1. Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine,
2. Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon 440-746, Korea
3. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
4. Department of Biochemistry, College of Medicine, Chung-Ang University, Seoul 156-756, Korea

Correspondence to: Yang-Gyun Kim⁴Kyeong Kyu Kim^1,2 Correspondence and requests for materials should be addressed to K.K.K (Email: kkim@med.skku.ac.kr) or Y.-G.K (Email: ygkimmit@cau.ac.kr). Coordinates and structure factor files have been deposited in the Protein Data Bank under the accession number 2ACJ

Abstract

Left-handed Z-DNA is a higher-energy form of the double helix, stabilized by negative supercoiling generated by transcription or unwrapping nucleosomes¹. Regions near the transcription start site frequently contain sequence motifs favourable for forming Z-DNA², and formation of Z-DNA near the promoter region stimulates transcription^{3, 4}. Z-DNA is also stabilized by specific protein binding; several proteins have been identified with low nanomolar binding constants^{5, 6, 7, 8, 9}. Z-DNA occurs in a dynamic state, forming as a result of physiological processes then relaxing to the right-handed B-DNA¹. Each time a DNA segment turns into Z-DNA, two B–Z junctions form. These have been examined extensively^{10, 11, 12}, but their structure was unknown. Here we describe the structure of a B–Z junction as revealed by X-ray crystallography at 2.6 Å resolution. A 15-base-pair segment of DNA is stabilized at one end in the Z conformation by Z-DNA binding proteins, while the other end remains B-DNA. Continuous stacking of bases between B-DNA and Z-DNA segments is found, with the breaking of one base pair at the junction and extrusion of the bases on each side (Fig. 1). These extruded bases may be sites for DNA modification.

Figure 1: A van der Waals view of the 15-base-pair DNA structure containing a junction between left-handed Z-DNA and right-handed B-DNA.

Two bases have been extruded from base stacking at the junction. The white line goes from phosphate to phosphate along the chain. O is shown red, N blue, P yellow and C grey.

High resolution image and legend (101K)

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