Comparison of a Left-Handed Z-DNA Molecular Structure Determined by X-Rays with That Simulated by a Molecular Dynamics

Crystals of left-handed Z-DNA [d(CGCGCG)]2 diffract X-rays to beyond 1 Å resolution, feature a small unit cell (∼18 × 31 × 44 Å) and are well hydrated, with around 90 water molecules surrounding the duplex in the asymmetric unit. The duplex shows regular hydration patterns in the narrow minor groove, on the convex surface and around sugar–phosphate backbones. Therefore, Z-DNA offers an ideal case to test the benefits of low-temperature neutron diffraction data collection to potentially determine the donor–acceptor patterns of first- and second-shell water molecules. Nucleic acid fragments pose challenges for neutron crystallography because water molecules are located on the surface rather than inside sequestered spaces such as protein active sites or channels. Water molecules can be expected to display dynamic behavior, particularly in cases where water is not part of an inner shell and directly coordinated to DNA atoms. Thus, nuclear density maps based on room-temperature diffraction data with a resolution of 1.6 Å did not allow an unequivocal determination of the orientations of water molecules. Here, cryo-neutron diffraction data collection for a Z-DNA crystal on the Macromolecular Neutron Diffractometer at the Spallation Neutron Source at Oak Ridge National Laboratory and the outcome of an initial refinement of the structure are reported. A total of 12 diffraction images were recorded with an exposure time of 3.5 h per image, whereby the crystal was static for each diffraction image with a 10° φ rotation between images. Initial refinements using these neutron data indicated the positions and orientations of 30 water molecules within the first hydration shell of the DNA molecule. This experiment constitutes a state-of-the-art approach and is the first attempt to our knowledge to determine the low-temperature neutron structure of a DNA crystal.

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The halting arrival of left-handed Z-DNA

Medical Hypotheses ◽

10.1016/s0306-9877(02)00418-8 ◽

2003 ◽

Vol 60 (3) ◽

pp. 418-423 ◽

Cited By ~ 6

Author(s):

C.E Gagna ◽

W.C Lambert

Keyword(s):

Left Handed ◽

Z Dna

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Thermodynamic Model for B-Z Transition of DNA Induced by Z-DNA Binding Proteins

Molecules ◽

10.3390/molecules23112748 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2748 ◽

Cited By ~ 5

Author(s):

Ae-Ree Lee ◽

Na-Hyun Kim ◽

Yeo-Jin Seo ◽

Seo-Ree Choi ◽

Joon-Hwa Lee

Keyword(s):

Dna Binding ◽

Dna Sequences ◽

Genomic Dna ◽

Binding Proteins ◽

Dna Binding Proteins ◽

Multiple Sequence ◽

Left Handed ◽

Transition Mechanism ◽

Dna Strands ◽

Z Dna

Z-DNA is stabilized by various Z-DNA binding proteins (ZBPs) that play important roles in RNA editing, innate immune response, and viral infection. In this review, the structural and dynamics of various ZBPs complexed with Z-DNA are summarized to better understand the mechanisms by which ZBPs selectively recognize d(CG)-repeat DNA sequences in genomic DNA and efficiently convert them to left-handed Z-DNA to achieve their biological function. The intermolecular interaction of ZBPs with Z-DNA strands is mediated through a single continuous recognition surface which consists of an α3 helix and a β-hairpin. In the ZBP-Z-DNA complexes, three identical, conserved residues (N173, Y177, and W195 in the Zα domain of human ADAR1) play central roles in the interaction with Z-DNA. ZBPs convert a 6-base DNA pair to a Z-form helix via the B-Z transition mechanism in which the ZBP first binds to B-DNA and then shifts the equilibrium from B-DNA to Z-DNA, a conformation that is then selectively stabilized by the additional binding of a second ZBP molecule. During B-Z transition, ZBPs selectively recognize the alternating d(CG)n sequence and convert it to a Z-form helix in long genomic DNA through multiple sequence discrimination steps. In addition, the intermediate complex formed by ZBPs and B-DNA, which is modulated by varying conditions, determines the degree of B-Z transition.

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Oligonucleotides DNA containing 8-trifluoromethyl-2′-deoxyguanosine for observing Z-DNA structure

Nucleic Acids Research ◽

10.1093/nar/gkaa505 ◽

2020 ◽

Cited By ~ 1

Author(s):

Hong-Liang Bao ◽

Tatsuki Masuzawa ◽

Takanori Oyoshi ◽

Yan Xu

Keyword(s):

Genetic Diseases ◽

Dna Structure ◽

2D Nmr ◽

Living Cells ◽

Molecular Probes ◽

Alternative Form ◽

Left Handed ◽

Z Dna ◽

And Function

Abstract Z-DNA is known to be a left-handed alternative form of DNA and has important biological roles as well as being related to cancer and other genetic diseases. It is therefore important to investigate Z-DNA structure and related biological events in living cells. However, the development of molecular probes for the observation of Z-DNA structures inside living cells has not yet been realized. Here, we have succeeded in developing site-specific trifluoromethyl oligonucleotide DNA by incorporation of 8-trifluoromethyl-2′-deoxyguanosine (FG). 2D NMR strongly suggested that FG adopted a syn conformation. Trifluoromethyl oligonucleotides dramatically stabilized Z-DNA, even under physiological salt concentrations. Furthermore, the trifluoromethyl DNA can be used to directly observe Z-form DNA structure and interaction of DNA with proteins in vitro, as well as in living human cells by19F NMR spectroscopy for the first time. These results provide valuable information to allow understanding of the structure and function of Z-DNA.

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