Modified nucleic acids are very interesting molecules because of their application in Biomedicine, as therapeutic agents, and in Nanoscience, as potential components of nano-devices. Of particular relevance is the substitution of a hydrogen atom at the 2’ position of the DNA deoxyribose by fluorine. Fluorine is the most electronegative element and alters the electronic distribution in its surroundings, provoking interactions that are not present, or are much weaker, in natural nucleic acids.

In two recent papers researchers of the IQFR, in collaboration with colleagues of McGill University in Canada and in the IRB in Barcelona, have described these effects at structural level and analysed their physico-chemical basis in double helical and guanine quadruplex structures.



N. Martín-Pintado, M. Yahyaee-Anzahaee, G. F. Deleavey, G. Portella, M. Orozco, M.J. Damha, and C. González.Dramatic effect of furanose C2´-substitution on structure and stability:  Directing the folding of the human telomeric quadruplex with a single fluorine atom.J. Am. Chem. Soc., 135, 5344-5347, 2013.doi: 10.1021/ja401954t

N. Martín-Pintado, G. F. Deleavey, G. Portella, R. Campos-Olivas, M. Orozco, M.J. Damha, and C. González.Backbone FC-H...O hydrogen bonds in 2´F-substituted nucleic acids.Angewandte Chemie Int Ed, en prensa, 2013.doi:10.1002/anie.201305710




Scientists from the Department of Biophysical Chemistry discovered novel water-soluble oxocines and azocines that produce blue fluorescence with 100% quantum yield. These molecules are the main product of a new fluorogenic reaction that converts non-emitting biocompounds as L-DOPA, dopamine, hydroxytyrosol, etc. into useful photostable fluorophores. The new molecular structures contain the rare four-ring chromophore which originated the first written account of fluorescence emission in 1565 (Acuña et al. Org. Lett. 2009, 11, 3020). At that time, the medical doctor N. Monardes from Sevilla reported the unusual blue “color” (fluorescence) of the infusion of a medicinal wood widely used in preHispanic Aztec culture.



Synthesis and photophysics of novel biocompatible fluorescent oxocines and azocines in aqueous solution.

A.Ulises Acuña, Mónica Älvarez-Pérez, Marta Liras, Pedro B. Coto and Francisco Amat-Guerri.

Phys. Chem. Chem. Phys. Sept. 2013 (DOI: 10:1039/c3cp52228h)


nap2pNab2p is an essential protein involved in mRNP (messenger ribonucleoprotein particles) formation and export in Saccharomyces cerevisiae. Its specific poly(A) RNA recognition ability resides on a region containing 7 CCCH-type zinc finger domains, of which, the last three zinc finger structure was previously known. In our group, we have solved the NMR structure of the first 4 zinc fingers that show novel elements in their fold. The first two zinc fingers (Zf1 and Zf2) form a compact tandem stabilized by a new -helix contacting both. Zf3 and Zf4 form a second tandem in which the metallic centres associate in a singular symmetric way with mutual recognition of the Zn2+ coordinating histidines. NMR, fluorescence anisotropy and mutagenesis studies identify the -helix in the first tandem and the exposed surface of Zf3 as the RNA binding interface. Our results allow us to propose a recognition model where Nab2p Zf1-4 cooperates with Nab2p Zf5-7 to reconstitute the poly(A) binding profile of the full-length protein.



Two Singular Types of CCCH Tandem Zinc Finger in Nab2p Contribute to Polyadenosine RNA Recognition.

Martínez-Lumbreras S1,3, Santiveri CM2,3, Mirassou Y1, Zorrilla S1,2, Pérez-Cañadillas JM1*.

Structure. 2013 Aug 28. doi: 10.1016/j.str.2013.07.019.

1 IQFR-CSIC; 2 CIB-CSIC; 3 equal contribution;*corresponding author


Figure-4A small

Bacterial cell wall is a polymer of considerable complexity that is in constant equilibrium between synthesis and recycling. AmpDh3 is a periplasmic zinc protease of Pseudomonas aeruginosa, which is intimately involved in cell-wall remodeling. In this report we document the reactions that this enzyme performs on the cell wall, which hydrolyze the peptide stems from the peptidoglycan, the major constituent of the cell wall. We document that the majority of the reactions of this enzyme takes place on the polymeric insoluble portion of the cell wall, as opposed to the fraction that is released from it. We show that AmpDh3 is tetrameric both in crystals and in solution. Based on the X-ray structures of the enzyme in complex with two synthetic cell-wall-based ligands, we present for the first time a model for a multivalent anchoring of AmpDh3 onto the cell wall, which lends itself to its processive remodeling.




Lee, M.; Artola-Recolons, C.; Carrasco-López, C.; Martínez-Caballero, S.; Hesek, D.; Spink, E.; Lastochkin, E.; Zhang, W.; Hellman, L.; Boggess, B.; Hermoso*, J.; Mobashery*, S.

      Cell-Wall Remodeling by the Zinc-Protease AmpDh3 from Pseudomonas aeruginosa

      J. Am. Chem. Soc. 2013; 12605-12607.


ampdh2-verybigThe zinc protease AmpDh2 is a virulence determinant of Pseudomonas aeruginosa, a problematic human pathogen. The mechanism of how the protease manifests virulence is not known, but it is known that it turns over the bacterial cell wall. A research conducted by the Instituto de Química-Física Rocasolano and the University of Notre Dame (Indiana, USA) provided insights into the mechanism of action of AmpDh2. The reaction of AmpDh2 with the cell wall was investigated and nine distinct turnover products were characterized by LC/MS/MS. The enzyme turns over both the crosslinked and non-crosslinked cell wall. Three high-resolution X-ray structures, of the apo enzyme and of two complexes with turnover products, were solved. The X-ray structures show how the dimeric protein interacts with the inner leaflet of the bacterial outer membrane and that the two monomers provide a more expansive surface for recognition of the cell wall. This binding surface can accommodate the three-dimensional solution structure of the crosslinked cell wall. We have disclosed in this report the nature of the reactions of AmpDh2 with the bacterial sacculus and have determined the structure of the protein, which reveals the importance of the dimeric nature in accommodating larger segments of the cell wall. The present study reveals at atomic detail the structural attributes of this important virulence factor of P. areruginosa in the reactions that it performs, which are at the roots of the manifestation of the virulence.


Siseth Martínez-Caballero, Mijoon Lee, Cecilia Artola-Recolons, César Carrasco-López, Dusan Hesek, Edward Spink, Elena Lastochkin, Weilie Zhang, Lance M. Hellman, Bill Boggess, Shahriar Mobashery* and Juan A. Hermoso*

Reaction products and the X-ray structure of AmpDh2, a virulence determinant of Pseudomonas aeruginosa.

Journal of the American Chemical Society (2013) 135, - (in press)  (doi:10.1021/ja405464b)