OFERTA DE CONTRATO PREDOCTORAL

Se ofrece un contrato predoctoral (FPU) por cuatro años para la realización de una tesis doctoral en biología estructural de ácidos nucleicos y sus complejos.

Se busca licenciad@ en Ciencias que haya superado los estudios de máster, con interés en la investigación, y que desee realizar una tesis doctoral altamente interdisciplinar sobre el tema indicado. Se valorará un buen expediente académico, buenas habilidades comunicativas y elevados conocimientos de inglés.

Se ofrece una sólida formación en técnicas de Resonancia Magnética Nuclear (RMN), así como en otras técnicas biofísicas y computacionales, aplicadas al estudio de procesos de reconocimiento molecular de ácidos nucleicos y a su caracterización estructural. El trabajo tendrá lugar en el entorno multidisciplinar del Instituto de Química Física Rocasolano, con amplias posibilidades de realizar estancias de colaboración con grupos internacionales. Las personas interesadas deben ponerse en contacto con el Prof. Carlos González en la dirección cgonzalez@iqfr.csic.es, adjuntando CV, o por teléfono 917459533.

1. DNAs modificados 2. Reconocimiento molecular 3. Estructuras no-canónicas Algunas publicaciones recientes de nuestro grupo (más información en http://rmnac.iqfr.csic.es/):

1. a) N. Martín-Pintado, et al. 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); b) N. Martín-Pintado, et al. Backbone FC-H...O hydrogen bonds in 2´F-substituted nucleic acid, Angewandte Chemie Int Ed, 52, 12065–12068 (2013); c) N. Martín-Pintado, et al The solution structure of double helical arabino-nucleic acids (ANA and 2'F-ANA): Effect of arabinoses in duplex-hairpin interconversion Nucleic Acids Res, 40, 9329-9339 (2012); d) J.K. Watts, et al. Differential Stability of 2'F-ANA•RNA and ANA•RNA Hybrid Duplexes: Roles of Structure, Pseudohydrogen Bonding, Hydration, Ion Uptake, and Flexibility. Nucleic Acids Res 38, 2498-2511 (2010).

2. a) M. Garavís, et al. Discovery of selective ligands for telomeric RNA G-quadruplexes (TERRA) through 19F-NMR based fragment screening ACS Chem Biol, 9, 1559−1566, (2014), b) I. Gómez-Pinto, et al. Carbohydrate-DNA interactions at G-quadruplexes: folding and stability changes by attaching sugars at the 5’-end Chemistry-A Eur J, 19, 1920-1927, (2013); c) E. Vengut-Climent, et al.. Glucose-nucleobase pseudo base pairs as a new binding motif in a DNA context. Angewandte Chemie Int Ed, 128, 8785-8789, (2016).

3. a) H. Abou-Assi, et al. Stabilization of i-Motif Structures by 2'-β-Fluorination of DNA. Nucleic Acids Res., 44, 4998-5009 (2016); b) M. Garavís, et al. Centromeric alpha-satellite DNA adopts dimeric i-motif structures capped by AT Hoogsteen base pairs. Chemistry-A Eur J, 21, 9816-9824 (2015); c) N. Escaja, et al. A minimal i-motif stabilized by minor groove G:T:G:T tetrads Nucleic Acids Res, 40, 11737-11747 (2012).

G

G

G G

GG

G

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a North conformation. No direct experimental evidence for thesugar conformation of C3, C8, and C9 was obtained due tosignal overlap.

Solution structure of HS2

The three-dimensional structure of HS2 was calculated on thebasis of 300 experimental distance constraints by using re-strained molecular dynamics methods, and by following stan-dard procedures used in our group.[23] A summary of the dis-tance constraints is shown in Table S4 and Figure S14 in theSupporting Information. Except for T4 and the correspondingresidue in the symmetry-related sub-unit, all residues are welldefined, with an RMSD of 0.8 ! (Table S4). The final AMBER en-ergies and NOE terms are reasonably low in all the structures,with no average distance constraint violation >0.7 !. Atomiccoordinates of HS2, have been deposited in the PDB (accessionnumber 2MRZ).

The resulting structure is a dimer, consisting of two mole-cules of d(TCCTTTTCCA) arranged head-to-tail (see schematicrepresentation in Figure 4 e). As reflected by the number of sig-nals in the NMR spectra, the dimer is symmetric. The two deca-mers associate with each other by forming four intercalatedhemi-protonated C:C+ base pairs (C2!C8 and C3!C9, and theirsymmetry related counterparts), sandwiched by two intermo-lecular T1:T7 base pairs. The structure is capped by two inter-molecular T6:A10 Hoogsteen base pairs, and the unpaired T5.The base-paired cytidines present the characteristic sugar–sugar contacts between adjacent strands through the minorgroove. The two sides of C:C+ stacks correspond with the cy-tosine located at 3’-end of the C-tracts (3’E type of i-motifstructures[20]). The two T:T base pairs, contiguous to the C:C+

core stack, follow the same pattern of alternate base pair be-tween parallel oriented strands (Figure 4 c). This feature con-firms the ability of thymines to fit into intercalative C:C+ struc-tures.[24] However, the Hoogsteen AT base pairs occur betweenantiparallel oriented strands and do not follow the alternatebase pair motif (Figure 4 d). In spite of this, extensive stackinginteractions occur between T6:A10 and T1:T7 base pairs. Asshown in Figure 4 a, residue T4 and its symmetry related resi-due are mainly disordered.

All glycosidic angles are anti, with values ranging from!1108 to !1508, with the exception of cytosines at the 3’-endof the tracts (C8, C9 and their symmetric counterparts) whichadopt a high anti glycosidic conformation of around !808 to!908. Sugar pucker of T1, C2, C3, and C9 are in the Northdomain, C8 adopts an East conformation, and the remainingresidues are in the general South domain. The dihedral torsionangles are shown in Table S5 in the Supporting Information.

Solution structure of the human A box (HS)

As mentioned above, all the NMR evidence indicate that thestructure of HS1 and HS are very similar to that of HS2. In fact,most signals in HS1 and HS2 spectra are almost identical (seeFigure 3, and Figure S5, S6 and S9 in the Supporting Informa-tion). Only some weak sequential cross-peaks between A10!

C11!C12 were detected in the NOESY spectra of HS1, sug-gesting that C11 and C12 are relatively disordered, and theyare not involved in additional base pairs. Interestingly, the CDmelting experiments show that addition of these two residuesreduces the thermal stability of HS1 vs. HS2 (Figure S2 in theSupporting Information). This is probably due to the presenceof two consecutive cytosines, which are partially charged atpH 4. Although dangling ends are usually stabilizing in duplexstructures, the opposite effect has been observed in nonca-nonical structures.[25]

Figure 4. Dimeric structure of HS2. a) Stereoview of the ensemble of the tencalculated structures. b) Stereoview of the average structure. c) Detail of thestacking interaction between C:C+ and T:T base pairs. d) Detail of the stack-ing interaction between T:T and the capping Hoogsteen A:T base pair.e) Schematic representation of the dimeric structure of HS2. Color code: cy-tosines in the two subunits are shown in blue and cyan, respectively; well-defined thymines and adenines in the two subunits are shown in magentaand green, respectively; no well-defined residues in grey; and backbone inblack. Hydrogen bonds are indicated in yellow

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