Three-dimensional solution structures of two DNA dodecamers through full relaxation matrix analysis

The solution structures of the two self-complementary oligonucleotides, d(A ATTTGCAAATT)(2) and d(GAGAAGCTTCTC)(2), were solved by using torsion angle dynamics and restrained energy minimization. Proton-proton distance constra ints were derived from NOE cross-peak volumes using a combination of relaxa tion matrix analysis and torsion angle dynamics. The final structures allow the recalculation of experimental NOE intensities with satisfactory agreem ent. The resulting families of conformers were energy minimized to include electrostatic energy terms and to remove some van der Waals clashes remaini ng at the end of torsion angle dynamics calculations. Both structures showe d a conformation close to B-form DNA, as shown by the similarity between th eir helix parameters and those of standard B-DNA. The latter parameters als o give an indication of the reliability of the present structure calculatio n approach. Copyright (C) 1999 John Wiley & Sons, Ltd.