Structural fluctuation observed in Z-DNA d(CGCGCG)₂ in the absence of divalent metal cations and polyamines.

Toshiyuki Chatake

doi:10.1107/s0909049513020773

Abstract

In the present study, Z-DNA d(CGCGCG)2 was crystallized from a DNA solution in the absence of divalent metal cations and polyamines, and its X-ray structure was determined at 0.98 Å resolution. Comparison of this structure and previously reported Z-DNA structures, containing Mg(2+) cations and/or polyamines, demonstrated that Z-DNA can have structural fluctuations with respect to phosphate groups and hydration in the minor groove. At the GpC steps, a two-state structural equilibrium between the ZI and ZII conformations was frequently observed. In contrast, at the CpG steps, the phosphate groups exhibited rotational fluctuation, which could induce distortion of sugar puckering. In addition, alternative positions of water molecules were found in the middle of the minor groove of the Z-DNA. These structural fluctuations were likely observable because of the absence of Mg(2+) cations and polyamines. The results related to these phenomena were supported by those of other experimental methods, suggesting the possibility of these fluctuations occurring in biological conditions.

Highlights

Z-DNA has a left-handed double helical structure, which is observably different from B-DNA
The Z-DNA structure that we report, which contained neither MgCl2 nor polyamine, showed behaviour different from that seen in previous studies with regard to the conformations of the phosphate groups at the GpC steps
The continual fluctuation at the CpG steps was frequent, and this fluctuation could be related to sugar puckering

Summary

Introduction

Z-DNA has a left-handed double helical structure, which is observably different from B-DNA. Associations have been found between Z-DNA and transcription (Schroth et al, 1992; Liu & Wang, 1987; Lipps et al, 1983), and Z-DNA binding proteins such as ADAR1 (Schwartz et al, 1999), ZALM1 (Schwartz et al, 2001) and DsrD (Mizuno et al, 2003) have been identified. The precise atomic structure of Z-DNA is applicable for understanding structural variety of DNA duplex and interactions of Z-DNA with protein and DNA-binding drugs. The DNA hexamer d(CGCGCG) is the most common DNA oligomer used in the crystallographic study of Z-DNA. Since high-quality crystals of the DNA hexamer can be obtained, many comparative studies were carried out at the atomic level under different conditions

Methods

Results

Conclusion