4GS2

DNA Holliday junction stabilized by iodine halogen bond. I1J construct in related reference.

Summary for 4GS2

• Entry DOI: 10.2210/pdb4gs2/pdb
• Related: 2ORF 2ORG 2ORH 3TOK 4GQD 4GRE 4GSG 4GSI
• Descriptor: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(5IU)P*CP*GP*G)-3'), DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3') (3 entities in total)
• Functional Keywords: dna holliday junction, halogen bond, dna
• Total number of polymer chains: 2
• Total formula weight: 6202.87

Authors

Ho, P.S.,Carter, M. (deposition date: 2012-08-27, release date: 2013-07-31, Last modification date: 2023-09-13)

Primary citation

Carter, M.,Voth, A.R.,Scholfield, M.R.,Rummel, B.,Sowers, L.C.,Ho, P.S.
Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions.
Biochemistry, 52:4891-4903, 2013

PubMed Abstract: Interest in noncovalent interactions involving halogens, particularly halogen bonds (X-bonds), has grown dramatically in the past decade, propelled by the use of X-bonding in molecular engineering and drug design. However, it is clear that a complete analysis of the structure-energy relationship must be established in biological systems to fully exploit X-bonds for biomolecular engineering. We present here the first comprehensive experimental study to correlate geometries with their stabilizing potentials for fluorine (F), chlorine (Cl), bromine (Br), or iodine (I) X-bonds in a biological context. For these studies, we determine the single-crystal structures of DNA Holliday junctions containing halogenated uracil bases that compete X-bonds against classic hydrogen bonds (H-bonds), estimate the enthalpic energies of the competing interactions in the crystal system through crystallographic titrations, and compare the enthalpic and entropic energies of bromine and iodine X-bonds in solution by differential scanning calorimetry. The culmination of these studies demonstrates that enthalpic stabilization of X-bonds increases with increasing polarizability from F to Cl to Br to I, which is consistent with the σ-hole theory of X-bonding. Furthermore, an increase in the X-bonding potential is seen to direct the interaction toward a more ideal geometry. However, the entropic contributions to the total free energies must also be considered to determine how each halogen potentially contributes to the overall stability of the interaction. We find that bromine has the optimal balance between enthalpic and entropic energy components, resulting in the lowest free energy for X-bonding in this DNA system. The X-bond formed by iodine is more enthalpically stable, but this comes with an entropic cost, which we attribute to crowding effects. Thus, the overall free energy of an X-bonding interaction balances the stabilizing electrostatic effects of the σ-hole against the competing effects on the local structural dynamics of the system.

PubMed: 23789744
DOI: 10.1021/bi400590h

Experimental method

X-RAY DIFFRACTION (1.9 Å)