Directing macromolecular conformation through halogen bonds

Abstract

The halogen bond, a noncovalent interaction involving polarizable chlorine, bromine, or iodine molecular substituents, is now being exploited to control the assembly of small molecules in the design of supramolecular complexes and new materials. We demonstrate that a halogen bond formed between a brominated uracil and phosphate oxygen can be engineered to direct the conformation of a biological molecule, in this case to define the conformational isomer of a four-stranded DNA junction when placed in direct competition against a classic hydrogen bond. As a result, this bromine interaction is estimated to be approximately 2-5 kcal/mol stronger than the analogous hydrogen bond in this environment, depending on the geometry of the halogen bond. This study helps to establish halogen bonding as a potential tool for the rational design and construction of molecular materials with DNA and other biological macromolecules.

Fig. 1.

Structure of the stacked-X DNA Holliday junction. The structure of d(CCGGTACCGG) (ACC-J) as a four-stranded junction (11) is shown with the inside cross-over strands colored in yellow and green and the outside noncrossing strands in blue and red. The pairs of stacked duplex arms are highlighted with cylinders. Details of the molecular interactions that stabilize junctions are in crystals are shown, with the essential H-bond from the C₈ cytosine to the phosphate of the cross-over C₇ nucleotide in the blue box, and the weaker H-bond from C7 to A6 in the ACC-J or the weak electrostatic interaction from the methyl of T7 to A6 in d(CCGATATCGG) (ATC-J) in the red boxes (12, 16).

Fig. 2.

Assay for competing X- against H-bonds. The isomeric forms of the stacked-X junction, resulting from restacking of the arms and migration of the junction (top), place an H-bond (H-isomer) or X-bond (X-isomer) at the junction cross-over. The crystal structures of H₂J in the H-isomer (with its H-bonding interaction) and Br₂J in the X-isomer (with its X-bond) are shown below. Bromines have been modeled at the outside strand of the H₂J structure to indicate their positions, if present, in the H-isomer of Br₂J.

Fig. 3.

Geometries of X-bonds in Br₂J and Br₁J. (a) Omit electron density maps contoured at 5σ comparing geometries at the tight U-turns of the Br₂J and Br₁J junctions. Closest distances from the bromines to the X-bonded phosphate oxygens are labeled. (b) Overlay of all common DNA atoms for nucleotides N₅, N₆, and N₇ at the core of the junctions of Br₂J (red), Br₁J (yellow), H₂J (blue), and the previously published structure of ATC-J (green). Conformational rearrangements are seen at the N₅ nucleotide to allow rotation of the phosphate to form a weak electrostatic interaction (green arrow) with the methyl group of T₇ in ATC-J, halogen bonds (magenta arrows) to the bromines in Br₂J and Br₁J, and a hydrogen bond (blue arrow) to the amino group of C₇ in H₂J.

Fig. 4.

Thermodynamic cycle to estimate the free energies of the X- relative to H-bonds. A free energy difference of ≈1 kcal/mol was estimated between the X- and H-isomers from the occupancies of bromine at the inside and outside strands of Br₁J (Br₁J-X and Br₁J-H) (Si Fig. 6) or ≈2 kcal/mol for 1 X-bond vs. 1 H-bond. Because there is very little contribution of hydration free energy to placing the bromine in the H- or X-isomeric forms (ΔG_hydration^o ≈0), we can assume that the primary effect on the energy of the X-bonds is electrostatic. Finally, if we assume that the is no difference in the energies of the H-isomer for either the Br₁J or Br₂J constructs (Br₁J-H and Br₂J-H, bottom of cycle, with the bromines on the outside strands), then the energy of the X-bond in the Br₂J construct (ΔG°Br₂J-X) can be estimated as the sum the Br₁J X-bond and the difference in electrostatic energy (ΔE) estimated from ab initio calculations (SI Fig. 7).