Structure of a left-handed DNA G-quadruplex

Abstract

Aside from the well-known double helix, DNA can also adopt an alternative four-stranded structure known as G-quadruplex. Implications of such a structure in cellular processes, as well as its therapeutic and diagnostic applications, have been reported. The G-quadruplex structure is highly polymorphic, but so far, only right-handed helical forms have been observed. Here we present the NMR solution and X-ray crystal structures of a left-handed DNA G-quadruplex. The structure displays unprecedented features that can be exploited as unique recognition elements.

Keywords: G-quadruplex; NMR; X-ray crystallography; left-handed helix; nucleic acid.

Fig. 1.

(A) One-dimensional imino proton NMR spectrum of Z-G4. (B) CD spectrum of Z-G4.

Fig. 2.

(A) Ten lowest-energy superimposed solution structures of Z-G4. (B) Crystal structure of Z-G4. The electron density corresponds to the final 2mFo-DFc map contoured at 1.0 σ. (C) Ribbon view of the crystal structure of Z-G4. Anti and syn guanine bases are colored in cyan and magenta, respectively; thymine bases are in orange; phosphate backbone are in gray; phosphate oxygens are in red; and O4′ oxygens are in yellow. Potassium ions and water molecules are colored in purple and red, respectively. (D) Schematic structure of Z-G4. Arrows represent the 5′-to-3′ strand progression.

Fig. 3.

Surface representation showing the capping of the top and bottom tetrad. (A) Side views. (B) Top view. (C) Bottom view. Anti and syn guanine bases are colored in cyan and magenta, respectively; thymine bases are in orange; phosphate backbone is colored in gray. Bases are labeled with their corresponding residue numbers.

Fig. 4.

(A) Surface representation of one block (two tetrad layers) of Z-G4 showing the left-handed directionality of the phosphate backbone. (B) Surface representation of T95-2T (Protein Data Bank code 2LK7) (three tetrad layers) showing the right-handed directionality of the phosphate backbone. Thymine residues are removed for clarity. (C) Top view from the 5′ end of Z-G4 showing the anticlockwise progression of the backbone, as depicted by the gray arrow. (D) Top view from the 5′ end of T95-2T showing the clockwise progression of the backbone, as depicted by the gray arrow. (E) Side view of a representative dinucleotide step of Z-G4. (F) Side view of a representative dinucleotide step of T95-2T. (G) (Top view) Stacking between two successive guanines within a subunit of Z-G4 with a relative rotation of −25.7°. (H) (Top view) Stacking between two successive guanines in T95-2T with a relative rotation of +29.4°.