Ion Channel-like Crystallographic Signatures in Modified Guanine

Communication pubs.acs.org/crystal

Ion Channel-like Crystallographic Signatures in Modified Guanine− Potassium/Sodium Interactions N. Nagapradeep, Suneeta Sharma, and Sandeep Verma* Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016 (UP), India S Supporting Information *

ABSTRACT: This communication describes crystallographic details of structures reminiscent of ion channels, formed from regioisomeric N7 and N9 guanine-carboxylate conjugates with potassium/sodium ions and their subsequent STM observations on Au(111) surface. Ion channel-like crystal structures were obtained with the observation of a notable shift in metal ion coordination from carbonyl to carboxylate oxygen. These results are expected to provide insight into competing sites for modified guanine−metal coordination, an entry into guaninebased ion channels and a route toward guanine-functionalized surfaces.

O

Scheme 1. Molecular Structures of Ligands 1 and 2

ptimum concentration and transport of potassium/ sodium ions, physiologically relevant monovalent cations, are crucial for biochemical actions ranging from nerve conduction, muscle contraction, to optimal fluid balance. These ions are transported in a facile fashion through specific cellular channels belonging to a family of membrane proteins.1 For example, crystallographic information has revealed the environment around potassium ions in ion channels, and it was shown that ion movement is facilitated via interactions with backbone carbonyl and aspartate/glutamate residues (Figure 1).2 It is also noted that preference for higher coordination numbers, relative free energies of hydration, and microsolvation determines ion channel selectivity.3 Potassium and other monovalent cations are also considered essential for the formation and stabilization of guanine tetrads and quadruplexes. Interestingly, O6 carbonyl is favorably oriented to coordinate monovalent cations in the tetrameric

motif, thus presenting structural features closely resembling protein cation channels.4 Thus, it is not surprising that metal ion-assisted G quartets are considered as promising building blocks for material synthesis and device construction.5 Looking at two distinct metal ion-binding structural elements, viz. carboxylate groups6 and guanine residues, in proteins and nucleic acids, respectively, we decided to rationally merge them to afford a modified guanine base bearing a carboxylate pendant. Interestingly, such guanine−carboxylate conjugates have been isolated from the fungal spores of Eremothecium ashbyii,7 thus raising the possibility of carboxylated guanine interactions with physiological monovalent cations like sodium and potassium ions, known to reverse the stress induced by other cations in fungal growth.8 Ligands 1 and 2, N7 and N9 carboxyl group-substituted regioisomers, respectively, were synthesized to study their interaction with K+/Na+ ions (Scheme 1).9 Notably, N7substituted guanines are known alkylation lesions resulting from the nucleophilicity of N7 imino nitrogen and display a wide range of toxic and mutagenic behavior,10 while N9substituted guanines are considered as N9-glycosylation

Figure 1. Schematic representation of a potassium channel: inset depicts an array of potassium ions interacting with backbone carbonyl oxygen atoms in KcsA K+ ion channel (adapted from: http://www. larapedia.com/biologia_appunti/biologia_appunti_parte_2.html). © 2013 American Chemical Society

Received: November 12, 2012 Revised: January 8, 2013 Published: January 14, 2013 455

dx.doi.org/10.1021/cg3016518 | Cryst. Growth Des. 2013, 13, 455−459

Crystal Growth & Design

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Figure 4. Ion channel-like view in G7Na similar to G7K when viewed along the c axis: inset box depicts the observed Na−Na distance in sodium ion arrays.

system (P21/c and C2/c for G7K and G9K, respectively), having one potassium ion and one ligand in their asymmetric units, along with water molecules. The potassium ion exhibited distorted trigonal bipyramidal and pentagonal bipyramidal geometries in G7K and G9K, respectively, with basal water coordination and apical coordinations to carboxylate oxygens from the pendant arms (Figure 2, panels a and c). In G7K, homodimerization of guanine residue, through the Watson−Crick face (Figure 2b) and the extended sugar edge, resulted in a ladderlike structure9 when viewed along the b axis, whereas cross-dimerization in G9K, through the Watson−Crick edge and carboxylate pendant arm (Figure 2d), revealed a herringbone-like pattern9 when viewed along the a axis. In both cases, potassium-mediated guanine dimers were stabilized by the hydrogen-bonding interaction from the metal ion-bound water molecules (K1−O1 = 2.73 Å, 2.75 Å in G7K; 2.358 Å in G9K).13 In G7K, each guanine was connected to two adjacent bases by six hydrogen bonds (two bonds of each N2−H2B···O6 = 2.157 Å; N2−H2A···N9 = 2.091 Å; N1−H1···N3 = 2.031 Å), resulting in the formation of infinite ribbons, when viewed along the c axis (Figure 2b). This DDA···AAD triple hydrogen bonding sequence in GG is rare (where D = donor, A = acceptor).14 Guanine ribbons possess a spacing of ∼3 Å and are stabilized by π−π interactions involving parallely offset rings.9 However, G9K afforded nonplanar zigzag ribbons, when viewed along the b axis, via hydrogen bonding between

Figure 2. (a and c) Potassium coordination in G7K and G9K, respectively. (b and d) Guanine−guanine hydrogen-bonding interactions in G7K and G9K, respectively.

models. Much chemistry is developed around substitution at the N7 and N9 nitrogens for the construction of nucleobase ligands for metal interaction studies.11 Colorless potassium coordinated crystals of 1 and 2 were grown from saturated aqueous methanolic solutions of K2CO3 by slow evaporation, to afford regioisomeric crystals G7K and G9K, respectively.12 Both crystallized in a monoclinic crystal

Figure 3. (a) K channel-like view in G7K when viewed along the a axis: inset box depicts the observed K−K distance in potassium ion arrays. b) K− channel-like view in G9K when viewed along the c axis: inset box depicts the observed K−K distance in potassium ion arrays. 456



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Figure 5. (a) STM image (It = 1.22 nA, Vt = 0.2 V) of G7K on Au(111) surface. (b) Magnified STM image of highlighted area in (a). (c and e) STM images (It = 1.22 nA, Vt = 0.2 V) of G9K on the Au(111) surface. (d) Magnified STM image of highlighted area in (c). (f) Magnified STM image of highlighted area in (e).

triple hydrogen bonded GG residues (N2−H2A···O6 = 2.124 Å; N2−H2B···N9 = 2.049 Å; N1−H1···N3 = 2.017 Å) and the ensuing guanine ribbons were stabilized by π−π interactions.9 Carbonyl O6 coordination was not observed again. The metal ions in arrays of G7Na are also equispaced (dNa−Na = 5.15 Å) and connected only through water molecules, unlike in G7K where both water and carboxylate oxygens are involved in potassium ion interactions.9 This difference could be perhaps attributed to a higher hydration energy and waterbinding ability of sodium over potassium ions.16 These results also suggest consistency of guanine−carboxylate conjugates in affording ion channel-like crystallographic signatures with alkali metals. Guanine and its derivatives are also known to form ordered structures on surfaces with or without the assistance of metal ions.17 Au(111) surface, in particular, allows nucleobases to adopt a flat-lying geometry; aromatic rings of bases remain parallel to the surface, without interfering with intermolecular hydrogen-bonding interactions.18 Given the interesting crystallographic features of G7K, G7Na, and G9K and our interest in force microscopy of coordination complexes and conjugates,19 we became interested in determining the deposition

guanine N1 and N2 and O1 and O2 of the carboxylate pendant (N1−H1···O2 = 1.949 Å; N2−H2B···O1 = 2.105 Å) (Figure 2d). These ribbons were further stabilized by π−π interactions and mediation of water.9 Infinite arrays of potassium ions in the G7K crystal lattice, reminiscent of K channels, were observed when viewed along the a axis. The potassium ions are equispaced (dK−K = 3.875 Å), and their separation is longer than the ionic radii but shorter than the sum of van der Walls radii (5.5 Å) (Figure 3a). G9K also exhibited similar equispaced arrays of potassium ions (dK−K = 9.59 Å), when viewed along the a axis (Figure 3b). Such alkali metal ion arrays were previously documented in the crystal structures of ion channels2 and G−quartets.15 Curiously, carbonyl O6 of guanine did not show interaction with potassium ions in these complexes, while remaining hydrogen-bonded to potassium-bound water molecules.9 Similar to potassium interaction, a sodium ion-containing crystal structure G7Na, similar to G7K, was also formed when 1 was treated with Na2CO3 under similar reaction conditions (Figure 4). The asymmetric unit of G7Na (monoclinic, P21/c) consists of an extra water molecule compared to G7K, sodium ions exhibiting distorted octahedral geometry with an apical coordination to oxygen of the carboxylate pendant group (Na1−O1 = 2.438 Å) and the rest to water molecules. The 457



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(2) (a) Zhou, Y. F.; Morais-Cabral, J. H.; Kaufman, A.; MacKinnon, R. Nature 2002, 414, 43−48. (b) Morais-Cabral, J.; Zhou, Y.; MacKinnon, R. Nature 2001, 414, 37−42. (c) Doyle, D. A.; Cabral, J. M.; Pfuetzner, R. A.; Kuo, A. L.; Gulbis, J. M.; Cohen, S. L.; Chait, B. T.; MacKinnon, R. Science 1998, 280, 69−77. (3) (a) Gu, J.; Leszczynski, J. J. Phys. Chem. A 2001, 105, 10366− 10371. (b) Meyer, M.; Sühnel, J. J. Biomol. Struct. Dyn. 2003, 20, 507− 518. (c) Meyer, M.; Hocquet, A.; Sühnel, J. J. Comput. Chem. 2005, 26, 352−364. (d) Hud, N. V.; Smith, F. W.; Anet, F. A. L.; Feigon, J. Biochemistry 1996, 35, 15383−15390. (4) (a) Akhshi, P.; Mosey, N. J.; Wu, G. Angew. Chem., Int. Ed. 2012, 51, 2850−2854 and references cited therein. (b) Forman, S. L.; Fettinger, J. C.; Pieraccini, S.; Gottarelli, G.; Davis, J. T. J. Am. Chem. Soc. 2000, 122, 4060−4067. (5) (a) Fahlman, R. P.; Hsing, M.; Sporer-Tuhten, C. S.; Sen, D. Nano Lett. 2003, 3, 1073−1078. (b) Likhitsup, A.; Yu, S.; Ng, Y.-H.; Chai, C. L. L.; Tam, E. K. W. Chem. Commun. (Cambridge, U.K.) 2009, 4070−4072. (c) Arnal-Hérault, C.; Pasc, A.; Michau, M.; Cot, D.; Petit, E.; Barboiu, M. Angew. Chem., Int. Ed. 2007, 46, 8409−8413. (d) Houbenov, N.; Nykänen, A.; Iatrou, H.; Hadjichristidis, N.; Ruokolainen, J.; Faul, C. F. J.; Ikkala, O. Adv. Funct. Mater. 2008, 18, 2041−2047. (e) González-Rodríguez, D.; Janssen, P. G. A.; MartìnRapún, R.; De Cat, I.; De Feyter, S.; Schenning, A. P. H. J.; Meijer, E. W. J. Am. Chem. Soc. 2010, 132, 4710−4719. (f) Mihai, S.; Le Duc, Y.; Cot, D.; Barboiu, M. J. Mater. Chem. 2010, 20, 9443−9448. (g) Betancourt, J. E.; Rivera, J. M. Org. Lett. 2008, 10, 2287−2290. (h) Arnal-Hérault, C.; Banu, A.; Barboiu, M.; Michau, M.; van der Lee, A. Angew. Chem., Int. Ed. 2007, 46, 4268−4272. (6) (a) Banerjee, D.; Parise, J. B. Cryst. Growth Des. 2011, 11, 4704− 4720. (b) Fromm, K. M. Coord. Chem. Rev. 2008, 252, 856−885. (7) (a) Al-Khalidi, U.; Greenberg, G. R. J. Biol. Chem. 1961, 236, 192−196. (b) Al-Khalidi, U.; Greenberg, G. R. J. Biol. Chem. 1961, 236, 189−191. (8) (a) Kurita, N.; Funabashi, M. Agric. Biol. Chem. 1984, 48, 887− 893. (b) Martínez, J. L.; Sychrova, H.; Ramos, J. Fungal Genet. Biol. 2011, 47, 177−184. (9) See Supporting Information. (10) (a) Gates, K. S.; Nooner, T.; Dutta, S. Chem. Res. Toxicol. 2004, 17, 839−856. (b) Boysen, G.; Pachkowski, B. F.; Nakamura, J.; Swenberg, J. A. Mutat. Res., Genet. Toxicol. Environ. Mutagen. 2009, 678, 76−94. (11) Selected references: (a) Price, C.; Shipman, M. A.; Rees, N. H.; Elsegood, M. R. J.; Edwards, A. J.; Clegg, W.; Houlton, A. Chem.−Eur. J. 2001, 7, 1194−1201. (b) Shipman, M. A.; Price, C.; Gibson, A. E.; Elsegood, M. R. J.; Clegg, W.; Houlton, A. Chem.−Eur. J. 2000, 6, 4371−4378. (c) Cerasino, L.; Intini, F. P.; Kobe, J.; De Clercq, E.; Natile, G. Inorg. Chim. Acta 2003, 344, 174−182. (d) Kozma, Á .; Ibáñez, S.; Silaghi-Dumitrescu, R.; Miguel, P. J. S.; Gupta, D.; Lippert, B. Dalton Trans. 2012, 41, 6094−6103. (e) Sigel, R. K. O.; Thompson, S. M.; Freisinger, E.; Glahé, F.; Lippert, B. Chem.−Eur. J. 2001, 7, 1968−1980. (f) Nagapradeep, N.; Verma, S. Chem. Commun. 2011, 47, 1755−1757. (g) Lippert, B. Coord. Chem. Rev. 2000, 200−202, 487− 516 and references cited therein. (h) Pérez-Yáñez, S.; Castillo, O.; Cepeda, J.; García-Terán, J. P.; Luque, A.; Román, P. Inorg. Chim. Acta 2011, 365, 211−219. (i) Verma, S.; Mishra, A. K.; Kumar, J. Acc. Chem. Res. 2010, 43, 79−91. (12) Crystallographic data for G7K: C7H12K1N5O6, Mr = 301.32, T = 100(2) K, monoclinic, space group P21/c, Z = 4, a = 16.239(5) Å, b = 9.884(4) Å, c = 7.574(3) Å, α = 90°, β = 100.516(5)°, γ = 90°, V = 1195.3(8) Å3, Dx = 1.674 Mg m−3, F(000) = 624, μ = 0.479 mm−1, 7615 reflections collected, 2936 unique (Rint = 0.0381) which were used in all calculations, R and Rw [I > 2σ(I)] = 0.0539 and 0.1347, R and Rw (all data) = 0.0796 and 0.2098, GOF = 1.208. Crystallographic data for G9K: C14H30K1N10O15, Mr = 617.58, T = 100(2) K, monoclinic, space group C2/c, Z = 4, a = 17.936(7) Å, b = 9.590(3) Å, c = 14.730(5) Å, α = 90°, β = 104.700(11)°, γ = 90°, V = 2450.8(15) Å3, Dx = 1.674 Mg m−3, F(000) = 1292, μ = 0.312 mm−1, 6766 reflections collected, 2407 unique (Rint = 0.0497) which were used in all calculations, R and Rw [I > 2σ(I)] = 0.0476 and 0.1155, R and Rw

pattern of our complexes on the Au(111) surface, through STM studies (Figures 5, panels a, c, and e). In the case of G7K, parallel rows composed of protruded double ridges were observed (Figure 5b), closely resembling the G7K lattice structure, when viewed along the c axis. The distance between two successive rows in the STM image was almost equal to the distance between potassium-bound water molecules and the plane through the nearest potassium ions in the crystal lattice.9 But, at the same resolution, G9K failed to reveal a visible pattern (Figure 5d). However, at slightly higher resolution, images composed of parallel rows containing protrusions, which resembled its lattice structure,9 were observed (Figure 5f). Relatively stable patterning of G7K over G9K can be ascribed to its robust flat ribbonlike structure formed with the assistance of six hydrogen bonds (Figure 2b). In addition, these patterns also reflect the relative stability of G7K and G9K in solution. A recent simulation study suggested that a centrosymmetric guanine−guanine homodimer, with two hydrogen bonds, is most stable, and it possesses significantly higher interaction energy with the Au(111) surface.20 Thus, formation of a triply hydrogen-bonded homodimer in G7K/G7Na is decidedly more stable, and such complexes may lead to higher affinity G− G surface patterns on gold substrates for material applications. In conclusion, ion channel-like structures were developed from alkaline solutions of guanine−carboxylate conjugates with a notable shift in metal ion coordination from carbonyl to carboxylate oxygen. These results may provide an expeditious entry into artificial ions channels21 based on guanine motif and a promising route toward guanine-functionalized surfaces for bioelectronics.22

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ASSOCIATED CONTENT

S Supporting Information *

Synthetic procedures, characterizations, experimental details, and crystal structure refinement parameters are given. The CCDC contains the supplementary crystallographic data for this paper with the following deposition numbers of CCDC: 862440 (G7K), 862441 (G9K), and 907744 (G7Na). Copies of this information can be obtained free of charge upon application to the CCDC, 12 Union Road, Cambridge CB21EZ, U.K. (Fax: +44-1223/336-033; E-mail: deposit@ ccdc.cam.ac.uk). This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We thank the single−crystal CCD X−ray facility at IIT− Kanpur. N.P. thanks CSIR for a predoctoral fellowship. This work is supported by an Outstanding Investigator Award from the Department of Atomic Energy, India, to S.V. We also thank DST Thematic Unit of Excellence for instrumentation support.

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REFERENCES

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(all data) = 0.0646 and 0.1306, GOF = 1.070. Crystallographic data for G7Na: C7H12Na1N5O7, Mr = 301.21, T = 100(2) K, monoclinic, space group P21/c, Z = 4, a = 17.566(5) Å, b = 9.743(4) Å, c = 7.361(3) Å, α = 90°, β = 96.875(5)°, γ = 90°, V = 1250.7(6) Å3, Dx = 1.600 Mg m−3, F(000) = 624, μ = 0.169 mm−1, 7906 reflections collected, 3074 unique (Rint = 0.0432) which were used in all calculations, R and Rw [I > 2σ(I)] = 0.0553 and 0.1355, R and Rw (all data) = 0.0890 and 0.1747, GOF = 1.083. More details about the crystallographic studies are given in the Supporting Information. (13) (a) Lv, Y.-K.; Feng, Y.-L.; Liu, J.-W.; Jiang, Z.-G. J. Solid State Chem. 2011, 184, 1339−1345 and references cited therein. (b) Makowski, S. J.; Hörmannsdorfer, M.; Schnick, W. Z. Anorg. Allg. Chem. 2010, 636, 2584−2588. (14) (a) Guille, K.; Clegg, W. Acta Crystallogr., Sect. C: Cryst. Struct. Commun. 2006, 62, o515−o517. (b) Bisacchi, G. S.; Singh, J.; Godfrey, J. D., Jr.; Kissick, T. P.; Mitt, T.; Malley, M. F.; Di Marco, J. D.; Gougoutas, J. Z.; Mueller, R. H.; Zahler, R. J. Org. Chem. 1995, 60, 2902−2905. (15) (a) Haider, S.; Parkinson, G. N.; Neidle, S. J. Mol. Biol. 2002, 320, 189−200. (b) Phillips, K.; Dauter, Z.; Murchie, A. I. H.; Lilley, D. M. J.; Luisi, B. J. Mol. Biol. 1997, 273, 171−182. (c) Laughlan, G.; Murchie, A. I. H.; Norman, D. G.; Moore, M. H.; Moody, P. C. E.; Lilley, D. M. J.; Luisi, B. Science 1994, 265, 520−524. (16) (a) Collins, K. D. Biophys. Chem. 2006, 119, 271−281. (b) Collins, K. D. Methods 2004, 34, 300−311. (17) (a) Xu, W.; Wang, J.-G.; Yu, M.; Lægsgaard, E.; Stensgaard, I.; Linderoth, T. R.; Hammer, B.; Wang, C.; Besenbacher, F. J. Am. Chem. Soc. 2010, 132, 15927−15929 and references cited therein. (b) Ciesielski, A.; Lena, S.; Masiero, S.; Spada, G. P.; Samorì, P. Angew. Chem., Int. Ed. 2010, 49, 1963−1966. (c) Ciesielski, A.; Perone, R.; Pieraccini, S.; Spada, G. P.; Samorì, P. Chem. Commun. (Cambridge, U.K.) 2010, 46, 4493−4495. (18) (a) Tao, N. J.; DeRose, J. A.; Lindsay, S. M. J. Phys. Chem. 1993, 97, 910−919. (b) Kelly, R. E. A.; Xu, W.; Lukas, M.; Otero, R.; Mura, M.; Lee, Y.-J.; Lægsgaard, E.; Stensgaard, I.; Kantorovich, L. N.; Besenbacher, F. Small 2008, 4, 1494−1500. (19) (a) Purohit, C. S.; Verma, S. J. Am. Chem. Soc. 2007, 129, 3488− 3489. (b) Purohit, C. S.; Verma, S. J. Am. Chem. Soc. 2006, 128, 400− 401. (c) Singh, P.; Kumar, J.; Maria Toma, F.; Raya, J.; Prato, M.; Fabre, B.; Verma, S.; Bianco, A. J. Am. Chem. Soc. 2009, 131, 13555− 13562. (d) Singh, P.; Venkatesh, V.; Nagapradeep, N.; Verma, S.; Bianco, A. Nanoscale 2012, 4, 1972−1974. (20) Maleki, A.; Alavi, S.; Najafi, B. J. Phys. Chem. C 2011, 115, 22484−22494. (21) (a) Sivakova, S.; Rowan, S. J. Chem. Soc. Rev. 2005, 34, 9−21. (b) Sakai, N.; Kamikawa, Y.; Nishii, M.; Matsuoka, T.; Kato, T.; Matile, S. J. Am. Chem. Soc. 2006, 128, 2218−2219. (c) Matile, S.; Som, A.; Sordé, N. Tetrahedron 2004, 60, 6405−6435. (d) Ma, L.; Melegari, M.; Colombini, M.; Davis, J. T. J. Am. Chem. Soc. 2008, 130, 2938−2939. (22) (a) Maruccio, G.; Visconti, P.; Arima, V.; D’Amico, S.; Biasco, A.; D’Amone, E.; Cingolani, R.; Rinaldi, R. Nano Lett. 2003, 3, 479− 483. (b) Rinaldi, R.; Branca, E.; Cingolani, R.; Masiero, S.; Spada, G. P. Appl. Phys. Lett. 2001, 78, 3541−3543. (c) Calzolari, A.; Di Felice, R.; Molinari, E.; Garbesi, A. Phys. E (Amsterdam, Neth.) 2002, 13, 1236− 1239. (d) Li, J.; Sarkar, A.; Morkoc, H.; Neogi, A. J. Disp. Technol. 2009, 5, 446−451.

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Ion Channel-like Crystallographic Signatures in Modified Guanine

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