PDBsum entry 2orh

DNA

PDB id: 2orh

Contents

DNA/RNA

Metals

_NA ×2

Waters ×99

References listed in PDB file

Key reference

Title

Directing macromolecular conformation through halogen bonds.

Authors

A.R.Voth, F.A.Hays, P.S.Ho.

Ref.

Proc Natl Acad Sci U S A, 2007, 104, 6188-6193. [DOI no: 10.1073/pnas.0610531104]

PubMed id

17379665

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.

Figure 1.
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 C[8] cytosine to the phosphate of the cross-over C[7] 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).

Figure 3.
Fig. 3. Geometries of X-bonds in Br[2]J and Br[1]J. (a) Omit electron density maps contoured at 5 comparing geometries at the tight U-turns of the Br[2]J and Br[1]J junctions. Closest distances from the bromines to the X-bonded phosphate oxygens are labeled. (b) Overlay of all common DNA atoms for nucleotides N[5], N[6], and N[7] at the core of the junctions of Br[2]J (red), Br[1]J (yellow), H[2]J (blue), and the previously published structure of ATC-J (green). Conformational rearrangements are seen at the N[5] nucleotide to allow rotation of the phosphate to form a weak electrostatic interaction (green arrow) with the methyl group of T[7] in ATC-J, halogen bonds (magenta arrows) to the bromines in Br[2]J and Br[1]J, and a hydrogen bond (blue arrow) to the amino group of C[7] in H[2]J.