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In this work, the effects of terminal adenines on the formation and stability of tetramolecular G-quadruplexes (G4s) have been studied by electrospray ionization mass spectrometry (ESI-MS), UV, CD and NMR spectroscopy. Several evidences suggested that the sequences d(AG n A) (n = 4 or 5) form stable uncompleted tetramolecular G4 at acidic condition which is different from the canonical one in the neutral condition. In addition, hydrolysis of guanine has also been observed in acidic condition that may occur for unpaired strands rather than in complete G4. Thus, a new G4 topology containing incomplete G-quartet is proposed that is very stable and particularly presents in acidic ammonium ions solution. The information presented in this study provides the new insight on the polymorphism of G4s in acidic environment, which may help understand of the special role of adenines on the formation of G4s. • A stable slipped tetramolecular G-quadruplex formed by d(AG n A) was proposed. • The hydrolysis of purines in G-quadruplex was observed by mass spectrometry. • The results give a new insight into the association polymorphism of G-quadruplex. [ABSTRACT FROM AUTHOR]

DNA G-quadruplexes (G4s) formed by guanine(G)-rich sequences show diversity of structural topologies. The detection of structural details is of great significance for understanding of their functions and for the target drug design, but is very challenging. Herein, we demonstrate that the surface-enhanced Raman spectroscopy (SERS) via Ag IANPs as substrates is able to identify the numbers of Adenine (A) located on the G-quartet of the G4s. Eight G4s are selected for SERS studies. Besides the detection of series of characteristic bands indicating the formation of G4s, the intensity of the band represented A base ring breath (ν A , ~733 cm−1) is observed particularly enhanced when there are A bases coplanar with G-quartet, and which is higher than the intensity of the band corresponding to G base ring breath (ν G, ~655 cm−1). Furthermore, the band intensity ratio of ν A to ν G versus the ratio of the numbers of A on the plane to the sum of numbers of A and G shows very good linear relationship. Thus, based on the band intensities of ν A to ν G and their ratio in the SERS spectrum, the G-quadruplexes with or without a coplanar A base and numbers of A bases on the plane of G-quartet can be facilely identified. The method is simple, fast, low cost and sensitive to provide particular details of the structure in aqueous solution, therefore, implies widespread applications. [Display omitted] • The adenine coplanar G-quartet structure in G-quadruplex was studied by SERS. • It was found that the SERS signal of adenine coplanar G-quartet was extra enhanced. • The number of A bases coplanar with G-quartet was quantitatively studied. [ABSTRACT FROM AUTHOR]