Work

The Crystal Structure of the GG-Rich DNA Quadruplex Sequence GGGGTTTTGGGG in Presence of Zn2+ and K+ Ions

Year: 2026

Type: article

Abstract: The structural characterization of GG-rich DNA sequences in presence of metal ions provides essential insight into quadruplex stability and ion-dependent conformational specifics. We report the crystal structure of the GG-quadruplex formed by the sequence GGGGTTTTGGGG in the presence of Zn2+, K+, and Na+. It was deposited in the RCSB Protein Data Bank under the accession code 9FTA. The structure was determined by single-crystal X-ray diffraction at a resolution of 2.49 Å in the space group P212121. It reveals a parallel-stranded, two-G-tetrad stabilized by K+ ions within the central channel, while Na+ and Zn2+ occupy peripheral and groove-associated sites. Zn2+ ions are engaged in noncanonical coordination interactions with phosphate oxygens and structured water molecules, contributing to lattice stabilization and subtle adjustments in groove dimensions. The T4 loop forms a compact, ordered motif that contributes to crystal packing rather than intramolecular G4 stabilization. The presence of mixed cations produces a sole lattice architecture mediated by ions that provides structural insight into how bivalent and monovalent metals mutually modulate G-quadruplex topology. These results suggest a basis for understanding the specific ion effects on G4 structures and may direct the design of metal open DNA architectures.

Source: Crystals

DOI: 10.3390/cryst16040223

Authors: Hristina Sbirkova-Dimitrova, Hristo Gerginov, Boris L. Shivachev

Institutions: Bulgarian Academy of Sciences, Institute of Mineralogy and Crystallography "Acad. Ivan Kostov" Bulgarian Academy of Sciences

Language: English

Topic: DNA and Nucleic Acid Chemistry

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,534

Funder: Bulgarian National Science Fund