Biblio

Ab initio study of naphtho-homologated DNA bases., Vazquez-Mayagoita, Alvaro, Huertas Oscar, Fuentes-Cabrera Miguel, Sumpter Bobby G., Orozco Modesto, and F Luque Javier , J Phys Chem B, 2008 Feb 21, Volume 112, p.2179-86, (2008)

Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives., Aviñó, Anna, Cubero Elena, González Carlos, Eritja Ramon, and Orozco Modesto , J Am Chem Soc, 2003 Dec 24, Volume 125, p.16127-38, (2003)

Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study., Pérez, Alberto, Sponer Jiri, Jurecka Petr, Hobza Pavel, F Luque Javier, and Orozco Modesto , Chemistry, 2005 Aug 19, Volume 11, p.5062-6, (2005)

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale., Islam, Barira, Sgobba Miriam, Laughton Charlie, Orozco Modesto, Sponer Jiri, Neidle Stephen, and Haider Shozeb , Nucleic Acids Res, 2013 Feb 1, Volume 41, p.2723-35, (2013)

Data mining of molecular dynamics trajectories of nucleic acids., Noy, Agnes, Meyer Tim, Rueda Manuel, Ferrer Carles, Valencia Antonion, Pérez Alberto, de la Cruz Xavier, López-Bes J M., Pouplana R, Fernandez-Recio J, et al. , J Biomol Struct Dyn, 2006 Feb, Volume 23, p.447-56, (2006)

Destabilization of quadruplex DNA by 8-aminoguanine., de la Osa, Jaime Lopez, González Carlos, Gargallo Raimundo, Rueda Manuel, Cubero Elena, Orozco Modesto, Aviñó Anna, and Eritja Ramon , Chembiochem, 2006 Jan, Volume 7, p.46-8, (2006)

Determining promoter location based on DNA structure first-principles calculations., J Goñi, Ramon, Pérez Alberto, Torrents David, and Orozco Modesto , Genome Biol, 2007, Volume 8, p.R263, (2007)

Direct measurement of the dielectric polarization properties of DNA., Cuervo, Ana, Dans Pablo D., Carrascosa José L., Orozco Modesto, Gomila Gabriel, and Fumagalli Laura , Proc Natl Acad Sci U S A, 2014 Sep 2, Volume 111, p.E3624-30, (2014)

DNAlive: a tool for the physical analysis of DNA at the genomic scale., J Goñi, Ramon, Fenollosa Carlos, Pérez Alberto, Torrents David, and Orozco Modesto , Bioinformatics, 2008 Aug 1, Volume 24, p.1731-2, (2008)

Dramatic effect of furanose C2’ substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom., Martín-Pintado, Nerea, Yahyaee-Anzahaee Maryam, Deleavey Glen F., Portella Guillem, Orozco Modesto, Damha Masad J., and González Carlos , J Am Chem Soc, 2013 Apr 10, Volume 135, p.5344-7, (2013)

Dynamics of B-DNA on the microsecond time scale., Pérez, Alberto, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2007 Nov 28, Volume 129, p.14739-45, (2007)

Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct., Gómez-Pinto, Irene, Cubero Elena, Kalko Susana G., Monaco Vania, van der Marel Gijs, van Boom Jacques H., Orozco Modesto, and González Carlos , J Biol Chem, 2004 Jun 4, Volume 279, p.24552-60, (2004)

Effects of local electric fields on the redox free energy of single stranded DNA., D’Abramo, Marco, Orozco Modesto, and Amadei Andrea , Chem Commun (Camb), 2011 Mar 7, Volume 47, p.2646-8, (2011)

Exploring polymorphisms in B-DNA helical conformations., Dans, Pablo D., Pérez Alberto, Faustino Ignacio, Lavery Richard, and Orozco Modesto , Nucleic Acids Res, 2012 Nov, Volume 40, p.10668-78, (2012)

Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?, Rueda, Manuel, Cubero Elena, Laughton Charles A., and Orozco Modesto , Biophys J, 2004 Aug, Volume 87, p.800-11, (2004)

Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions., J Goñi, Ramon, Vaquerizas Juan Manuel, Dopazo Joaquin, and Orozco Modesto , BMC Genomics, 2006, Volume 7, p.63, (2006)

Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad., Escaja, Núria, Gelpí Josep-Lluis, Orozco Modesto, Rico Manuel, Pedroso Enrique, and González Carlos , J Am Chem Soc, 2003 May 14, Volume 125, p.5654-62, (2003)

Frontiers in molecular dynamics simulations of DNA., Pérez, Alberto, F Luque Javier, and Orozco Modesto , Acc Chem Res, 2012 Feb 21, Volume 45, p.196-205, (2012)

Functionalization of the 3’-ends of DNA and RNA strands with N-ethyl-N-coupled nucleosides: a promising approach to avoid 3’-exonuclease-catalyzed hydrolysis of therapeutic oligonucleotides., Terrazas, Montserrat, Alagia Adele, Faustino Ignacio, Orozco Modesto, and Eritja Ramon , Chembiochem, 2013 Mar 4, Volume 14, p.510-20, (2013)

Fuzziness and noise in nucleosomal architecture., Flores, Oscar, Deniz Ozgen, Soler-López Montserrat, and Orozco Modesto , Nucleic Acids Res, 2014 Apr, Volume 42, p.4934-46, (2014)

G-quadruplexes can maintain their structure in the gas phase., Rueda, Manuel, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2006 Mar 22, Volume 128, p.3608-19, (2006)

Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling., Nadal-Ribelles, Mariona, Conde Núria, Flores Oscar, González-Vallinas Juan, Eyras Eduardo, Orozco Modesto, de Nadal Eulàlia, and Posas Francesc , Genome Biol, 2012, Volume 13, p.R106, (2012)

Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives., Cubero, Elena, Aviñó Anna, de la Torre Beatriz G., Frieden Miriam, Eritja Ramon, F Luque Javier, González Carlos, and Orozco Modesto , J Am Chem Soc, 2002 Mar 27, Volume 124, p.3133-42, (2002)

Hydrophobic similarity between molecules: a MST-based hydrophobic similarity index., Muñoz, J, Barril X, Hernández B, Orozco Modesto, and F Luque Javier , J Comput Chem, 2002 Apr 15, Volume 23, p.554-63, (2002)

Impact of methylation on the physical properties of DNA., Pérez, Alberto, Castellazzi Chiara Lara, Battistini Federica, Collinet Kathryn, Flores Oscar, Deniz Ozgen, Ruiz Maria Luz, Torrents David, Eritja Ramon, Soler-López Montserrat, et al. , Biophys J, 2012 May 2, Volume 102, p.2140-8, (2012)

The impact of monovalent ion force field model in nucleic acids simulations., Noy, Agnes, Soteras Ignacio, F Luque Javier, and Orozco Modesto , Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10596-607, (2009)

The (in)dependence of alternative splicing and gene duplication., Talavera, David, Vogel Christine, Orozco Modesto, Teichmann Sarah A., and de la Cruz Xavier , PLoS Comput Biol, 2007 Mar 2, Volume 3, p.e33, (2007)

MD and NMR analyses of choline and TMA binding to duplex DNA: on the origins of aberrant sequence-dependent stability by alkyl cations in aqueous and water-free solvents., Portella, Guillem, Germann Markus W., Hud Nicholas V., and Orozco Modesto , J Am Chem Soc, 2014 Feb 26, Volume 136, p.3075-86, (2014)

Multiple routes to characterize the folding of a small DNA hairpin., Portella, Guillem, and Orozco Modesto , Angew Chem Int Ed Engl, 2010 Oct 11, Volume 49, p.7673-6, (2010)

NAFlex: a web server for the study of nucleic acid flexibility., Hospital, Adam, Faustino Ignacio, Collepardo-Guevara Rosana, González Carlos, Gelpí Josep-Lluis, and Orozco Modesto , Nucleic Acids Res, 2013 Jul, Volume 41, p.W47-55, (2013)

Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps., Sponer, Jiri, Jurecka Petr, Marchán Ivan, F Luque Javier, Orozco Modesto, and Hobza Pavel , Chemistry, 2006 Mar 20, Volume 12, p.2854-65, (2006)

On the nature of DNA hyperchromic effect., D’Abramo, Marco, Castellazzi Chiara Lara, Orozco Modesto, and Amadei Andrea , J Phys Chem B, 2013 Jul 25, Volume 117, p.8697-704, (2013)

Nature of minor-groove binders-DNA complexes in the gas phase., Rueda, Manuel, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2005 Aug 24, Volume 127, p.11690-8, (2005)

Non-coding recurrent mutations in chronic lymphocytic leukaemia., Puente, Xose S., Beà Sílvia, Valdés-Mas Rafael, Villamor Neus, Gutiérrez-Abril Jesús, Martín-Subero José I., Munar Marta, Rubio-Pérez Carlota, Jares Pedro, Aymerich Marta, et al. , Nature, 2015 Oct 22, Volume 526, p.519-24, (2015)

Nucleic acid simulations themed issue., Laughton, Charles A., and Orozco Modesto , Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10541-2, (2009)

Parmbsc1: a refined force field for DNA simulations., Ivani, Ivan, Dans Pablo D., Noy Agnes, Pérez Alberto, Faustino Ignacio, Hospital Adam, Walther Jurgen, Andrio Pau, Goni Ramon, Balaceanu Alexandra, et al. , Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast., Deniz, Ozgen, Flores Oscar, Battistini Federica, Pérez Alberto, Soler-López Montserrat, and Orozco Modesto , BMC Genomics, 2011, Volume 12, p.489, (2011)

Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines., Aviñó, Anna, Frieden Miriam, Morales Juan Carlos, de la Torre Beatriz García, García Ramón Güimil, Azorín Ferran, Gelpí Josep-Lluis, Orozco Modesto, González Carlos, and Eritja Ramon , Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)

Real-time atomistic description of DNA unfolding., Pérez, Alberto, and Orozco Modesto , Angew Chem Int Ed Engl, 2010 Jun 28, Volume 49, p.4805-8, (2010)

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers., Pérez, Alberto, Marchán Ivan, Svozil Daniel, Sponer Jiri, Cheatham Thomas E., Laughton Charles A., and Orozco Modesto , Biophys J, 2007 Jun 1, Volume 92, p.3817-29, (2007)

The relative flexibility of B-DNA and A-RNA duplexes: database analysis., Pérez, Alberto, Noy Agnes, Lankaš Filip, F Luque Javier, and Orozco Modesto , Nucleic Acids Res, 2004, Volume 32, p.6144-51, (2004)

Relative flexibility of DNA and RNA: a molecular dynamics study., Noy, Agnes, Pérez Alberto, Lankaš Filip, F Luque Javier, and Orozco Modesto , J Mol Biol, 2004 Oct 22, Volume 343, p.627-38, (2004)

Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases., Blas, José Ramón, Huertas Oscar, Tabares Carolina, Sumpter Bobby G., Fuentes-Cabrera Miguel, Orozco Modesto, Ordejón Pablo, and F Luque Javier , J Phys Chem A, 2011 Oct 20, Volume 115, p.11344-54, (2011)

The structural impact of DNA mismatches., Rossetti, Giulia, Dans Pablo D., Gómez-Pinto Irene, Ivani Ivan, González Carlos, and Orozco Modesto , Nucleic Acids Res, 2015 Apr 30, Volume 43, p.4309-21, (2015)

The structure and dynamics of DNA in the gas phase., Rueda, Manuel, Kalko Susana G., F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2003 Jul 2, Volume 125, p.8007-14, (2003)

Structure and Dynamics of Oligonucleotides in the Gas Phase, Arcella, Annalisa, Dreyer Jens, Ippoliti Emiliano, Ivani Ivan, Portella Guillem, Gabelica Valérie, Carloni Paolo, and Orozco Modesto , Angewandte Chemie International Edition, 01/2015, Volume 54, p.467–471, (2015)

Structure and properties of DNA in apolar solvents, Arcella, Annalisa, Portella Guillem, Collepardo-Guevara Rosana, Chakraborty Debayan, Wales David J., and Orozco Modesto , J Phys Chem B, 2014 Jul 24, Volume 118, p.8540-8, (2014)

The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane., Fort, Joana, de la Ballina Laura R., Burghardt Hans E., Ferrer-Costa Carles, Turnay Javier, Ferrer-Orta Cristina, Usón Isabel, Zorzano Antonio, Fernandez-Recio Juan, Orozco Modesto, et al. , J Biol Chem, 2007 Oct 26, Volume 282, p.31444-52, (2007)

Structure of triplex DNA in the gas phase., Arcella, Annalisa, Portella Guillem, Ruiz Maria Luz, Eritja Ramon, Vilaseca Marta, Gabelica Valérie, and Orozco Modesto , J Am Chem Soc, 2012 Apr 18, Volume 134, p.6596-606, (2012)

Structure, recognition properties, and flexibility of the DNA.RNA hybrid., Noy, Agnes, Pérez Alberto, Márquez Manuel, F Luque Javier, and Orozco Modesto , J Am Chem Soc, 2005 Apr 6, Volume 127, p.4910-20, (2005)