Publications

Here you will find some selected publications about the study of conformational equilibria of nucleic acids by means of spectroscopic and chemometric techniques. Most recent articles describe the solution equilibria of several G-quadruplex and i-motif-forming DNA sequences. Previous research was mainly focused on the equilibria involving homopolynucleotides like poly(C), poly(I) or poly(U) acids, and mixtures of them.

Concomitantly to the study of solution equilibria of DNAs, effort has been also focused on the development of chemometric methods. We would like to remark the application of Multivariate Curve Resolution to the analysis of DNA microarray data.

Reviews

Experimental methods to study the interaction of G-quadruplex structures with ligands. Jaumot, J.; Gargallo, R. Current Pharm. Design. 2012, in press

Application of multivariate resolution methods to the study of Biochemical and Biophysical processes, Jaumot, J.; Vives, M.; Gargallo, R., Anal. Biochem., 2004, 327, 1 - 13

Solution equilibria of DNA

Combination of chromatographic and chemometric methods to study the interactions between DNA strands. Ruiz, S.; Checa, A.; Gargallo, R.; Jaumot, J. Anal. Chim. Acta, 2012, in press

Influence of pH, temperature and cationic porphyrin TMPyP4 on the stability of the i-motif formed by the 5'-(C3TA2)4-3' sequence of the human telomere. Fernández, S.; Jaumot, J.; Aviñó, A.; Eritja, R.; Gargallo, R. International Journal of Biological Macromolecules'2011, 49, 729-736

Chemical equilibria studies using multivariate analysis methods. Jaumot, J.; Eritja, R.; Gargallo, R. Anal. Bioanal. Chem. 2011, 399, 1983-1997

Spectrometric study of the folding process of i-motif-forming DNA sequences upstream of the c-kit transcription initiation site. Bucek, P.; Gargallo, R.; Kudrev, A. Anal. Chim. Acta, 2010, 683, 69-77

Synthesis and G-quadruplex binding properties of defined acridine oligomers. Ferreira, R.; Aviñó, A.; Pérez-Tomás, R.; Gargallo, R.; Eritja, R. Journal of Nucleic Acids, 2010, article ID 489060, doi:10.4061/2010/489060

Spectrometric study of the oligodeoxyribonucleotide protonation in aqueous solution. Gargallo, R.; Eritja, R.; Kudrev, A. Russian Journal of General Chemistry 2010, 3, 485. DOI: 10.1134/S1070363210030205

Structural properties of G,T-parallel duplexes carrying 8-aminopurine residues. Aviñó, A.; Cubero, E.; Gargallo, R.; González, C.; Orozco, M.; Eritja, R. Journal of Nucleic Acids, 2010, Article ID 763658, doi:10.4061/2010/763658

pH-modulated Watson-Crick duplex - quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 bp upstream of the c-kit transcription initiation site. Bucek, P.; Jaumot, J.; Aviñó, A.; Eritja, R.; Gargallo, R. Chemistry - A European Journal, 2009, 15, 12663-12671

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 strand. del Toro, M.; Bucek, P.; Aviñó, A.; Jaumot, J.; González, C.; Eritja, R.; Gargallo, R. Biochimie 2009, 91, 894-902

Study of the interaction between the G-quadruplex-forming Thrombin Binding Aptamer and the porphyrin TmPyP4. del Toro, M.; Gargallo, R.; Eritja, R.; Jaumot, J. Anal. Biochem. 2008, 379, 8 - 15

Triplex formation using oligonucleotide clamps carrying 8-aminopurines. Aviñó, A.; Grimau, M.G.; Alvira, M.; Eritja, R.; Gargallo, R.; Orozco, M.; González, C. Nucleosides, Nucleotides, and Nucleic Acids 2007, 26, 979 - 983

Solution Equilibria of the i-motif-forming Region Upstream of the B-Cell Lymphoma-2 P1 Promoter. Khan N.; Aviñó, A.; Tauler, R.; González, C.; Eritja, R.; Gargallo, R. Biochimie 2007, 89, 1562 - 1572

Spectroscopic study of the interaction of actinomycin D with oligonucleotides carrying the central base sequences -XGCY- and -XGGCCY- using multivariate methods.  Vives, M.; Tauler, R.; Eritja, R.; Gargallo, R. Analytical and Bioanalytical Chemistry 2007, 387, 311-320

Resolution of a structural competition involving dimeric G-quadruplex and its C-rich complementary strand. Jaumot, J.; Eritja, R.; Tauler, R.; Gargallo, R. Nucleic Acids Research 2006, 34, 206 - 216

Tetraplex DNA Transitions within the human c-myc promoter detected by Multivariate Curve Resolution of Fluorescence Resonance Energy Transfer. Kumar, P.; Verma, A.; Maiti, S.; Gargallo, R.; Chowdhury, S. Biochemistry, 2005, 44, 16426 - 16434

Application of multivariate curve resolution for the study of folding processes of DNA monitored by Fluorescence Resonance Energy Transfer. Kumar, P.; Kanchan, K.; Gargallo, R.; Chowdhury, S. Anal. Chim. Acta 2005, 536, 135 - 143

Synthesis and Triplex-Forming Properties of Cyclic Oligonucleotides with G,A-Antiparallel Strands, Grimau, M.G.; Aviñó, A.; Gargallo, R.; Eritja, R. Chemisty and Biodiversity 2005, 2, 275 - 285

Synthesis, Stability and Protonation studies of a self-complementary dodecamer containing the modified nucleoside 2'-deoxyzebularine, Vives, M.; Eritja, R.; Tauler, R.; Márquez, V.E.; Gargallo, R. Biopolymers 2004, 73, 27 - 43

Resolution of Parallel and Antiparallel Oligonucleotide triple helices formation and melting processes by Multivariate Curve Resolution, Jaumot, J.; Aviñó, A.; Eritja, R.; Tauler, R.; Gargallo, R. Journal of Biomolecular Structure & Dynamics 2003, 21, 267 - 278

Multivariate Curve Resolution: a powerful tool for the analysis of conformational transitions in nucleic acids. Jaumot, J.; Escaja, N.; Gargallo, R.; Pedroso, E..; Tauler, R., Nucleic Acids Research 2002, 30(17), e92

Study of the influence of metal ions on tRNAPhe thermal unfolding equilibria by UV spectroscopy and multivariate curve resolution Gargallo, R.; Vives, M.; Tauler, R., J. Inorg. Biochem., 2002, 89, 115 - 122

Study of the interaction of cis dichloro-(1,2 diethyl-3 aminopyrrolidine)Pt(II) complex with poly(I), poly(C) and poly(I)•poly(C). Vives, M.; Gargallo, R.; Tauler, R.; Moreno, V. J. Inorg. Biochem.2001, 85, 279 - 290

Protonation studies and Multivariate Curve Resolution on oligodeoxynucleotides carrying the mutagenic base 2-aminopurine. Gargallo,R.; Vives, M.; Tauler, R.; Eritja, R., Biophys. J., 2001, 81, 2886 - 2896

Study of the intercalation equilibria between the polynucleotide poly(adenylic)-poly(uridylic)acid and the ethidium bromide dye by means of Multivariate Curve Resolution and the multivariate extension of the continuous variation and mole-ratio methods. Vives, M.; Gargallo, R.; Tauler, R. Anal. Chem., 1999, 71, 4328 - 4337

Study of the acid-base and copper(II) complexation equilibria of poly(inosinic) -poly(cytidylic) acid. Gargallo, R.; Tauler, R.; Izquierdo-Ridorsa, A. Biopolymers, 1997, 42, 271 - 283

Application of a soft modeling curve resolution method to the study of the melting behavior of synthetic and natural polynucleotides. Gargallo, R.; Tauler, R.; Izquierdo-Ridorsa, A. Anal. Chem., 1997, 69, 1785 - 1792

 

Development and application of Chemometric tools to study complex systems in Chemistry and Biophysics

Using Principal Component Analysis to find hidden correlations between loop-related and thermodynamic variables for G-quadruplex-forming sequences. Jaumot, J.; Gargallo, R. Biochimie 2010, 92, 1016-1023

Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra. Jaumot, J.; Eritja, R.; Navea, S. Gargallo, R. Anal. Chim. Acta 2009, 642, 117-126

Exploratory data analysis of DNA microarrays by multivariate curve resolution. Jaumot, J.; Tauler, R.; Gargallo, R. Anal. Biochem. 2006, 358, 76 - 89

A user friendly interface for MCR-ALS: a new tool for Multivariate Curve Resolution in MATLAB. Jaumot, J.; Gargallo, R.; de Juan, A.; Tauler, R. Chemom. Intel. Lab. Syst. 2005, 76, 101 - 110

Multivariate Curve Resolution applied to the analysis and resolution of two - dimensional [1H, 15N]-NMR reaction spectra. Jaumot, J.; Marchán, V.; Gargallo, R.; Grandas, A.; Tauler, R. Anal. Chem., 2004, 76, 7094 - 7101

Validation of the alternating least squares multivariate curve resolution for the chromatographic resolution and quantitation. Gargallo, R.; Cuesta-Sánchez, F.; Massart, D.L.; Tauler, R. Trends in Anal. Chem., 1996, 15, 279

Application of Eigenstructure Tracking Analysis and SIMPLISMA to the study of the protonation equilibria of cCMP and several polynucleotides. Gargallo, R.; Cuesta-Sánchez, F.; Izquierdo-Ridorsa, A.; Massart,D.L. Anal. Chem. 1996,68, 2241