1,721,062 research outputs found
Configuration assignment in small organic molecules via residual dipolar couplings
No full textHere we propose a new method to assign relative configurations of stereocenters in small organic molecules by using residual dipolar couplings; the main advantage of this method is that spatial proximity of the stereocenters is not required
The Introduction of Inversion of Polarity Sites in DNA G-Quadruplex Structures: Effects and Perspectives
No full textThe natural sequences of nucleic acids generally consist of nucleotides linked together by canonical 3'-5' phosphodiester bonds. An inversion of polarity site (IPS) can be defined as the point of the sequence in which a 3'-3' or a 5'-5' phosphodiester bond occurs. By extending this definition, an IPS can be described as that part of the sequence in which two 3'- or two 5'-hydroxyl groups are connected by a linker, variable in size or in chemical nature. In G-quadruplex structures an IPS can be introduced in three different positions: inside a non G-tract, inside a G-tract and just between a non Gtract and a G-tract. Investigations have been reported concerning all the three types of modification. This review describes the effects of the presence of one or more IPSs in G-quadruplex structures, particularly regarding their topological and structural characteristics, glycosidic bond preference, and thermal stability, with special attention to biologically active Gquadruplex forming aptamers. The perspectives and potential developments of this research area are also discussed
Studio 1H-NMR dell’ interazione tra la distamicina A e la netropsina con strutture di duplex e quadruplex DNA
No full textA novel equilibrium relating to the helix handedness in G-quadruplexes formed by heterochiral oligonucleotides with an inversion of polarity site
No full textInvestigations of heterochiral oligodeoxynucleotides 50-TD1GD2GD3-
30-30-GL3GL2TL1-50 (L33) and 30-TD1GD2GD3-50-50-GL3GL2TL1-30 (L55)
forming quadruplex structures are reported. Data indicate the
presence of enantiomeric left- and right-handed quadruplex
helices. In the case of L55, NMR experiments point to an unusual
equilibrium between them
NMR Solution Structure of a Parallel LNA Quadruplex
No full textThe soln. structure of a locked nucleic acid (LNA) quadruplex, formed by the oligomer d(TGGGT), contg. only conformationally restricted LNA residues is reported. NMR and CD spectroscopy, as well as mol. dynamics and mechanic calcns., has been used to characterize the complex. The mol. adopts a parallel stranded conformation with a 4-fold rotational symmetry, showing a right-handed helicity and the guanine residues in an almost planar conformation with three well-defined G-tetrads. The thermal stability of Q-LNA has been found to be comparable with that of [r(UGGGU)]4, while a Tm increment of 20° with respect to the corresponding DNA quadruplex structure [d(TGGGT)]4 has been obsd. The structural features of the LNA quadruplex reported here may open new perspectives for the biol. application of LNAs as novel versatile tools to design aptamer or catalyst oligonucleotides
Structural study of four-stranded quadruplex structures containing 2'-deoxy-8-(propyn-1-yl)adenosine
No full textIn this paper, we report the NMR structural study of two quadruplex structures formed by truncations of the human telomeric sequence and contg. a modified base, namely d(AprGGGT) and d(TAprGGGT), where Apr indicates 2'-deoxy-8-(propyn-1-yl)adenosines. Both oligonucleotides have been found to form 4-fold sym. G-quadruplex structures with all strands parallel and equiv. to each other and characterized by higher thermal stabilities than the natural counterparts. The presence of the propynyl groups affects the conformations of the 5' edge of both quadruplexes in such a way to prevent the formation of one of the two possible H-bond patterns obsd. for a canonical A-tetrad. The increased thermal stabilities of the modified quadruplexes seem to be mostly due to a prevalent syn glycosidic conformation assumed by the Apr residues
More than one non-canonical phosphodiester bond in the G-tract: formation of unusual parallel G-quadruplex structures
No full textIn this article, we report an investigation, based on NMR and CD spectroscopic and electrophoretic techniques, of 5′TGGGGT3′ analogues containing two or three 3′-3′ or 5′-5′ inversion sites in the G-run, namely 5′TG3′-3′G5′- 5′GGT3′ (Q350), 5′TG3′-3′GG5′- 5′GT3′ (Q305), 5′TGG3′-3′G5′- 5′GT3′ (Q035), 5′TG3′-3′G5′- 5′G3′-3′GT5′ (Q353) and 3′TG5′- 5′G3′-3′G5′-5′GT3′ (Q535). Although the sequences investigated contain either no or only one natural 3′-5′ linkage in the G-tract, all modified oligodeoxyribonucleotides (ODNs) have been shown to form stable tetramolecular quadruplex structures. The ability of the 3′-3′ or 5′-5′ inversion sites to affect the glycosidic conformation of guanosines and, consequently, base stacking, has also been investigated. The results of this study allow us to propose some generalizations concerning strand arrangements and the glycosidic conformational preference of residues adjacent to inverted polarity sites. These rules could be of general interest in the design of modified quadruplex structures, in view of their application as G-wires and modified aptamers
8-Methyl-2'-deoxyguanosine incorporation into parallel DNA quadruplex structures
No full textThis paper concerns the CD and NMR structural studies of the quadruple helix arrangements adopted by three tailored oligodeoxyribonucleotide analogs, namely d(TGMeGGT), d(TGGMeGT) and d(TGGGMeT), where dGMe represents a 8-methyl-2'-deoxyguanosine residue. The results of this study clearly demonstrate that the effects of the incorporation of dGMe instead of a dG residue are strongly dependent upon the positioning of a single base replacement along the sequence. As such, d(TGMeGGT), d(TGGMeGT) have been found to form 4-fold sym. quadruplexes with all strands parallel and equiv. to each other, each more stable than their natural counterpart. NMR expts. clearly indicate that [d(TGMeGGT)]4 possesses a GMe-tetrad with all dGMe residues in a syn-glycosidic conformation while an anti-arrangement is apparent for the four dGMe of [d(TGGMeGT)]4. As the two complexes show a quite different CD behavior, a possible relationship between the presence of residues adopting syn-glycosidic conformations and CD profiles is briefly discussed. As far as d(TGGGMeT) is concerned, NMR data indicate that at 25°C it exists primarily as a single-strand conformation in equil. with minor amts. of a quadruplex structure
A new class of DNA quadruplexes formed by oligodeoxyribonucleotides containing a 3'-3' or 5'-5' inversion of polarity site
No full textUnprecedented DNA quadruplex structures containing a 3′-3′ or 5′-5′ inversion of polarity site in the G-tract are presented; the quadruplexes are characterized by different elements of symmetry and glycosidic angle conformations. © The Royal Society of Chemistry 2005
EFFECTS OF THE SYN/ANTI EQUILIBRIUM MODULATION ON THE STRUCTURAL PROPERTIES OF TETRAMOLECULAR QUADRUPLEXES,
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