1,720,964 research outputs found
A further contribution to the extreme variability of quadruplex structures from oligodeoxyribonucleotides containing inversion of polarity sites in the G-tract
No full textStructural insight into DNA quadruplex structures formed by oligodeoxyribonucleotides 3'TG5'-5'GGGT3' (QS55) and 5'TG3'-3'GGGT5' (QS33) is presented. NMR anal. reveals that QS33 forms a parallel-like four-fold sym. quadruplex, while QS55 possesses a two-fold symmetry and is characterized by a tetrameric antiparallel quadruplex embedded between two parallel tracts. The results reported here describe unprecedented quadruplex complexes provided by peculiar structural features never reported to date. These structures might inspire the design of new aptameric nucleic acids characterized by novel structural motifs hardly realizable with unmodified DNA/RN
Effect of rubidium and cesium ions on the dimeric quaduplex formed by the Oxytricha nova telomeric repeat oligonucleotide d(GGGGTTTTGGGG)
No full textThe DNA sequence d(GGGGTTTTGGGG) consists of 1.5 units of the repeat in telomeres of Oxytricha nova. It has been shown by NMR and x-ray crystallographic analysis that it is capable to form a dimeric quadruplex structure and that a variety of cations, namety K+, Na+, and NH4+, are able to interact with this complex with different affinity, leading to complexes characterized by different local conformations. Thus, in order to improve the knowledge of this kind of molecule, and in particular to Providejurther insight into the role of monovalent cations in the G-quadruplex folding and conformation, we have investigated by H-1-NMR the effect of the addition of Rb+ and Cs+ to the quadruplex formed by the oligonucleotide d(GGGGTTTTGGGG)
A MINI-LIBRARY OF TBA ANALOGUES CONTAINING 3'-3' AND 5'-5' INVERSION OF POLARITY SITES
No full textSeveral researches have been devoted to structure-activity relationship and to post-SELEX modifications of the thrombin binding aptamer (TBA), one of the first aptamers discovered by the SELEX methodol. However, no studies on TBA dealing with the effects of introduction of inversion of polarity sites have been reported yet. In this frame, we have undertaken the synthesis and the study of a mini-library composed of several TBA analogs contg. a 3'-3' or a 5'-5' inversion of polarity site at different positions into the sequence. Particularly, in this article, we present preliminary results about their structural and biol. properties
Competitive binding exchange between alkali metal ions (K(+), Rb(+), and Cs(+)) and Na(+) ions bound to the dimeric quadruplex [d(G(4)T(4)G(4))](2): a (23)Na and (1)H NMR study
No full textA comparative study of the competitive cation exchange between the alkali metal ions K(+), Rb(+), and Cs(+) and the Na(+) ions bound to the dimeric quadruplex [d(G(4)T(4)G(4))](2) Was performed in aqueous solution by a combined use of the (23)Na and (1)H NMR spectroscopy. The titration data confirm the different binding affinities of these ions for the G-quadruplex and, in particular, major differences in the behavior of Cs(+) as compared to the other ions were found. Accordingly, Cs(+) competes with Na(+) only for the binding sites at the quadruplex surface (primarily phosphate groups), while K(+) and Rb(+) are also able to replace sodium ions located inside the quadruplex. Furthermore, the (1)H NMR results relative to the CsCl titration evidence a close approach of Cs(+) ions to the phosphate groups in the narrow groove of [d(G(4)T(4)G(4))](2). Based on a three-site exchange model, the (23)Na NMR relaxation data lead to an estimate of the relative binding affinity of Cs(+) versus Na(+) for the quadruplex surface of 0.5 at 298 K. Comparing this value to those reported in the literature for the surface of the G-quadruplex formed by 5'-guanosinemonophosphate and for the surface of double-helical DNA suggests that topology factors may have an important influence on the cation affinity for the phosphate groups on DNA. Copyright (C) 2009 John Wiley & Sons, Ltd
Molecular Modelling Studies of Four Stranded Quadruplexes Containing a 3’-3’ or 5’-5’ Inversion of Polarity Site
No full textRecently we reported a preliminary study on the structure of two novel quadruplex structures, Q33 and Q55, formed by the oligodeoxynucleotides 5'TGG3'-3'GGT5' and 3'TGG5'-5'GGT3', resp. Here we report their soln. structures at the at. level. The obtained structures reveal that Q55 and Q33 possess a different stacking among G-quartets and different twist angle (and therefore different helical winding) at the inversion of polarity level
EFFECT OF THE INTRODUCTION OF AN A-RESIDUE INTO A QUADRUPLEX FORMING OLIGONUCLEOTIDE CONTAINING A 5'-5' POLARITY OF INVERSION SITE
No full textPreliminary NMR studies on structure formed by sequence 3'-TGA-5'-5'-GGT-3' are described. We proposed the formation of a tetramol. quadruplex in which strands are equiv. to each other and three G-tetrads are present. The possibility of the occurrence of an A-tetrad also is discussed
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