Article Biochemistry, Vol. 49, No. 12, 2010 2621 FIGURE 7: 1H NOESY spectrum (tile plot) showing the NOEs between etheno protons and imino protons from neighboring base pairs. The NOESY spectrum was recorded at 7 C with a mixing time of 250 ms. FIGURE 8: Chemical shift differences observed for the 1-BD duplex when compared to those of the corresponding unmodified 1-BD duplex. restraints, including seven intranucleotide, nine internucleotide, and eight internucleotide cross-strand distance restraints, were employed at nucleotide X6, which allowed the position of X6 in the duplex to be determined with confidence. Structure Refinement. The randomly seeded rMD calcula- tions were performed starting with initial structures that were created with either A- or B-form geometries and energy mini- mized before rMD calculations. Ten structures were calculated from each starting structure. Figure S3 (Supporting Information) shows an ensemble of structures of the 1-BD duplex obtained from randomly seeded rMD calculations from starting A-form and B-form DNA. The precision of the rMD calculations was determined by pairwise root-mean-square deviation (rmsd) cal- culations (Table 2). Maximum pairwise rmsd values of 0.62 and 0.80 A˚ were obtained for the structures calculated from starting A-form and B-form DNA, respectively, suggesting convergence. The accuracies of these structures were verified using CORMA (36). This calculation was based on the compari- son of the experimental NOE intensities with the NOE intensities calculated from CORMA. A plot of the distribution of the sixth