Crystal structure at 1.5-.ANG. resolution of d(CGCICICG), an octanucleotide containing inosine, and its comparison with d(CGCG) and d(CGCGCG) structures

Abstract

The octadeoxyribonucleotide d(CGCICICG) has been crystallized in space group P(6)5(22) with unit cell dimensions of a = b = 31.0 A and c = 43.7 A, and X-ray diffraction data have been collected to 1.5-A resolution. Precession photographs and the self-Patterson function indicate that 12 base pairs of Z-conformation DNA stack along the c-axis, and the double helices pack in a hexagonal array similar to that seen in other crystals of Z-DNA. The structure has been solved by both Patterson deconvolution and molecular replacement methods and refined in space group P(6)5 to an R factor of 0.225 using 2503 unique reflections greater than 3.0 sigma (F). Comparison of the molecules within the hexagonal lattice with highly refined crystal structures of other Z-DNA reveals only minor conformational differences, most notably in the pucker of the deoxyribose of the purine residues. The DNA has multiple occupancy of C:I and C:G base pairs, and C:I base pairs adopt a conformation similar to that of C:G base pairs.

Specificity and Catalytic Mechanism in Family 5 Uracil DNA Glycosylase

“…The T/I and A/I base pairs have a similar level of higher stability than the G/I base pair. The C/I base pair has the highest level of stability, in keeping with its structural similarity to a C/G base pair (34). The outcome of the computational analysis on the stability of the hypoxanthinecontaining base pairs is consistent with experimental analyses previously reported (35)(36)(37).…”

Strand Breaks in X-Irradiated Crystalline DNA: Alternating CG Oligomers

“…Because the crystal structure of CG10 had not been determined previously, x-ray diffraction data was taken and analyzed by two of us (SBH and LDW). CG10 was found be nearly isomorphous to CG8 (10) and to the closely related crystal of d(CGCICICG) 2 (11). In each case, the Z-DNA duplexes are packed so as to form parallel columns of continuously stacked CG base pairs.…”

Studies on the base pairing properties of deoxyinosine by solid phase hybridisation to oligonucleotides

“…It has a similar structure to guanosine, but lacks the 2-amino group, and pairs with the natural bases as shown in Figure 1 (2)(3)(4)(5)(6)(7)(8)(9). Deoxyinosine has been investigated as a universal base for use in oligonucleotide probes and primers (10)(11)(12).…”