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International Review of Biophysical Chemistry (IRe.Bi.C) - June 2011 (Vol. 2 N. 3) - Papers

 

 

          SPECIAL SECTION ON

 

                    "3rd International Meeting on G-Quadruplexes and G-assembly"

                            Sorrento (Italy), June 28th - July 1st, 2011 

 

   

 

 


 

 

 

International Review of Biophysical Chemistry - Papers

 

go to top   Editorial

         by Concetta Giancola, Antonio Randazzo

         Vol. 2, n. 3, pp. 65-67

   


 

go to top   Do anions exert any structural changes on dimeric d(G4T4G4)2 quadruplex in aqueous solution?
         by Primož Šket, Rok Pirh, Janez Plavec

         Vol. 2, n. 2, pp. 68-73

       

Abstract - It is well known that the presence of cations is necessary for G-quartet formation due to their role in reducing repulsions amongst guanine carbonyl oxygen atoms and additionally enhancing base-base stacking interactions. However, not much is known about the influence of anions on G-quadruplex formation by G-rich oligonucleotides in aqueous solution. In the presence of sodium halides, acetate, nitrate and BPh4- folding was almost complete, while only partial folding has been observed with NaBF4 and NaPF6. Detailed evaluation of 1H NMR spectra of d(G4T4G4)2 in the presence of nine different sodium salts indicates minor differences in loop regions as well as in structure of G-quadruplex core. Comparison of inter-proton distances obtained from NOESY spectra showed slightly different orientations of thymine residues in loop regions and changes in stacking interactions between G-quartets, which are most pronounced in the case of G-quadruplex folded in the presence of NaPF6.

Copyright © 2011 Praise Worthy Prize S.r.l. - All rights reserved

 

Keywords: Quadruplex, Cations, Anions, NMR Spectroscopy.

 


 

go to top  Preparation and AFM-Characterization of Self-Assembled Monolayers Functionalized with a Thrombin Binding Aptamer
         by Brendan Manning, Isaac Gállego, María Tintoré, Mª Carme Fàbrega, Anna Aviñó, Ramon Eritja

         Vol. 2, n. 2, pp. 74-77

       

Abstract - Self-assembled monolayers on silicon oxide surfaces functionalized with a unimolecular DNA G-quadruplex derived from the thrombin binding aptamer have been prepared. The formation of the G-quadruplex in the presence of potassium ions is observed by atomic force microscopy (AFM). The results presented here are interesting for the fabrication of nanostructured systems for sensing applications.

Copyright © 2011 Praise Worthy Prize S.r.l. - All rights reserved

 

Keywords: G-Quadruplex, Self-Assembled Monolayers, DNA, Thrombin Binding Aptamer, AFM.

 


 

go to top   Template Assembled Synthetic G-Quadruplex: A Novel Biomolecular System for Investigating the Interactions of Ligands with Constrained Quadruplex Conformation
         by R. Bonnet, P. Murat, N. Spinelli, A. Van Der Heyden, P. Labbé, P. Dumy, E. Defrancq

         Vol. 2, n. 2, pp. 78-81

      

Abstract - We report on the design of a new biomolecular device based on the concept of Template Assembled Synthetic G-Quadruplex (TASQ), where quadruplex DNA structures are assembled on a scaffold for constraining G-quadruplex conformation. As a proof of concept, parallel-stranded conformation of G-quadruplex was prepared by using a cyclodecapeptide as the template. As anticipated the use of the scaffold allows the precise control of the conformation of the quadruplex and increases dramatically the stability of the motif. This device was used for investigating by Surface Plasmon Resonance the affinity of ligands for G-quadruplex DNA.

Copyright © 2011 Praise Worthy Prize S.r.l. - All rights reserved

 

Keywords: Click-Chemistry, G-Quadruplex, Surface Plasmon Resonance, Template.

 


 

go to top   Density Functional Study of the Structure of Guanine Octets in Aqueous Medium
         by Mykola M. Ilchenko, Igor Ya. Dubey

         Vol. 2, n. 2, pp. 82-86

       

Abstract - The structures and energies of guanine quartets and octets in water were determined by DFT (Density Functional Theory) calculations using M06-2X functional and 6-31G(d, p) basic set. Guanine quartets in vacuum were found to have not only the Hoogsteen or bifurcated, but also mixed system of hydrogen bonds; in water the latter two forms are transformed into the classic Hoogsteen-type structure. Four stable configurations of G-octets with D4, C4 and S4 symmetry formed by the pairs of guanine quartets with Hoogsteen, bifurcated or mixed system of H-bonds were identified. The most advantageous structure of the G-octet molecular system in aqueous medium was shown to be S4-symmetric structure consisting of the pair of mixed Hoogsteen-bifurcated type G-quartets.

Copyright © 2011 Praise Worthy Prize S.r.l. - All rights reserved

 

Keywords: DFT, G-Octets, G-Quartets, Guanine, H-Bonds.

 


 

go to top   Switching between Supramolecular Assemblies of Lipophilic Guanosine Derivatives Triggered by External Stimuli
         by Stefano Masiero, Lucia Gramigna, Paolo Neviani, Rosaria C. Perone, Silvia Pieraccini, Gian Piero Spada

         Vol. 2, n. 2, pp. 87-95
       

Abstract - Depending on the experimental conditions, lipophilic guanosines (LipoGs) can undergo different self-assembly pathways based on different H-bonded motifs, e.g. the cyclic discrete G-quartet and the “infinite” tape-like G-ribbon. The switching between different supramolecular motifs have been obtained by a variety of external stimuli. After a general presentation of the LipoG self-assembly, in this mini-review we will discuss, the case of three different stimuli. A first example is represented by chemical stimuli: addition of an alkali metal ion stabilizes the G-quartet while its removal shifts the equilibrium toward the G-ribbon. In the second case, a lipoG armed with a terthiophene unit undergoes a pronounced variation of its supramolecular organisation by changing the polarity of the solvent: in chloroform the derivative assembles via H-bonding in a guanosine driven structure, while in the more polar (and H-bond competing) acetonitrile different aggregates are observed, where the terthiophene chains are π-π stacked in a helicoidal arrangement. Finally, a third type of stimulus is represented by light: the photocontrolled self-assembly of a modified guanosine nucleobase with a photoactive unit at C8 is obtained selecting the appropriate wavelength.

Copyright © 2011 Praise Worthy Prize S.r.l. - All rights reserved

 

Keywords: Guanosine, G-Quartet, Self-Assembly, Supramolecular Chemistry, Switch.

 


 

go to top   PNA oligomers as tools for targeting G-quadruplex structures
         by Jussara Amato

         Vol. 2, n. 2, pp. 96-101
       

Abstract - G-quadruplex-forming sequences (QFS) are widely distributed in the human genome, including chromosomal telomeres and regulatory regions of oncogenes, and are involved in a variety of biological contexts. Molecular probes that selectively target QFS have been investigated to delineate their biological role and to identify potential therapeutic agents. Peptide nucleic acids (PNAs) targeting to QFS can be designed using two different approaches. In the first, complementary cytosine-rich PNAs can hybridize to the target QFS by forming PNA:DNA or PNA:RNA hybrid duplexes. In the second, guanine-rich PNAs can hybridize to the homologous DNA or RNA target by forming the corresponding heteroquadruplexes. This review discusses the principles and the recent improvements of the complementary and homologous hybridization modes of PNA oligomers.

Copyright © 2011 Praise Worthy Prize S.r.l. - All rights reserved

 

Keywords: G-Quadruplex, Peptide Nucleic Acid (PNA), Hybridization.

 


 

go to top   Structural and Functional Characterization of Thrombin Binding Aptamer Minor Loop
         by Giuseppe Marson, Manlio Palumbo, Claudia Sissi

         Vol. 2, n. 2, pp. 102-104
       

Abstract - The thrombin binding aptamer (29hTBA), identified with a SELEX approach, shows a significant affinity for the coagulation factor thrombin by recognizing the protein Exosite II (heparin binding site). The structure of 29hTBA consists of a G-quadruplex core flanked by two partially paired terminal strands. Literature data underline that the structure and stability of intramolecular G-quadruplexes can be profoundly influenced by the length and composition of the loops. Here, we investigated the role of the minor loop (10-11) composition by introducing a single A-T mutation at position 11. A comparative structural investigation of the wild type and the mutant aptamers evidenced that this loop is not largely impairing the folding of the G-quadruplex core. Additionally, thrombin binding analysis suggested that this loop is not directly involved in protein binding at exosite II.

Copyright © 2011 Praise Worthy Prize S.r.l. - All rights reserved

 

Keywords: Thrombin, Aptamer, G-quadruplex.


 
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