Guanine Amine Derivatives Promote Forming a Base-Vacancy-G Quadruplex Structure

G-quadruplex (G4) structures are important in both biological and medical fields. A unique G4 type containing G vacancies allowing stabilization by guanine or guanine derivatives is widely used in the treatment of diseases, such as cancer. However, the identification of ligands with suitable affinities and specificities for G4 structures remains challenging. This study investigated the assisting effect of guanine derivatives in the formation of G-vacancy G4 structures. Focusing on the EAD2 sequence, we designed EAD2 sequences with one or two missing G bases. Circular dichroism (CD) assays revealed negligible impact of guanine and its derivatives on intact EAD2 structures but notable alterations in single-G-base-deficient EAD2 sequences. The formation of G4 structures in the EAD2 sequence lacking two G bases was difficult, even with the assistance of guanine derivatives. Moreover, experimental results demonstrated that the guanine derivatives M2 had better auxiliary effects on base-deficient sequences than other compounds, which may be due to the enhanced pairing capability of G4 caused by M2. Lastly, the experiment demonstrates that the hemin/G4 DNAzyme-catalyzed ABTS confirmed the auxiliary role of the guanine derivatives in the formation of G4 in G base-deficient sequences. Overall, the findings indicated the significant impact of G base deficiency on G4 assembly, with the guanine derivative M2 effectively aiding stable G4 formation in G base-deficient sequences.