STRUCTURE OF PY-CENTER-DOT-PU-CENTER-DOT-PY DNA TRIPLE HELICES - FOURIER-TRANSFORMS OF FIBER-TYPE X-RAY-DIFFRACTION OF SINGLE-CRYSTALS

Well-formed hexagonal crystals of oligomeric DNA triple helices exhibi t fiber-type x-ray diffraction patterns [cf., Lilt et al. (1994) Natur e Struct. Biol. I, II], which can be interpreted in terms of Fourier t ransforms of these helices. Precession photographs of a triplex formed of DA and dr chains show that it has 13 residues per trim. In contras t, a sequence containing the four natural bases A, G, C, and T has 12 residues per turn. In this sense the triple helices exhibit a sequence -dependent polymorphism, though both have C2'-endo sugar pucker and B rather than A conformation. New models are constructed, using constrai nts from x-ray diffraction, and Fourier transforms of the models are c alculated. Good agreement in the amplitudes and positions of the calcu lated and observed diffraction intensities confirms the structures for both triple helices. These are the first stereochemically satisfactor y DNA triple helices for which coordinates based on adequate experimen tal data were provided. Sequences for crystallization are designed to achieve unique base alignments and are screened for the presence of sh arp bands on gel electrophoresis to assure the absence of multiple spe cies caused by strand slippage. Despite intensive efforts to observe n ormal crystal diffraction by varying sequences and conditions, all cry stals exhibited only fiber-type diffraction. We suggest that this beha vior may be an intrinsic property of triple helices and discuss possib le reasons for the results. Spectroscopic and chemical experiments est ablish that the oligonucleotides exist in solution as triple helices u nder the conditions of crystallization. (C) 1996 John Wiley & Sons, In c.