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Refinement Of The Solution Structure Of A Branched Dna Three-Way Junction, Neocles B. Leontis, Igor V. Ouporov

Chemistry Faculty Publications

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 …