Physico-chemical analysis of G-quadruplex containing bunch-oligonucleotides

Petraccone, Luigi; Martino, Luigi; Duro, Ida; Oliviero, Giorgia; Borbone, Nicola; Piccialli, Gennaro; Giancola, Concetta

doi:10.1016/j.ijbiomac.2006.07.013

Cited by 4 publications

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References 41 publications

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“…Further evidence for quadruplex formation came from circular dichroism spectroscopy. In particular, upon incubation in quadruplex forming conditions, both ODN 1 and control ODN 7 exhibited the characteristic profile for a parallel quadruplex structure, with a strong positive circular dichroism peak at 263 nm and a relatively weak negative peak at 242 nm (Figure b, inset). , In an effort to discern the thermal stability of the quadruplexes, we performed thermal denaturation experiments. As can be gauged from Figure b both quadruplex 2 ( 1 4 ) and quadruplex 7 4 are thermally very stable and show no significant denaturation.…”

Section: Resultsmentioning

confidence: 99%

Photonic DNA-Chromophore Nanowire Networks: Harnessing Multiple Supramolecular Assembly Modes

et al. 2013

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Photonic DNA nanostructures are typically prepared by the assembly of multiple sequences of long DNA strands that are conjugated covalently to various dye molecules. Herein we introduce a non-covalent method for the construction of porphyrin-containing DNA nanowires and their networks that uses the programmed assembly of a single, very short, oligodeoxyribonucleotide sequence. Specifically, our strategy exploits a number of supramolecular binding modalities (including DNA base-pairing, metal-ion coordination, and β-cyclodextrin-adamantane derived host-guest interactions) for simultaneous nanowire assembly and porphyrin incorporation. Furthermore, we also show that the resultant DNA-porphyrin assembly can be further functionalized with a complementary “off-the-shelf” DNA binding dye resulting in photonic structures with broadband absorption and energy transfer capabilities.

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Section: Resultsmentioning

confidence: 99%

Photonic DNA-Chromophore Nanowire Networks: Harnessing Multiple Supramolecular Assembly Modes

et al. 2013

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Synthesis and Structural Characterization of Stable Branched DNA G‐Quadruplexes Using the Trebler Phosphoramidite

et al. 2012

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Guanine (G)-rich sequences can form a noncanonical four-stranded structure known as the G-quadruplex. G-quadruplex structures are interesting because of their potential biological properties and use in nanosciences. Here, we describe a method to prepare highly stable G-quadruplexes by linking four G-rich DNA strands to form a monomolecular G-quadruplex. In this method, one strand is synthesized first, and then a trebler molecule is added to simultaneously assemble the remaining three strands. This approach allows the introduction of specific modifications in only one of the strands. As a proof of concept, we prepared a quadruplex where one of the chains includes a change in polarity. A hybrid quadruplex is observed in ammonium acetate solutions, whereas in the presence of sodium or potassium, a parallel G-quadruplex structure is formed. In addition to the expected monomolecular quadruplexes, we observed the presence of dimeric G-quadruplex structures. We also applied the method to prepare G-quadruplexes containing a single 8-aminoguanine substitution and found that this single base stabilizes the G-quadruplex structure when located at an internal position.

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Problems with molecular mechanics implementations on the example of 4-benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide

2011

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Results from force fields implemented in HyperChem, a program frequently used in studies of bioactive compounds, have been compared using the example of the conformational analysis of a 1-carbonylthiosemicarbazide that exhibits strong antibacterial activity. By comparing these results with the original force fields and the experimental NMR ROESY spectrum, it was shown that these implementations can lead to erroneous results.

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Physico-chemical analysis of G-quadruplex containing bunch-oligonucleotides

Cited by 4 publications

References 41 publications

Photonic DNA-Chromophore Nanowire Networks: Harnessing Multiple Supramolecular Assembly Modes

Photonic DNA-Chromophore Nanowire Networks: Harnessing Multiple Supramolecular Assembly Modes

Synthesis and Structural Characterization of Stable Branched DNA G‐Quadruplexes Using the Trebler Phosphoramidite

Problems with molecular mechanics implementations on the example of 4-benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide

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