Refinement of the Solution Structure of a Branched DNA Three-Way Junction

We have refined the structure of the DNA Three-Way Junction complex, TWJ- TC, described in the companion paper by quantitative analysis of two 2D NOESY spectra (mixing times 60 and 200 ms) obtained in D2O solution. NOESY crosspeak intensities extracted from these spectra were used in two kinds of refinement procedure: 1) distance-restrained energy minimization (EM) and molecular dynamics (MD) and 2) full relaxation matrix back calculation refinement. The global geometry of the refined model is very similar to that of a published, preliminary model (Leontis, 1993). Two of the helical arms of the junction are stacked. These are Helix 1, defined by basepairs S1-G1/S3- C12 through S1-C5/S3-G8 and Helix 2, which comprises basepairs S1-C6/S2-G5 through S1-G10/S2-G1. The third helical arm (Helix 3), comprised of basepairs S2-C6/S3-G5 through S2-C10/S3-G1 extends almost perpendicularly from the axis defined by Helices 1 and 2. The bases S1-C5 and S1-C6 of Strand 1 are continuously stacked across the junction region. The conformation of this strand is close to that of B-form DNA along its entire length, including the S1-C5 to S1-C6 dinucleotide step at the junction. The two unpaired bases S3- T6 and S3-C7 lie outside of the junction along the minor groove of Helix 1 and largely exposed to solvent. Analysis of the refined structure reveals that the glycosidic bond of S3-T6 exists in the syn conformation, allowing the methyl group of this residue to contact the hydrophobic surface of the minor groove of Helix 1, at S3-G11. The helical parameters of the three helical arms of the structure exhibit only weak deviations from typical values for right-handed B-form DNA. Unusual dihedral angles are only observed for the sugar-phosphate backbone joining the \u27hinge\u27 residues, S2-G5 and S2- C6, and S3-G5 through S3-G8. The glycosidic bond of S3-G8 also lies within the syn range, allowing favorable Watson-Crick base-pairing interactions with S1-C5. The stability of this structure was checked in 39 ps molecular dynamic simulation at 330 K in water. The structure of TWJ-TC retained the geometrical features mentioned above at the end of the simulation period. The final R(1/6)-factor of the refined structure is 5%