title: DNA-based nanostructures: The effect of the base sequence on octamer formation from d(XGGYGGT) tetramolecular G-quadruplexes.
abstract: In a previous work we have demonstrated that the DNA sequence CGGTGGT folds into a higher order G-quadruplex structure (2Q), obtained by the 5'-5' stacking of two unusual G(:C):G(:C):G(:C):G(:C) planar octads belonging to two identical tetra-stranded parallel quadruplexes, when annealed in the presence of ammonium or potassium ions. In the present paper, we discuss the role played by the title nucleosides X and Y (where X and Y stand for A, C, G, or T) on the formation and stability of 2Q structures formed by the XGGYGGT oligodeoxynucleotides. We found that the above mentioned dimerization pathway is not peculiar to the CGGTGGT sequence, but is possible for all the remaining CGGYGGT sequences (with Y = A, C, or G). Furthermore, we have found that the TGGAGGT sequence, despite the absence of the 5'-ending C, is also capable of forming a 2Q-like higher order quadruplex by using a slightly different dimerization interface, as characterized by NMR spectroscopy. To the best of our knowledge, this is the first characterization of a quadruplex multimer formed by an oligodeoxynucleotide presenting a thymine at its 5'-end. Examples of such structures were observed previously only in crystals and in the presence of non-physiological cations. Our results expand the repertoire of DNA quadruplex nanostructures of chosen length and add further complexity to the structural polymorphism of G-rich DNA sequences.
authors: Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors: Valentina
authors: V
authors: D'Atri
authors: Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy. Electronic address: nicola.borbone@unina.it.
authors: Nicola
authors: N
authors: Borbone
authors: Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors: Jussara
authors: J
authors: Amato
authors: Univ. Bordeaux, IECB, ARNA Laboratory, F-33600 Pessac, France; INSERM, U869, ARNA laboratory, F-33000 Bordeaux, France.
authors: Valérie
authors: V
authors: Gabelica
authors: Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors: Stefano
authors: S
authors: D'Errico
authors: Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors: Gennaro
authors: G
authors: Piccialli
authors: Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors: Luciano
authors: L
authors: Mayol
authors: Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors: Giorgia
authors: G
authors: Oliviero
mesh_terms: D001483:Base Sequence; D002942:Circular Dichroism; D054856:G-Quadruplexes; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*
chemical_list: D009838:Oligodeoxyribonucleotides
keywords: A-tetrads; DNA nanostructures; G-quadruplex multimers; Higher order assemblies; NMR