Structure of d(TGCGCA)₂ and a Comparison to Other DNA Hexamers

Abstract

The X-ray crystal structure of d(TGCGCA) 2 has been determined at 120 K to a resolution of 1.3 A Ê . Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the`pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388±11402] but with signi®cantly different cell dimensions. The phosphate backbone exists in two equally populated discrete conformations at one nucleotide step, around phosphate 11. The structure contains two ordered cobalt hexammine molecules which have roles in stabilization of both the Z-DNA conformation of the duplex and in crystal packing. A comparison of d(TGCGCA) 2 with other Z-DNA hexamer structures available in the Nucleic Acid Database illustrates the elusive nature of crystal packing. A review of the interactions with the metal cations Na + , Mg 2+ and Co 3+ reveals a relatively small proportion of phosphate binding and that close contacts between metal ions are common. A prediction of the water structure is compared with the observed pattern in the reported structure.

Exploration of the influence of 5-iodo-2′-deoxyuridine incorporation on the structure of d[CACG(IDU)G]

“…2c). These contacts are quite similar to those seen for the second cobalt hexammine in ZDF060 (Harper et al, 1998). In our case the extra contacts that appear can be explained by the tighter packing.…”

“…The Z II conformation has also been observed at P3 in two other Z-DNA hexamers (Schroth et al, 1993;Harper et al, 1998).…”

“…The only other Z-DNA structure (containing no overhanging bases) crystallized with cobalt hexammine, d(TGCGCA) 2 , also adopts this mode (Harper et al, 1998). The reduction of the unit-cell volume when going from mode 1 (25036 A Ê 3 ) to mode 2 (24436 A Ê 3 ), and caused by a compression along the helical axis (Egli et al, 1991), is even more pronounced in the reported structure (22 895 A Ê 3 ).…”

A DNA structural alphabet provides new insight into DNA flexibility

“…The sizes of the tetrahedrons represent the confal values for each step. The tetranucleotide with PDB entry 1ana (Conner et al, 1984) is a typical A-DNA, PDB entry 1bna (Drew et al, 1981) is B-DNA overall but with pronounced A-like features, PDB entry 362d (Harper et al, 1998) is a typical Z-DNA, and PDB entry 190d (Chen et al, 1994) is DNA folded as an i-motif with several A-like steps but with most steps unassigned. The quadruplex with PDB entry 1jpq (Haider et al, 2002) has most steps in the B-DNA form; some steps have syn bases assigned (in orange) and a few are not assigned.…”

Nucleic‐acid structural deformability deduced from anisotropic displacement parameters

“…Each structure meets the following criteria: (i) refinement at a resolution of 1.3 Å or better, (ii) chain length of at least six nucleotides on each strand, (iii) anisotropic displacement parameters reported for both strands, and (iv) no major chemical modifications or structural abnormalities. The data include three right‐handed A‐DNA decamers (NDB_IDs AD0007, AD0027, and AD0028),22–24 six right‐handed Dickerson‐Drew B‐DNA dodecamers (NDB_IDs BD0007, BD0012, BD0030, BD0041, BD0054, and BD0060),19, 22, 25–28 one B‐DNA decamer with 3′‐terminal overhanging bases (NDB_ID BD0018),29 one right‐handed AB‐DNA intermediate dodecamer (NDB_ID BD0026),30 two left‐handed Z‐DNA hexamers (NDB_IDs ZD0005, ZDF060),31, 32 one drug‐DNA complex with a cytotoxic platinum(II) compound associated through a novel backbone‐binding motif (NDB_ID DD0086),33 one protein‐bound DNA structure in which the DNA is bound to Escherichia coli endonuclease VIII (NDB_ID PD0254),34 and one RNA structure containing two coaxially stacked double‐stranded fragments (NDB_ID AR0013) 35…”