Behavior of the Guanine Base in G‐quadruplexes Probed by the Fluorescent Guanine Analog, 6‐Methyl Isoxanthopterin

Abstract

In this study, circular dichroism (CD) spectrum and fluorescence techniques were used to examine the dynamic properties and microenvironment of the guanine base (G) at the central loop and at the middle of the G‐stem of the G‐quadruplex formed from the G3T2G3TGTG3T2G3 sequence (G‐quadruplex 1), in which the G base at the 10th and 13th position were replaced with a fluorescent G analog, 6‐methyl isoxanthopterin (6MI) (G‐quadruplex 2 and 3, respectively). For all G‐quadruplexes, the CD spectrum revealed a positive band at 263 nm and a shoulder at 298 nm, and the thermal melting profiles were the sum of at least two sigmoidal curves. These observations indicated the presence of two conformers in the G‐quadruplex. The fluorescence intensity of G‐quadruplex 2 was greater than 3, as expected from the extent of stacking interaction, which is larger in the G(6MI)G sequence than the T(6MI)T sequence. The efficiency of fluorescence quenching by the polar acrylamide quencher and negatively charged I− quencher were larger for G‐quadruplex 3, suggesting that 6MI in the G(6MI)G stem is exposed more to the aqueous environment compared to that in the T(6MI)T central loop. In the latter case, 6MI may direct to the center of the top G‐quartet layer. The possibility of hydrogen bond formation between the carbonyl group of 6MI and the acrylamide of the G‐quadruplex 3 was proposed.