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Crystal structure of Z-DNA in com­plex with the polyamine putrescine and potassium cations at ultra-high resolution1

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aCenter for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland, and bDepartment of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
*Correspondence e-mail: mariuszj@amu.edu.pl

Edited by A. Nangia, CSIR–National Chemical Laboratory, India (Received 12 November 2020; accepted 10 March 2021; online 6 May 2021)

The X-ray crystal structure of the d(CGCGCG)2/putrescine(2+)/K+ com­plex has been determined at 0.60 Å resolution. Stereochemical restraints were used only for the putrescinium dication, and 23 bonds and 18 angles of the Z-DNA nucleotides with dual conformation. The N atoms of the putrescine(2+) dication form three direct hydrogen bonds with the N7_G atoms of three different Z-DNA molecules, plus three water-mediated hydrogen bonds with cytosine, guanine and phosphate acceptors. A unique potassium cation was also unambiguously identified in the structure, albeit at a ∼0.5 occupation site shared with a water molecule, providing the first example of such a com­plex with Z-DNA. The K+ cation has coordination number of eight and an irregular coordination sphere, formed by four water molecules and four O atoms from two phosphate groups of the Z-DNA, including ligands present at fractional occupancy. The structural disorder of the Z-DNA duplex is manifested by the presence of alternate conformations along the DNA backbone. Comparison of the position and interactions of putrescine(2+) in the present structure with other ultra-high-resolution structures of Z-DNA in com­plexes with Mn2+ and Zn2+ ions shows that the dicationic putrescinium moiety can effectively substitute these metal ions for stabilization of Z-type DNA duplexes. Furthermore, this comparison also suggests that the spermine(4+) tetracation has a higher affinity for Z-DNA than K+.

1. Introduction

Biogenic polyamine cations are essential for cell growth and differentiation, and their biochemical significance in a wide spectrum of physiological functions has been repeatedly reviewed (Gugliucci, 2004[Gugliucci, A. (2004). Clin. Chim. Acta, 344, 23-35.]; Moinard et al., 2005[Moinard, C., Cynober, L. & de Bandt, J.-P. (2005). Clin. Nutr. 24, 184-197.]; Larqué et al., 2007[Larqué, E., Sabater-Molina, M. & Zamora, S. (2007). Nutrition, 23, 87-95.]; Igarashi & Kashiwagi, 2010[Igarashi, K. & Kashiwagi, K. (2010). Int. J. Biochem. Cell. Biol. 42, 39-51.]; Jastrzab et al., 2016[Jastrzab, R., Lomozik, L. & Tylkowski, B. (2016). Phys. Sci. Rev. 1, 20160003.]). Common com­pounds in this group include the di­amines 1,3-di­amino­propane(2+) (Dap2+), putrescine(2+) (Put2+) and cadaverine(2+) (Cad2+), the tri­amines spermidine(3+) (Spd3+) and norspermidine(3+), and the tetramine spermine(4+) (Spm4+). Put2+ and Cad2+ are the two most common biogenic di­amines in bacteria. For example, at a concentration of 10–30 mM, putrescine is the predominant polyamine in Escherichia coli (Cohen, 1997[Cohen, S. S. (1997). In A Guide to the Polyamines. New York: Oxford University Press Inc.]). Polyamines(n+) are involved in maintaining the cell-envelope integrity of bacteria. They are also crucial to the virulence phenotype of many bacterial pathogens (Shah & Swiatlo, 2008[Shah, P. & Swiatlo, E. (2008). Mol. Microbiol. 68, 4-16.]; Di Martino et al., 2013[Di Martino, M. L., Campilongo, R., Casalino, M., Micheli, G., Colonna, B. & Prosseda, G. (2013). Int. J. Med. Microbiol. 303, 484-491.]). Moreover, polyamines(n+) are important resources for viruses, which evolved mechanisms to maintain, enhance or manipulate polyamine(n+) metabolism to support viral infection (Firpo & Mounce, 2020[Firpo, M. R. & Mounce, B. C. (2020). Biomolecules, 10, 628.]). For instance, Mounce et al. (2017[Mounce, B. C., Olsen, M. E., Vignuzzi, M. & Connor, J. H. (2017). Microbiol. Mol. Biol. Rev. 81, e00029-17.]) showed the enhancement of viral polymerase activity by polyamines(n+). Polyamines(n+) are important factors stabilizing nucleic acids and stimulating their replication; only ∼7–10% of the total cell content exists as free polyamines(n+), the vast majority remaining in association with nucleic acids (Gugliucci, 2004[Gugliucci, A. (2004). Clin. Chim. Acta, 344, 23-35.]). It was also shown that both polyamines(n+) and metal polycations (even at low concentration) can stimulate B to Z conversion of DNA and promote DNA condensation (Ohishi et al., 2008[Ohishi, H., Odoko, M., Grzeskowiak, K., Hiyama, Y., Tsukamoto, K., Maezaki, N., Ishida, T., Tanaka, T., Okabe, N., Fukuyama, K., Zhou, D. Y. & Nakatani, K. (2008). Biochem. Biophys. Res. Commun. 366, 275-280.]; Vijayanathan et al., 2001[Vijayanathan, V., Thomas, T., Shirahata, A. & Thomas, T. J. (2001). Biochemistry, 40, 13644-13651.]). Generally, both polyamines(n+) and metal cations can interact with Z-DNA molecules in one of two different modes. Polyamine(n+) cations are found to bind to the O atoms of different phosphate groups either directly or through water-mediated bridges. In the second mode, the cations are coordinated simultaneously by the guanine bases from different helices and also by the O atoms of dual-conformation phosphate groups (Tomita et al., 1989[Tomita, K., Hakoshima, T., Inubushi, K., Kunisawa, S., Ohishi, H., van der Marel, G. A., van Boom, J. H., Wang, A. H.-J. & Rich, A. (1989). J. Mol. Graph. 7, 71-75.]; Gao et al., 1993[Gao, Y.-G., Sriram, M. & Wang, A. H.-J. (1993). Nucleic Acids Res. 21, 4093-4101.]).

Among all Z-DNA (Wang et al., 1979[Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., Crawford, J. L., van Boom, J. H., van der Marel, G. & Rich, A. (1979). Nature, 282, 680-686.]) com­plexes, the largest number of crystal structures in the Protein Data Bank (PDB; Berman et al., 2000[Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). Nucleic Acids Res. 28, 235-242.]) and Nucleic Acid Database (NDB; Narayanan et al., 2014[Coimbatore Narayanan, B., Westbrook, J., Ghosh, S., Petrov, A. I., Sweeney, B., Zirbel, C. L., Leontis, N. B. & Berman, H. M. (2014). Nucleic Acids Res. 42, D114-D122.]) is available for com­plexes with magnesium and sperminium cations (Table 8 in Drozdzal, 2014[Drozdzal, P. (2014). PhD thesis. A. Mickiewicz University, Poznan, Poland. https://repozytorium.amu.edu.pl/handle/10593/10090.]). Z-DNA com­plexes with Dap2+ (PDB ID 2f8w), Spd3+ (2elg and 293d), N-(2-aminoethyl)-1,4-di­aminobutane (292d), thermospermine(4+) (336d), trientine(4+) (1dj6) and N1-{2-[2-(2-aminoethyl­amino)ethyl­amino]ethyl}ethane-1,2-di­amine (2ie1) are also deposited in the PDB. Besides the Mg2+ cation, there are PDB structures of Z-DNA or Z-DNA-RNA (Gilski et al., 2016[Gilski, M., Drozdzal, P., Kierzek, R. & Jaskolski, M. (2016). Acta Cryst. D72, 211-223.]) duplexes with many other metal(n+) cations, including Ba2+, Mn2+, Cu2+, Zn2+, Cr3+, Co3+ and Ru3+. There is currently no structure, however, of a Z-DNA/K+ com­plex.

While the structure of the Put2+ cation has been thoroughly studied (Woo et al., 1979[Woo, N. H., Seeman, N. C. & Rich, A. (1979). Biopolymers, 18, 539-552.]; Bratek-Wiewiorowska et al., 1986[Bratek-Wiewiorowska, M. D., Alejska, M., Perkowska, A., Wiewiorowski, M., Jaskolski, M. & Cramer, F. (1986). Bull. Acad. Pol. Sci. Chim. 34, 229-249.]; Jaskólski, 1987[Jaskólski, M. (1987). Acta Cryst. C43, 1761-1763.]; Pospieszna-Markiewicz et al., 2007[Pospieszna-Markiewicz, I., Radecka-Paryzek, W. & Kubicki, M. (2007). Acta Cryst. E63, o3650.]), including the structures of phosphate salts (Jaskólski et al., 1986[Jaskólski, M., Alejska, M. & Wiewiórowski, M. (1986). J. Crystallogr. Spectrosc. Res. 16, 31-39.]; Bartoszak & Jaskólski, 1990[Bartoszak, E. & Jaskólski, M. (1990). Acta Cryst. C46, 2158-2160.]) and a study at helium temperature (Jaskólski & Olovsson, 1989[Jaskólski, M. & Olovsson, I. (1989). Acta Cryst. B45, 78-85.]), it is rather poorly characterized as a component of nucleic acid structures. The Put2+ dication was specified as a nucleic acid ligand only in nine structures deposited in the PDB, all of them corresponding to E. coli ribosome.

In this article, we describe a very-high-resolution crystal structure of Z-DNA with the sequence d(CGCGCG)2, which for the first time provides insight into the interaction of Z-DNA with Put2+ and K+ cations. We also discuss the questions of competition and effectiveness of polyamine and metal cations in interactions with Z-DNA.

2. Materials and methods

2.1. Oligonucleotide synthesis, purification and crystallization

The methods of synthesis, deprotection and purification of the oligo­deoxy­nucleotide have been described previously (Xia et al., 1998[Xia, T., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C. & Turner, D. H. (1998). Biochemistry, 37, 14719-14735.]; Drozdzal et al., 2013[Drozdzal, P., Gilski, M., Kierzek, R., Lomozik, L. & Jaskolski, M. (2013). Acta Cryst. D69, 1180-1190.]). A 1.5 mM water solution of the DNA oligonucleotide with the self-com­plementary seq­uence d(CGCGCG) was heated at 338 K for 10 min and then annealed slowly to room temperature overnight. Single crystals of the d(CGCGCG)2/Put2+/K+ complex were grown at 292 K by the hanging-drop vapour-diffusion method by mixing a 2 µl nucleic acid solution and a 2 µl precipitating solution consisting of 10%(v/v) (+/−)-2-methyl-2,4-pentane­diol (MPD), 40 mM sodium cacodylate pH 6.0, 80 mM KCl, 12 mM NaCl and 14 mM putrescinium dichloride. The drops were equilibrated against 0.5 ml 80%(v/v) MPD. Crystals appeared within one week and grew to dimensions of 0.3 mm × 0.1 mm × 0.1 mm.

2.2. X-ray data collection and processing

X-ray diffraction data for the Z-DNA/Put2+/K+ com­plex were collected to a resolution of 0.60 Å on the EMBL beamline P13 (Cianci et al., 2017[Cianci, M., Bourenkov, G., Pompidor, G., Karpics, I., Kallio, J., Bento, I., Roessle, M., Cipriani, F., Fiedler, S. & Schneider, T. R. (2017). J. Synchrotron Rad. 24, 323-332.]) of the PETRA III storage ring at DESY, Hamburg. The crystal was vitrified in a stream of cold nitro­gen gas at 100 K. The mother liquor served as the cryoprotectant solution. The diffraction data were collected in two passes using two wavelengths and the following crystal-to-detector distances, oscillation ranges and numbers of images: λ 0.6880 and 0.7293 Å, 134 and 134 mm, 0.5 and 0.1° and 360 and 1800, respectively. The diffraction data were indexed, integrated and scaled using the XDS package (Kabsch, 2010[Kabsch, W. (2010). Acta Cryst. D66, 125-132.]). The X-ray data statistics are summarized in Table 1[link].

Table 1
Data collection and refinement statistics for d(CGCGCG)2/Put2+/K+

Data collection  
Radiation source P13, Petra III, DESY, Hamburg
Wavelength (Å) 0.6880, 0.7293
Temperature (K) 100
Space group P212121
Cell dimensions (Å) a = 17.97, b = 31.02, c = 43.86
Resolution range (Å) 25.33–0.60 (0.61–0.60)a
Number of reflections 107 989b
Completeness native (%) 90.5 (22.6)
Redundancy 3.7 (1.2)
I/σI 29.8 (2.9)
CC[1 \over 2]c 99.9 (81.1)
Rmerged (%) 2.4 (26.4)
Wilson B-factor (Å2) 5.17
   
Refinement  
Refinement program SHELXL (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.])
Resolution (Å) 25.33–0.60
No. of reflections in working set 106 103b
No. of reflections in test set 1876
R, Rfreee (%) 8.77, 9.50
No. of atoms (nucleic acid, solvent, polyamine, metal) 240, 123, 6, 1
B〉 (Å2) (nucleic acid chain A, B, solvent, polyamine, metal) 4.56, 3.99, 11.93, 4.27, 6.56
R.m.s. deviations from ideal bond lengths (Å), angles (°) 0.010, 1.56
Notes: (a) values in parentheses correspond to the last resolution shell; (b) Bijvoet pairs separated; (c) correlation between intensities from random half-sets as defined by Karplus & Diederichs (2012[Karplus, P. A. & Diederichs, K. (2012). Science, 336, 1030-1033.]); (d) Rmerge = ΣhΣj |Ij − 〈I〉|/ΣhΣjIj, where Ij is the intensity of observation j of reflection h; (e) R = Σh||Fo| − |Fc||/Σh|Fo| for all reflections, where Fo and Fc are the observed and calculated structure factors, respectively. Rfree was calculated analogously for the test reflections, which were randomly selected and excluded from the refinement.

2.3. Structure solution and refinement

The structure was solved by molecular replacement using PHASER (McCoy et al., 2007[McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J. Appl. Cryst. 40, 658-674.]). The DNA part of the PDB structure 4hig, corresponding to our earlier model of the d(CGCGCG)2/Spm4+/Mn2+ com­plex (Drozdzal et al., 2013[Drozdzal, P., Gilski, M., Kierzek, R., Lomozik, L. & Jaskolski, M. (2013). Acta Cryst. D69, 1180-1190.]), served as a molecular probe. At the initial stages of the refinement, the model was refined using REFMAC5 (Murshudov et al., 2011[Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355-367.]) from the CCP4 program suite (Winn et al., 2011[Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A. & Wilson, K. S. (2011). Acta Cryst. D67, 235-242.]). The final anisotropic refinement was carried out with SHELXL (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) using the full resolution of the diffraction data. The details of the SHELXL refinement were the same as described for our previous Z-DNA structures (Drozdzal et al., 2013[Drozdzal, P., Gilski, M., Kierzek, R., Lomozik, L. & Jaskolski, M. (2013). Acta Cryst. D69, 1180-1190.], 2015[Drozdzal, P., Gilski, M., Kierzek, R., Lomozik, L. & Jaskolski, M. (2015). J. Biol. Inorg. Chem. 20, 595-602.]), except for the use of the DISP instruction, which allows the definition of the dispersion and absorption coefficients of a particular element without having to use the full format of the SFAC instruction. The instruction OMIT was used to exclude ten of the most disagreeable reflections (error/e.s.d. > 10) from the refinement. The model was validated using the NuCheck program (Feng et al., 1998[Feng, Z., Westbrook, J. & Berman, H. M. (1998). Report NDB-407. Rutgers University, New Brunswick, New Jersey, USA.]) and the free R test (Brünger, 1992[Brünger, A. T. (1992). Nature, 355, 472-475.]), with 1876 reflections selected at random and set aside for Rfree calculations.

It should be noted that the atomic scattering factor for the K+ site was declared on the SFAC instruction by specifying a neutral K atom. This small inaccuracy means assigning one excess electron per 18 actual electrons. This should have very little, if any, effect on the refinement, possibly under­estimating the refinable occupancy of the K+ cation by a factor of 18/19.

At the wavelengths used in the diffraction experiments (0.6880, 0.7293 Å), the imaginary component of the anomalous scattering (f′′) of K and P atoms are, respectively, 0.236, 0.286 and 0.095, 0.104 electron units (Cromer, 1983[Cromer, D. T. (1983). J. Appl. Cryst. 16, 437.]). The anomalous signal is significant in the diffraction data set up to ∼0.9 Å resolution, as illustrated by clear peaks at the K+ ion and P atoms in the anomalous electron-density map (Fig. 1[link]).

[Figure 1]
Figure 1
Stereoview of the d(CGCGCG)2/Put2+/K+ com­plex with anomalous difference map (gray) peaks for the K+ ion (purple sphere) and P atoms. The map is contoured at 3σ. Note the alternative conformations (I is green and II is orange) along the DNA chain.

At this resolution, no stereochemical restraints are necessary to supplement the experimental observations (Jaskolski, 2017[Jaskolski, M. (2017). In Protein Crystallography: Methods and Protocols, Vol. 1607, pp. 549-563 in the series Methods in Molecular Biology edited A. Wlodawer, Z. Dauter & M. Jaskolski. Totowa, New Jersey: Springer - Humana Press.]). However, restraints may still be needed for some disordered or highly mobile fragments. In the present structure, restraints were applied only to the putrescinium dication and to bonds and angles (33 for the sugar and eight for the phospho­diester moieties) of dual-conformation Z-DNA fragments. The ideal geometry targets for Put2+ were taken from Pospieszna-Markiewicz et al. (2007[Pospieszna-Markiewicz, I., Radecka-Paryzek, W. & Kubicki, M. (2007). Acta Cryst. E63, o3650.]). Conformation-dependent geometrical restraints on bond lengths (DFIX) and bond angles (DANG) for the polynucleotide chains were generated using the RestraintLib server (http://achesym.ibch.poznan.pl/restraintlib/) as described by Kowiel et al. (2016[Kowiel, M., Brzezinski, D. & Jaskolski, M. (2016). Nucleic Acids Res. 44, 8479-8489.], 2020[Kowiel, M., Brzezinski, D., Gilski, M. & Jaskolski, M. (2020). Nucleic Acids Res. 48, 962-973.]) and Gilski et al. (2019[Gilski, M., Zhao, J., Kowiel, M., Brzezinski, D., Turner, D. H. & Jaskolski, M. (2019). Acta Cryst. B75, 235-245.]). The CSD-derived conformation-dependent RestraintLib dictionary supersedes the classic nucleic acid restraints compiled by Parkinson et al. (1996[Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T. & Berman, H. M. (1996). Acta Cryst. D52, 57-64.]). The final cycles of CGLS (conjugate-gradient least-squares) refinement converged with R/Rfree values of 8.88/9.50%. The very last round of refinement, calculated with the test reflections included in the working set, converged with R = 8.77%. In order to provide estimations of standard uncertainties in all individual refined parameters and of all derived geometrical parameters, at the final stage of the refinement, one cycle of full-matrix least-squares minimization was calculated. Model placement in the unit cell was standardized with the Achesym server (Kowiel et al., 2014[Kowiel, M., Jaskolski, M. & Dauter, Z. (2014). Acta Cryst. D70, 3290-3298.]).

The final model includes all the H atoms of the oligonucleotides and Put2+ added as riding contributions to Fc. The ammonium –NH3+ groups of Put2+ were refined using the instruction AFIX 33. The rotatable O3′/5′—H groups of the terminal sugars were refined using the instruction AFIX 87.

Figures presenting the model and electron density were prepared with PyMOL (DeLano, 2002[DeLano, W. L. (2002). The pyMOL Molecular Graphics System, Version 2.0. Schrödinger, LLC, New York, USA. https://pymol.org/2/.]). The Coot (Emsley et al., 2010[Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.]) program was used for visualization of the electron-density maps and manual rebuilding of the atomic model. The program 3DNA (Lu & Olson, 2003[Lu, X. J. & Olson, W. K. (2003). Nucleic Acids Res. 31, 5108-5121.]) was used to calculate the Z-DNA helical parameters. The pseudorotation parameters were calculated by the method of Jaskólski (1984[Jaskólski, M. (1984). Acta Cryst. A40, 364-366.]) using the PseudoRotation server (http://www.cryst.ump.edu.pl/pseudorotation.php).

2.4. Data deposition in public repositories

Atomic coordinates and anisotropic ADPs, as well as the processed structure factors corresponding to the final model presented in this work, were deposited in the PDB with accession code 7atg. Raw X-ray diffraction images were deposited in the Integrated Resource for Reproducibility in Macromolecular Crystallography repository (proteindiffraction.org; Grabowski et al., 2016[Grabowski, M., Langner, K. M., Cymborowski, M., Porebski, P. J., Sroka, P., Zheng, H., Cooper, D. R., Zimmerman, M. D., Elsliger, M.-A., Burley, S. K. & Minor, W. (2016). Acta Cryst. D72, 1181-1193.]) with DOI https://dx.doi.org/10.18430/m37atg.

3. Results and discussion

3.1. Quality of the results

The estimated standard uncertainties (e.s.u.) of the fully occupied DNA atomic positions in the structure are in the range 0.003–0.01 Å for C atoms, 0.003–0.007 Å for N atoms, 0.003–0.009 Å for O atoms and 0.001–0.002 Å for P atoms. The e.s.u. values for the full-occupancy covalent bonds are ∼0.005, ∼0.004, ∼0.004 and ∼0.003 Å for C—C, C—O, C—N and P—O, respectively. The agreement with stereochemical standards (r.m.s.d.) is 0.010 Å for bond lengths and 1.56° for bond angles. These results are comparable in terms of accuracy and precision with the record-setting model of Z-DNA (0.55 Å, R = 7.77%, PDB ID 3p4j) described by Brzezinski et al. (2011[Brzezinski, K., Brzuszkiewicz, A., Dauter, M., Kubicki, M., Jaskolski, M. & Dauter, Z. (2011). Nucleic Acids Res. 39, 6238-6248.]).

3.2. Overall structure and helical parameters

The overall structural parameters of the DNA moieties of the d(CGCGCG)2/Put2+/K+ com­plex classify them within the Z-DNA family. The average helical twist Ωh (i.e. the angle of rotation about the helical axis that brings successive base pairs into coincidence) per CG/GC tandem of base pairs is −60°. Other average base-pair and base-pair-step parameters are as follows: helical rise 4.37 Å, inclination (η) 14.55°, tip 2.6°, tilt 0.44°, roll −3.32°, shift −0.02 Å, slide 2.77 Å and rise 3.45 Å. Comparison of these helical parameters and base-pair geometries for the present and previously described Z-DNA com­plexes shows that they are within the range typical for Z-DNA duplexes (see supplementary Table S3 in Drozdzal et al., 2015[Drozdzal, P., Gilski, M., Kierzek, R., Lomozik, L. & Jaskolski, M. (2015). J. Biol. Inorg. Chem. 20, 595-602.]).

The 5′-d(CGCGCG) nucleotides of chain A in the asymmetric unit are numbered 1–6 and the com­plementary 3′-d(GCGCGC) nucleotides of chain B are numbered 12–7. There are only five internucleotide phospho­diester groups on each strand, which are numbered, respectively, P2–P6 and P12–P8. Alternative conformations are clearly visible in the electron-density map and are designated as I/II at the C3–G4, G4–C5 and C5–G6 internucleotide phosphate linkages, whose refined occupancies converged at 0.687 (8)/0.313 (8), 0.710 (4)/0.290 (4) and 0.650 (12)/0.350 (12), respectively. The major (I) and minor (II) conformations of C3 have C2′-endo and C1′-exo sugar puckers with pseudorotation (P) angles of 162.0 (7) and 138.2 (6)°, respectively. Differences in sugar pucker are also observed at G4, where conformation I is C3′-endo [P = 20.2 (7)°] and conformation II is C4′-exo [P = 38 (1)°]. Moreover, the mFo–DFc electron-density maps indicate three additional discrete positions (peaks) for the phosphate atoms at the C3 (6.7σ), C9 (6.0σ) and C11 (6.7σ) nucleotides. However, additional phosphate groups placed at these peaks refined with an occupancy below 0.20. Therefore, no atoms were modelled to interpret the peaks near the P_C3, P_C9 and P_C11 atoms. No alternative conformations were observed for the base moieties.

In the present com­plex, the sugars at the 3′-termini do not have the alternating C2′-endo/C3′-endo pucker of the pyrimidine/purine nucleotides, as is typical for Z-DNA, but all assume the C2′-endo conformation. The ZII conformation of the phosphate group can be assigned only to G4(I) with ζ = 64.6° [ζ is a backbone torsion angle defined as: C3′—O3′—P(i + 1)—O5′(i + 1)]. This ZII conformation is stabilized by a water-mediated OP2(I)_G4⋯Wat81⋯N2_G4 hydrogen bond.

3.3. Coordination of the polyamine cation

The entire putrescinium dication is clearly visible in the electron-density map (Fig. 2[link]) despite its fractional occupancy, which converged on refinement at 0.378 (7). The putrescinium dication has a gauchetransgauche+ conformation, with the following torsion angles: −72.5 (7), 172.9 (5) and 71.0 (8)°. The Put2+ dication is involved in direct hydrogen-bond contacts only with the guanine N7 atoms of three DNA duplexes (Fig. 2[link]). The N1 atom is anchored by the N7 atoms of two neighbouring DNA duplexes at the following distances: N1_Put2+⋯N7_G12 = 2.915 (6) Å and N1_Put2+⋯N7_G10i = 2.755 (6) Å [symmetry code: (i) x − [1 \over 2], −y + [3 \over 2], −z + 1]. The N2 atom is hydrogen bonded to N7_G6ii at a distance of 2.839 (7) Å [symmetry code: (ii) −x + [3 \over 2], −y + 1, z − [1 \over 2]]. The remaining three N—H donors of the putrescinium dication form water-mediated hydrogen bonds with the O6_G10i, N4_C9i and OP1(I)_C5ii atoms of two Z-DNA duplexes.

[Figure 2]
Figure 2
The putrescinium(2+) dication in the crystal structure of the d(CGCGCG)2/Put2+/K+ com­plex. The 2mFo-DFc map is contoured at the 1.6σ level. Some water molecules have been omitted for clarity. Hydrogen bonds are marked by dashed lines, with DA distances in Å.

The electron-density maps indicate six water molecules in the vicinity of the Put2+ dication as alternative species populating the polyamine(2+) site at com­plementary occupancy. It should be noted that there was a ∼20-fold molar excess of Put2+ relative to the Z-DNA duplex in the crystallization mixture. The low occupancy of the Put2+ site is, therefore, not the result of insufficient supply of the ligand, but rather reflects the natural equilibrium of components required for growing those high-quality (from the point of view of diffraction quality) crystals.

There is very little literature information on putrescine(2+) interactions with longer d(CG)n sequences. Putrescine had no effect on the conformation of a plasmid (pDHg16) with a 23-base pair d(GC)23 insert up to a 3 mM concentration (Thomas et al., 1991[Thomas, T. J., Gunnia, U. B. & Thomas, T. (1991). J. Biol. Chem. 266, 6137-6141.]). Our results indicate that the putrescine(2+) cation has preference for interactions with Z-DNA bases, which may explain why a 3 mM putrescine concentration was not sufficient for the B- to Z-DNA transition in the above plasmid. For longer d(GC)n sequences in vitro, high concentrations of the putrescine(2+) cation may be needed to lower the energetic cost of Z-DNA formation.

3.4. Coordination of the K+ cation

The electron-density maps clearly revealed one metal co­ordi­nation site with an occupancy of 0.49 (3), interpreted as potassium. Due to the partial occupation of the potassium cation, a com­plementary water molecule (Wat202) was also modeled in the 2mFo–DFc map at this site with an occupancy of 0.34 (6). After the refinement of this model, the R factor was reduced from 8.82 to 8.77%. The refined distance between the K+ and Wat202 sites is 0.195 (14) Å.

The metal was unambiguously identified as potassium using the following pieces of evidence. The length of the M—O bonds supports the presence of K+ rather than, for example, the presence of Na+ at higher occupancy. In the anomalous difference map, its peak (6.1σ) had a height similar to that of a full-occupancy P atom (P_11 at 6.4σ). The bond-valence method of Brese & O'Keeffe (1991[Brese, N. E. & O'Keeffe, M. (1991). Acta Cryst. B47, 192-197.]), which correlates bond valences with the identity of the metal atom, is a popular method in coordination chemistry, and is especially reliable at high resolution. The application of this method gives values of the valence (VK) and bond-valence (RKO) parameters of 1.18, 1.09 and 2.07, 2.10 (the expected values for K+ being VK = 1.00 and RKO = 2.13) for the coordination sphere including Wat110(I)/Wat110(II), respectively (vide infra). Also, the application of the CBVS method of Müller et al. (2003[Müller, P., Köpke, S. & Sheldrick, G. M. (2003). Acta Cryst. D59, 32-37.]) confirmed the identity of the metal site as K+ (calcium bond-valence sum CBVS = 0.53; according to the CBVS method, the reference value for K+ is 0.64). Finally, the CheckMyMetal server (Zheng et al., 2014[Zheng, H., Chordia, M. D., Cooper, D. R., Chruszcz, M., Müller, P., Sheldrick, G. M. & Minor, W. (2014). Nat. Protoc. 9, 156-170.]) also predicted potassium as the most likely cation at this site.

The K+ cation is located between two Z-DNA phosphate groups. There are eight O atoms (four from Z-DNA backbone and four from water molecules) in the immediate vicinity (up to a distance of 3.20 Å) of the K+ cation (Table 2[link]). However, one of the water molecules (Wat110) and one phosphate group (OP1_G6) interacting with the potassium cation are disordered and were modelled in two com­plementary positions. In the presence of the OP1(I) and O5′(I) atoms (CN = 8), the coordination sphere can be considered as highly distorted square antiprismatic or dodecahedral. The K+ ion is coordinated simultaneously by OP1(I), O5′(I) from G6 and OP1, OP2 from C9iii [symmetry code: (iii) −x + 1, y − [1 \over 2], −z + [3 \over 2]], as well as by four water sites, one of which (Wat110) has dual occupancy (Fig. 3[link] and Table 2[link]). The K+—O bond distances are in the range 2.612 (22)–3.185 (11) Å. The angles within the coordination sphere are irregular (Table 2[link]).

Table 2
Coordination geometry (Å, °) around the metal ion in the d(CGCGCG)2/Put2+/K+ structure, with standard uncertainties in parentheses

  Distance Angles
W109 2.661 (8)                
W110(I) 2.612 (22) 80.3 (6)              
W110(II) 2.831 (39) 72.3 (10) 12.4 (8)            
W111 2.887 (20) 157.3 (8) 77.8 (8) 87 (1)          
OP1(I)_6 2.715 (8) 108.8 (2) 97.1 (7) 90.1 (10) 80.0 (4)        
O5′(I)_6 3.047 (11) 73.4 (2) 123.6 (6) 111 (1) 124.5 (6) 49.5 (2)      
W117 3.172 (29) 168.0 (5) 107.4 (7) 117 (1) 29.8 (6) 79.9 (3) 108.3 (5)    
OP1_9iii 3.185 (11) 80.4 (2) 151.4 (7) 150.7 (9) 117.3 (5) 109.1 (4) 69.9 (3) 89.0 (5)  
OP2_9iii 2.792 (7) 88.3 (2) 108.6 (7) 118 (1) 93.1 (4) 151.4 (5) 119.2 (4) 80.5 (4) 49.9 (2)
- K+ W109 W110(I) W110(II) W111 OP1(I)_6 O5′(I)_6 W117 OP1_9iii
Symmetry code: (iii) −x + 1, y − [1 \over 2], −z + [3 \over 2].
[Figure 3]
Figure 3
The coordination sphere of the hydrated com­plex of K+ (purple) at G6. The 2mFo–DFc map is contoured at 1.0σ. Coordination bonds are marked as gray dashed lines and hydrogen bonds are marked as orange dashed lines. Bond distances are in Å.

3.5. Hydration

The asymmetric unit contains 123 water sites. All water molecules were refined anisotropically without positional restraints. There was no attempt to model the H atoms of the water molecules. While for some water molecules it might be possible to try to locate their H atoms from difference Fourier maps, such H atoms have notoriously very poor geometry, even in small-molecule structures, and in macromolecular structures the dubious gain from their inclusion in the model usually does not compensate the burden of their individual handling in the refinement (Jaskolski, 2017[Jaskolski, M. (2017). In Protein Crystallography: Methods and Protocols, Vol. 1607, pp. 549-563 in the series Methods in Molecular Biology edited A. Wlodawer, Z. Dauter & M. Jaskolski. Totowa, New Jersey: Springer - Humana Press.]). Summation of all the water occupancies in the asymmetric unit gives a total water content of 93.15. The positions of many disordered water molecules are correlated with the alternate I/II conformations of the Z-DNA backbones. With respect to their occupancy parameters, those water molecules for which the occupancies converged on refinement to values close to unity (>0.93) had their occupancy fixed at 1.0 (22 sites). Close pairs of sites for which the sum of their refined occupancies converged close to unity (36 pairs) had their combined occupancy constrained to 1.0. The remaining 65 sites had their occupancies refined freely to fractional values (all ≥0.20). The common patterns of solvent structure, as noted previously for Z-DNA crystals (Drozdzal et al., 2013[Drozdzal, P., Gilski, M., Kierzek, R., Lomozik, L. & Jaskolski, M. (2013). Acta Cryst. D69, 1180-1190.], 2015[Drozdzal, P., Gilski, M., Kierzek, R., Lomozik, L. & Jaskolski, M. (2015). J. Biol. Inorg. Chem. 20, 595-602.]), such as water molecules between N2_G and phosphate O atoms, the spine of hydration (Chevrier et al., 1986[Chevrier, B., Dock, A. C., Hartmann, B., Leng, M., Moras, D., Thuong, M. T. & Westhof, E. (1986). J. Mol. Biol. 188, 707-719.]), two water molecules hydrogen bonded to each O6_G group or the absence of water molecules hydrogen bonded to the N3_G atoms, are also ob­served in the present Z-form structure.

4. Discussion

In this work, we have presented a new crystal structure of Z-DNA/polyamine(n+), in com­plex with putrescine(2+) and K+ cations. It describes the first example of the interactions of putrescine(2+) with a DNA duplex. It is also the first case of Z-DNA crystallized in a com­plex with potassium ions. Moreover, the structure has the highest resolution and accuracy of the refined parameters among all DNA com­plexes with biogenic polyamines and/or metal cations deposited in the PDB.

Although the crystallization systems for all the Z-DNA com­plexes presented in our previous studies (Drozdzal et al., 2013[Drozdzal, P., Gilski, M., Kierzek, R., Lomozik, L. & Jaskolski, M. (2013). Acta Cryst. D69, 1180-1190.], 2015[Drozdzal, P., Gilski, M., Kierzek, R., Lomozik, L. & Jaskolski, M. (2015). J. Biol. Inorg. Chem. 20, 595-602.]) always contained KCl at a concentration of 40–80 mM in the crystallization drop, the K+ cation has been identified in the electron-density maps only in the present Z-DNA structure in com­plex with putrescine(2+). Comparison of the Z-DNA/Spm4+/Mn2+ and Z-DNA/Spm4+/Zn2+ structures with the present Z-DNA/Put2+/K+ com­plex in their common unit cell shows that the N1+ atoms of Spm4+ coincide almost exactly with the site of the K+ cation. This may indicate that the Spm4+ cation has a higher affinity for Z-DNA binding than the K+ cation and is preferentially selected when both are present in the crystallization buffer. It should also be stressed that the Z-DNA/K+ interaction has not been described in the literature so far in any crystallographic studies of Z-DNA structures. It is interesting to note that the general location of the N1+ and N2+ atoms of the putrescinium(2+) dication in the unit cell of the Z-DNA/Put2+/K+ com­plex is analogous to the positions of certain divalent metal cations, such as Mn2+ (PDB ID 4hig) or Zn2+(1) and Zn2+(2) (4hif) (Drozdzal et al., 2013[Drozdzal, P., Gilski, M., Kierzek, R., Lomozik, L. & Jaskolski, M. (2013). Acta Cryst. D69, 1180-1190.]) (Fig. 4[link]). Therefore, Put2+, having the same net charge as Mn2+ or Zn2+, can effectively replace these cations in interactions with the Z-DNA duplex. It is also worth mentioning that putrescine(2+) has a com­pletely different interaction pattern than 1,3-di­amino­propane(2+) (Dap2+) and 1,5-pentanedi­amine(2+) [cadaverine(2+)]. The structure of Z-DNA with Dap2+ (PDB ID 2f8w) indicates that this one-carbon-link-shorter polyamine interacts only with the phosphate groups of the Z-DNA (Narayana et al., 2006[Narayana, N., Shamala, N., Ganesh, K. N. & Viswamitra, M. A. (2006). Biochemistry, 45, 1200-1211.]). In a similar way, cadaverine(2+) (one carbon longer than Put2+) exhibits a preference for binding with Z-DNA phosphates only (Drozdzal et al., to be published).

[Figure 4]
Figure 4
The d(CGCGCG)2/Spm4+/Mn2+ (red), d(CGCGCG)2/Spm4+/Zn2+ (blue) and d(CGCGCG)2/Put2+/K+(green) com­plexes in their common reference frame (unit cell). The interactions of the Mn2+, Zn2+(1) and Zn2+(2) ions and of the putrescinium(2+) N atoms with N7_G6, N7_G6ii and N7_G10i are indicated. A different location of G10i in the com­plex with Zn2+ cations is also visible.

The putrescinium dication has been characterized in several crystal structures of its salts and in some of them it has the gauchetransgauche+ conformation, while in the remaining cases it is all-trans (Woo et al., 1979[Woo, N. H., Seeman, N. C. & Rich, A. (1979). Biopolymers, 18, 539-552.]; Jaskólski et al., 1986[Jaskólski, M., Alejska, M. & Wiewiórowski, M. (1986). J. Crystallogr. Spectrosc. Res. 16, 31-39.]; Pospieszna-Markiewicz et al., 2007[Pospieszna-Markiewicz, I., Radecka-Paryzek, W. & Kubicki, M. (2007). Acta Cryst. E63, o3650.]).

Our study provides insight into the effectiveness and competition of polyamine and metal cations for interactions with Z-DNA, and confirms that even a simple di­amine can adopt different conformations and consequently enter into a variety of interactions with biomacromolecular partners.

The partial occupancy of the K+ ion confirms previous research findings suggesting that most observed monovalent cation sites in DNA crystals are partially occupied positions (Tereshko et al., 2001[Tereshko, V., Wilds, C., Minasov, G., Prakash, T. P., Maier, M., Howard, A., Wawrzak, Z., Manoharan, M. & Egli, M. (2001). Nucleic Acids Res. 29, 1208-1215.]; Dong, 2003[Dong, X. (2003). Acta Cryst. D59, 1336-1338.]). These cations are mobile and easily exchange sites with water molecules. This result also agrees both with (i) the conclusion from molecular-dynamic simulations which suggested that the structures of monovalent counter-ions in DNA are dynamic (Young et al., 1997[Young, M. A., Jayaram, B. & Beveridge, D. L. (1997). J. Am. Chem. Soc. 119, 56-69.]) and with (ii) the crystallographic studies on which the hybrid solvent model for the solvent structure around DNA is based and in which the solvent sites are occupied by water–cation hybrids (Shui et al., 1998[Shui, X., Sines, C., McFail-Isom, L., VanDerveer, D. & Williams, L. (1998). Biochemistry, 37, 16877-16887.]).

Footnotes

1Dedicated as a birthday tribute to Professor Wladek Minor, champion of quality and reproducibility in biostructural research, and a longtime friend.

Acknowledgements

We are grateful to Professor Ryszard Kierzek for the use of a DNA synthesizer. The synchrotron X-ray diffraction data were collected at beamline P13 operated by EMBL Hamburg at the PETRA III storage ring (DESY, Hamburg, Germany). We would like to thank Michele Cianci for assistance in using the beamline. This work was supported in part by a National Science Centre (NCN) grant.

Funding information

The following funding is acknowledged: National Science Centre (Poland) (grant No. 2013/10/M/NZ1/00251 to MJ).

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Journal logoSTRUCTURAL SCIENCE
CRYSTAL ENGINEERING
MATERIALS
ISSN: 2052-5206
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