Pucker restraints

Figure 9. Models of the control (A) and alphaA (B) decamer duplexes. The initial models were based on the PDB coordinates of the Dickerson dodecamer (22), and energy minimized with AMMP, Another Molecular Modeling Program (25), as outlined previously (9 JO). A dielectric screen with 5 A correlation length and no cut-off for non-bonded interactions were used also no NMR (i.e., NOE or J) restraints were incorporated into the calculations. a-Anomeric nucleotides are displayed in red. Both duplex models are nearly identical, with an RMSD of 0.32 A (excluding the a-anomeric residues and their counterparts in the control), and total energies of -12419 kJmol 1 for alphaA and -12461 kJmol for the control. The sugar puckering for each nucleotide in the models shown, including A5 in alphaA, is of the S-type.

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