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Example text
For D N A fragments, the choice is relatively easy, since any right-handed doublehelical crystal structure is a good structural approximation. For initial M A R D I G R A S calculations, we typically utilize canonical B- and A-DNA models, energy-minimized for the respective nucleotide sequence (vide supra). As already described, M A R D I G R A S will refine a hybrid relaxation matrix until a user-defined threshold is reached for the iteration, defined by a sixth-root residual index, RX: [(ao)i 1/6 -- (ac)il/6 I RX ~ l ~ .
Egan, and T. L. James, Biochemistry 33, 354 (1994); (6) K. D. Bishop, F. Blocker, W. Egan, and T. L. James, Biochemistry 33, 427 (1994); (7) A. Mujeeb, S. M. Kerwin, W. Egan, G. L. Kenyon, and T. L. James, Biochemistry 31, 9325 (1992); (8) M. Tonelli and T. L. James, unpublished results (1995); (9) C, Gonzalez, W. Stec, A. Kobylanska, R. I. Hogrefe, M. Reynolds, and T. L. James, Biochemistry 33, 11062 (1994). type of COSY technique, where spectra are recorded for individual peaks, results in much higher digital resolution and ultimately in narrower error margins for the coupling constants.
We note that the accuracy of integrated peak intensities and general spectral quality is worse for 1H20 datasets. Consequently, one might be tempted to commingle the additional cross-peaks involving exchangeable protons from ~H20 spectra, with the higher quality data obtained from 2H20 solutions. Aside from surmountable normalization problems, however, the fundamental problem is that cross45 K. Weisz, R. H. Sharer, W. Egan, and T. L. James, Biochemistry 31, 7477 (1992). 46 K. D. Bishop, F. Blocker, W.