Biophysical Properties of Quadruplexes Containing Two or Three 8-Bromodeoxyguanosine Residues

Petraccone, Luigi; Duro, Ida; Randazzo, Antonio; Virno, Ada; Mayol, Luciano; Giancola, Concetta

doi:10.1080/15257770701490589

Cited by 12 publications

(5 citation statements)

References 6 publications

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“…For example, in quadruplex structures [d(TG 3 T)] 4 and [d(TG 4 T)] 4 the effects of an 8-methyl-2′-deoxyguanosine incorporation are sequence dependent (34): the replacement of the first guanosine in sequence results in the formation of an all- syn tetrad never observed before in solution, while the replacement of the second guanosine in sequence, surprisingly, does not affect the original anti preference of the residue, notwithstanding the presence of the methyl group in the 8 position usually promoting a syn glycosidic conformation. Since, to the best of our knowledge, only one investigation concerning the introduction of more than one 8-substituted deoxyguanosine analogues in parallel quadruplexes has been reported to date (51), we have explored the ability to form G-quadruplexes and their structural properties of ODNs analogues of TG 3 T and TG 4 T in which two canonical guanines have been replaced by 8-methyl-2′-deoxyguanosine residues (Table 1). Results obtained for ODNs T12 and F12 confirm the findings obtained for ODNs analogues of TG 3 T and TG 4 T in which one canonical guanine has been replaced by an 8-methyl-2′-deoxyguanosine residue (33,34): these ODNs adopt a tetramolecular parallel G-quadruplex characterized by an all- syn M-tetrad stacked to an all- anti M-tetrad.…”

Section: Discussionmentioning

confidence: 99%

The insertion of two 8-methyl-2′-deoxyguanosine residues in tetramolecular quadruplex structures: trying to orientate the strands

Virgilio

Esposito

Citarella

et al. 2011

Nucleic Acids Research

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In this article, we report a structural study, based on NMR and CD spectroscopies, and molecular modelling of all possible d(TG3T) and d(TG4T) analogues containing two 8-methyl-2′-deoxyguanosine residues (M). Particularly, the potential ability of these modified residues to orientate the strands and then to affect the folding topology of tetramolecular quadruplex structures has been investigated. Oligodeoxynucleotides (ODNs) TMMGT (T12) and TMMGGT (F12) form parallel tetramolecular quadruplexes, characterized by an all-syn M-tetrad at the 5′-side stacked to all-anti M- and G-tetrads. ODNs TMGMT (T13) and TMGGMT (F14) form parallel tetramolecular quadruplexes, in which an all-anti G core is sandwiched between two all-syn M-tetrads at the 5′- and the 3′-side. Notably, the quadruplex formed by T13 corresponds to an unprecedented structure in which the syn residues exceed in number the anti ones. Conversely, ODN TGMGMT (F24) adopts a parallel arrangement in which all-anti G-tetrads alternate with all-syn M-tetrads. Most importantly, all data strongly suggest that ODN TMGMGT (F13) forms an unprecedented anti-parallel tetramolecular quadruplex in which G and M residues adopt anti and syn glycosidic conformations, respectively. This article opens up new understandings and perspectives about the intricate relationship between the quadruplex strands orientation and the glycosidic conformation of the residues.

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Section: Discussionmentioning

confidence: 99%

The insertion of two 8-methyl-2′-deoxyguanosine residues in tetramolecular quadruplex structures: trying to orientate the strands

Virgilio

Esposito

Citarella

et al. 2011

Nucleic Acids Research

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“…Another example reported in the literature deals once again with the study of modified d(TGGGT). 31 In this case, two or three Gs have been replaced by G Br residues. In particular, four modified oligonucleotides have been studied, namely d(TG Br G Br GT), d(TG Br GG Br T), d(TGG Br G Br T) and d(TG Br G Br G Br T).…”

Section: The CD Of Chemically Modified G4-dna Revisitedmentioning

confidence: 99%

A non-empirical chromophoric interpretation of CD spectra of DNA G-quadruplex structures

et al. 2010

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G-quadruplex DNA (G4-DNA) structures are four-stranded helical DNA (or RNA) structures, comprising stacks of G-tetrads, which are the outcome of planar association of four guanines in a cyclic Hoogsteen hydrogen-bonding arrangement. In the last decade the number of publications where CD spectroscopy has been used to study G4-DNAs, is extremely high. However, with very few exceptions, these investigations use an empirical interpretation of CD spectra. In this interpretation two basic types of CD spectra have been associated to a single specific difference in the features of the strand folding, i.e. the relative orientation of the strands, "parallel" (all strands have the same 5' to 3' orientation) or "antiparallel". Different examples taken from the literature where the empirical interpretation is not followed or is meaningless are presented and discussed. Furthermore, the case of quadruplexes formed by monomeric guanosine derivatives, where there is no strand connecting the adjacent quartets and the definition parallel/antiparallel strands cannot apply, will be discussed. The different spectral features observed for different G-quadruplexes is rationalised in terms of chromophores responsible for the electronic transitions. A simplified exciton coupling approach or more refined QM calculations allow to interpret the different CD features in terms of different stacking orientation (head-to-tail, head-to-head, tail-to-tail) between adjacent G-quartets irrespectively of the relative orientation of the stands (parallel/antiparallel).

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“…Exceptions to this ''guanine only'' rule are guanine analogs modified at position 8. [1][2][3] Given the position of that substituent, which does not perturb the cyclic arrangement of H-bonds but favors the syn sugar base conformation, we wondered what would be the effect of other substituents at this position. 8-Amino guanine was previously found to stabilize triplexes 4 but destabilize quadruplexes 5 when inserted in the position 1 of an intramolecular quad-ruplex.…”

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8-Amino guanine accelerates tetramolecular G-quadruplex formation

et al. 2008

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Biophysical Properties of Quadruplexes Containing Two or Three 8-Bromodeoxyguanosine Residues

Cited by 12 publications

References 6 publications

The insertion of two 8-methyl-2′-deoxyguanosine residues in tetramolecular quadruplex structures: trying to orientate the strands

The insertion of two 8-methyl-2′-deoxyguanosine residues in tetramolecular quadruplex structures: trying to orientate the strands

A non-empirical chromophoric interpretation of CD spectra of DNA G-quadruplex structures

8-Amino guanine accelerates tetramolecular G-quadruplex formation

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