Solution structure of the EcoRI DNA sequence: refinement of NMR-derived distance geometry structures by NOESY spectrum back-calculations

Abstract

The solution structure of the self-complementary DNA duplex [d(CGCGAATTCGCG)]2, which contains the EcoRI restriction site sequence GAATTC at the center, has been studied by two-dimensional nuclear magnetic resonance spectroscopy. Time-dependent nuclear Overhauser effect spectra were used to obtain the initial cross-relaxation rates between 155 pairs of protons. These initial cross-relaxation rates were converted into interproton distances and entered into a distance (bounds) matrix. A distance geometry algorithm (DSPACE) was used to create embedded starting structures and to refine these structures until they showed good agreement with the distance matrix; symmetry constraints were included in the refinement procedure, making the two strands in the refined distance geometry structures virtually identical and significantly improving the agreement with the distance matrix. The NOESY spectrum for one of these distance geometry structures was then calculated from the explicit coordinates by numerically integrating all the z-magnetization transfer pathways among neighboring protons within a specified radius. Distances in this distance geometry structure that did not agree with the experimental NOESY time course were then adjusted accordingly. This process was iterated until a good agreement between calculated and experimental NOESY spectra was reached. The final structure, which generates good agreement with the experimental NOESY spectrum, displays kinks at the C3-G4 base step and at the A6-T7 base step that appear to be similar to those reported for the EcoRI restriction site DNA bound to its endonuclease. The solution structure is not the same as the crystal structure of this DNA duplex.

Kinetics of DNA hydration

“…While the solution structure is surely not identical with the crystal structure, there appears to be no signi®cant differences in the narrow AATT region of the minor groove (Nerdal et al, 1989). Figures 1 and 2 show the ®ve water molecules in the spine of hydration, located in the narrow AATT region of the minor groove.…”

A NOESY NMR Study of the Interaction between Sodium Dodecyl Sulfate and Poly(Ethylene Oxide)

“…cross-peak volume indicate mostly primary magnetization transfer at 0.5 s mixing time ( 14 ) . In summary, these three NOESY experiments at 283.1 K indicate proximity ( õ5 Å ) of the polymer protons and the EXPERIMENTAL main part of the surfactant hydrocarbon chain ( called SDS3, see Eq.…”

Synthesis and Characterization of the Diastereomers Λ‐ and Δ‐[Ru(bpy)2(m‐bpy‐Gly‐L‐His‐L‐Lys)]Cl2−1H NMR Studies on Their Interactions with the Deoxynucleotide Duplex d[(5′‐CGCGAATTCGCG‐3′)2]

“…[5,6] The DNA binding properties of the complex we designed were tested on the spectroscopically and crystallographically characterized DickersonϪDrew dodecamer, d(5Ј-CGCGAATTCGCG-3Ј) 2 which forms a self-complementary duplex the structure of which is known. [16,17] This paper describes the synthesis and characterization of the diastereomeric complexes Λ-and ∆-[Ru(bpy) 2 (m-bpy-GHK)]Cl 2 , derived from the compounds Λ-and ∆-cis-[Ru(bpy) 2 (py) 2 ]A (where A ϭ O,OЈ-dibenzoyltartaric acid) [18,19] by a substitution of the two py molecules with the chelate ligand m-bpy-COOH followed by a solid-phase peptide synthesis. This was also our first attempt to investigate, by means of NMR, ESI-MS and CD spectroscopic techniques, their binding properties with the deoxynucleotide duplex d(5Ј-CGCGAATTCGCG-3Ј) 2 .…”