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Proc. Natl. Acad. Sci. USA Vol. 87, pp. 2526-2530, April 1990 Biochemistry Molecular structure of nicked DNA: A substrate for DNA repair enzymes (x-ray diffraction/DNA conformation) JUAN AYMAMI*t, MIQUEL COLL*t, Gus A. VAN DER MAREL§, JACQUES H. VAN BooM§, ANDREW H.-J. WANG?, AND ALEXANDER RICH* *Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; §Gorlaeus Laboratories, Leiden State University, Leiden, 2300RA, The Netherlands; and IDepartment of Physiology and Biophysics, University of Illinois at Urbana-Champaign, Urbana, IL 61801 Contributed by Alexander Rich, January 5, 1990 ABSTRACT The molecular structure of a nicked dodeca- mer DNA double helix, made of a ternary system containing d(CGCGAAAACGCG) + d(CGCGTT) + d(TTCGCG) oligo- nucleotides, has been determined by x-ray diffraction analysis at 3 A resolution. The molecule adopts a B-DNA conformation, not unlike those found in intact dodecamer DNA molecules crystallized in a somewhat different crystal lattice, despite a gap due to the absence of a phosphate group in the molecule. The helix has a distinct narrow minor groove near the center of the molecule at the AAAA region. This suggests that the internal stabilizing forces due to base stacking and hydrogen- bonding interactions are sufficient to overcome the loss of connectivity associated with the disruption of the covalent backbone of DNA. DNA is known to be damaged in a number of ways and biological systems have developed a variety of enzymes to FIG. 1. Schematic drawings of the two related orthorhombic crystal packing arrangements of the DNA dodecamers. (A) d(CGC- repair different types of DNA damage (1). A common DNA GATATCGCG) + netropsin complex (6). (B) d(CGC- damage is the limited hydrolysis of a sugar-phosphate bond GAAAACGCG) + d(CGCGTT) + d(TTCGCG). The b axis is followed by the removal of the phosphate group. This pro- horizontal and the c axis is v