target cytosine residue... - Magnetically trigged direct electrochemical detection of DNA hybridization using Au67 quantum dot as electrical tracerMartin Pumera
Grup de Sensors i Biosensors, , Universitat Autonoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
Langmuir 21:9625-9. 2005.... - New developments in the synthesis of oligonucleotide-peptide conjugatesCecilia Portela
Dipartamento de Química Orgánica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
Nucleosides Nucleotides Nucleic Acids 26:963-7. 2007..This conjugate has a long peptide sequence with a large number of trifunctional amino acids... - Solution equilibria of the i-motif-forming region upstream of the B-cell lymphoma-2 P1 promoterNasiruddin Khan
Department of Analytical Chemistry, University of Barcelona, Diagonal 647, E 08028 Barcelona, Spain
Biochimie 89:1562-72. 2007..6 yield identical interaction species with stoichiometries 1:2 (DNA:ligand) and logarithms of formation constant 12.4+/-0.2 and 11.7+/-0.1, respectively. The initial i-motif structure at pH 6.1 is lost upon interaction with TmPyP4... - Analysis of interaction between dendriplexes and bovine serum albuminDzmitry Shcharbin
Department of General Biophysics, University of Lodz, Lodz, Poland
Biomacromolecules 8:2059-62. 2007..Dendriplex formation significantly decreased the interactions between ODNs and albumin. Thus, the formation of dendriplexes between carbosilane dendrimers and ODNs may improve ODN delivery... - Water-soluble carbosilane dendrimers protect phosphorothioate oligonucleotides from binding to serum proteinsLouis Chonco
Laboratorio de Inmunobiologia Molecular, Hospital General Universitario Gregorio Maranon, Madrid, Spain
Org Biomol Chem 5:1886-93. 2007..As examples, transfection processes on normal primary peripheral blood cells and diagnosis of HIV infection in the presence of serum have been assayed... - ds-Oligonucleotide-peptide conjugates featuring peptides from the leucine-zipper region of Fos as switchable receptors for the oncoprotein JunCecilia Portela
, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
Chembiochem 8:1110-4. 2007 - Synthesis and triplex-forming properties of cyclic oligonucleotides with (G,A)-antiparallel strandsMarta G Grimau
Department of Structural Biology, Institut de Biologia Molecular de Barcelona, C.S.I.C, Jordi Girona 18-26, E-08034 Barcelona
Chem Biodivers 2:275-85. 2005..Although the differences in binding affinity between cyclic oligonucleotides and their corresponding linear precursors are small, the use of cyclic oligonucleotides offers a clear advantage over conventional duplex recognition... - Water-soluble carbosilane dendrimers: synthesis biocompatibility and complexation with oligonucleotides; evaluation for medical applicationsJesus F Bermejo
Laboratorio de Inmunobiologia Molecular, Hospital General Universitario Gregorio Maranon, Madrid, Spain
Chemistry 13:483-95. 2007..Also a preliminary transfection assay has been accomplished. These results demonstrate that the new ammonium-terminated carbosilane dendrimers are good base molecules to be considered for biomedical applications... - Trimethylguanosine nucleoside inhibits cross-linking between Snurportin 1 and m3G-CAPPED U1 snRNADiana Bahia
Institut de Biologia Molecular de Barcelona, CSIC IBMB CSIC, Barcelona
Nucleosides Nucleotides Nucleic Acids 25:909-23. 2006..These results indicate that the free nucleoside TMG could be a candidate to be an inhibitor of the interaction between Snurportin 1 and U snRNAs. We also show the behavior of free TMG nucleoside in in vitro U snRNPs nuclear import... - Efficient sequence-specific purification of Listeria innocua mRNA species by triplex affinity capture with parallel tail-clampsAnna Nadal
Institute of Food and Agricultural Technology (INTEA, University of Girona, , Spain
Chembiochem 7:1039-47. 2006..As an example, our tail-clamp-based triplex affinity capture assay allowed the specific capture and recovery of iap mRNA molecules from an L. innocua total RNA solution with 45 % yield... - Resolution of a structural competition involving dimeric G-quadruplex and its C-rich complementary strandJoaquim Jaumot
Department of Analytical Chemistry, University of Barcelona Diagonal, 647, Barcelona, E-08028 Spain
Nucleic Acids Res 34:206-16. 2006..In addition to melting temperatures, equilibrium constants for the parallel/antiparallel G-quadruplex equilibrium and for the G-quadruplex/duplex equilibrium were determined from the concentration profiles... - Strand displacement of double-stranded DNA by triplex-forming antiparallel purine-hairpinsSilvia Coma
Department of Biochemistry, School of Pharmacy, University of Barcelona, Barcelona, Spain
Oligonucleotides 15:269-83. 2005..Thus, triplexforming antiparallel purine-hairpins can be a potentially useful strategy for both single-strand and double-strand nucleic acid recognition... - Nanotechnology: carbon nanotubes with DNA recognitionKeith A Williams
Department of Nanoscience, Delft University of Technology, 2628 CJ Delft, The Netherlands
Nature 420:761. 2002 - Synthesis and structural properties of oligonucleotides covalently linked to acridine and quindoline derivatives through a threoninol linkerAnna Aviñó
Institute for Research in Biomedicine, Networking Centre on Bioengineering, Biomaterials and Nanomedicine CIBER BBN, CSIC, Baldiri Reixac 10, E 08028 Barcelona, Spain
Bioorg Med Chem 18:7348-56. 2010..Self-complementary oligonucleotides and thrombin binding aptamers (TBA) carrying the acridine and quindoline molecules are studied by NMR... - "Parallel" and "antiparallel tail-clamps" increase the efficiency of triplex formation with structured DNA and RNA targetsAnna Nadal
, Institut de Biologia Molecular de Barcelona, , Jordi Girona 18-26, 08034 Barcelona, Spain
Chembiochem 6:1034-42. 2005..In addition, the reported triplex-stabilizing property of 8-aminopurine residues was confirmed for tail-clamps. Finally, we discuss the possible use of this improved triplex technology as a new tool for applications in molecular biology... - Synthesis and properties of oligonucleotides carrying isoquinoline imidazo[1,2-a]azine fluorescent unitsSónia Pérez-Rentero
Institute for Research in Biomedicine, IQAC CSIC, CIBER BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 10, Barcelona, Spain
Bioconjug Chem 21:1622-8. 2010..Cell uptake studies allow observation of these fluorescently labeled oligonucleotides internalized into HeLa cells... - Triplex formation using oligonucleotide clamps carrying 8-aminopurinesAnna Aviñó
Instituto de Biologia Molecular de Barcelona, C S I C, Barcelona, Spain
Nucleosides Nucleotides Nucleic Acids 26:979-83. 2007..The stability of triple helices is enhanced by replacing purine bases with 8-aminopurine residues. These enhanced binding properties are used for the specific capture of polypyrimidine RNA/DNA sequences of interest... - Synthesis of oligonucleotide-peptide conjugates carrying the c-myc peptide epitope as recognition systemMiriam Frieden
Department of Structural Biology, , C.S.I.C, Jordi Girona 18-26, E-08034 Barcelona
Chem Biodivers 1:930-8. 2004..Oligonucleotides carrying the c-myc peptide were specifically recognized by the anti-c-myc monoclonal antibody... - Triplex-stabilizing properties of parallel clamps carrying LNA derivatives at the Hoogsteen strandMargarita Alvira
Institute for Research in Biomedicine, IQAC CSIC, CIBER BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Edifici Helix, Baldiri Reixac 15, ES 08028 Barcelona, Spain
Chem Biodivers 7:376-82. 2010..DNA Parallel clamps with a polypurine strand linked to a polypyrimidine Hoogsteen strand containing locked nucleic acids bind their corresponding polypyrimidine targets with high affinity... - Synthesis of labelled PNA oligomers by a post-synthetic modification approachBeatriz G de la Torre
Institut de Biologia Molecular de Barcelona, C.S.I.C, Jordi Girona 18-26, E-08034 Barcelona, Spain
Bioorg Med Chem Lett 13:391-3. 2003..In both cases, the desired fluorescently-labelled PNA oligomer was obtained in good yields...