DNA has the genetic information storage and transmission capacity according to the sequential order of the monomer and creates a central role in the chemical evolution by copying itself with the proliferation feature. Watson-Crick base pairs define two base pairs with hydrogen bonds. If metal coordination bonds replace hydrogen bonds more stable alternative metallo-DNA sequence can be established. If the replication feature can be obtained for the metallo-DNA, this will greatly benefit the creation of DNA computer keys. In this study, a new type of benzimidazole based metallo-DNA sensors consisting of a connector unit that unsaturated azinil bridge linked to Watson-Crick base pairs with Ni2+, Hg2+, Zn2+, Ag+, Pt2+, Pd2+ metal cations and a benzimidazole has been designed. Absorption and emission spectrum of the newly designed aqua medium based fluorophore and their metallo-DNA sensors with selected cations have been theoretically investigated by using DFT method. The logic gates of selected possible sensors which response in the visible region have also been examined in detail in acidic and water phase. As a result of calculated absorption-emission spectrum data show that T-Hg-A-Bnz, A-Ni-T-Bnz, C-Pt-G-Bnz, C-Ni-C-Bnz complexes produce OR gate. T-Zn-T-Bnz and G-Pt-C-Bnz results demonstrated XOR and AND logic gate, respectively.
References
[1]
Holliday, B.J. and Mirkin, C.A. (2001) Strategies for the Construction of Supramolecular Compounds through Coordination Chemistry. Angewandte Chemi, 40, 2022-2043.
http://dx.doi.org/10.1002/1521-3773(20010601)40:11<2022::AID-ANIE2022>3.0.CO;2-D
[2]
Panja, K.S., Dwivedi, N. and Saha, S. (2016) Highly Stable Naphthalene Core Based Novel Cleftshaped Strain Molecule: Influence of Intermolecular H-Bonding Architectures. The Royal Society of Chemistry, 6, 59574-59581.
http://dx.doi.org/10.1039/c6ra06855c
[3]
Mahmudov, K.T., Kopylovich, M.N., Silva, F.C. and Pombeiro, A.J.L. (2016) Non-Covalent Interactions in the Synthesis of Coordination Compounds: Recent Advances. Coordination Chemistry Reviews.
http://dx.doi.org/10.1016/j.ccr.2016.09.002
[4]
Hisamatsu, Y., Miyazawa, Y., Yoneda, K., Miyauchi, M., Zulkefeli, M. and Aoki, S. (2016) Supramolecular Complexes Formed by the Self-Assembly of Hydrophobic Bis(Zn2+-cyclen) Complexes, Copper, and Dior Triimide Units for the Hydrolysis of Phosphate Mono- and Diesters in Two-Phase Solvent Systems (Cyclen = 1,4,7,10-Tetraazacyclododecane). Chemical and Pharmaceutical Bulletin, 64, 451-464.
http://dx.doi.org/10.1248/cpb.c15-01014
[5]
Smith, S.J., Radford, R.J., Subramanian, R.H., Barnett, B.R., Figueroa, J.S. and Tezcan, F.A. (2016) Tunable Helicity, Stability and DNA-Binding Properties of Short Peptides with Hybrid Metal Coordination Motifs. Chemical Science, 7, 5453-5461.
http://dx.doi.org/10.1039/c6sc00826g
[6]
Santamaria-Diaz, N., Mendez-Arriaga, M.J., Salas, J.M. and Galindo, M.A. (2016) Highly Stable Double-Stranded DNA Containing Sequential Silver (I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs. Angewandte Chemie, 55, 6170-6174. http://dx.doi.org/10.1002/anie.201600924
[7]
Léon, J.C., Sinha, I. and Müller, J. (2016) 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes. International Journal of Molecular Sciences, 17, 554-564. http://dx.doi.org/10.3390/ijms17040554
[8]
Camacho, C.C., Ruiz, A.E., Hueso P.A., Mijangos, E., Garcia, I.R., Contreras, R. and Parra, A.F. (2013) Organometallic Tin Compounds Derived from 2-Benzimidazole Propionic Acid. Zeitschrift für anorganische und allgemeine Chemie, 7, 1122-1128.
http://dx.doi.org/10.1002/zaac.201300108
[9]
Mallajosyula, S.S. and Pati, S.K. (2008) Benzimidazole-Modified Single-Stranded DNA: Stable Scaffolds for 1-Dimensional Spintronics Constructs. Journal of Physical. Chemistry B, 112, 16982-16989. http://dx.doi.org/10.1021/jp8080782.
[10]
Miyake, Y., Togashi, M., Tashiro, M., Yamaguchi, H., Oda, S., Kudo, M., Tanaka, Y., Kondo, Y., Sawa, R., Fujimoto, T., Machinami, T. and Ono, A. (2005) MercuryII-Mediated Formation of Thymine-HgII-Thymine Base Pairs in DNA Duplexes. Journal of the American Chemical Society, 128, 2172-2173.
http://dx.doi.org/10.1021/ja056354d
[11]
Miyachi, H., Matsui, T., Shigetac, Y. and Hirao, K. (2009) Effects of Mercury (II) on Structural Properties, Electronic Structure and UV Absorption Spectra of a Duplex Containing Thymine-Mercury(II)-Thymine Nucleobase Pairs. Physical Chemistry Chemical Physics, 12, 909-917. https://doi.org/10.1039/B912807G
[12]
Takezawa, Y. and Shionoya, M. (2012) Metal-Mediated DNA Base Pairing: Alternatives to Hydrogen-Bonded Watson Crick Base Pairs. Accounts of Chemical Research, 45, 2066-2076. https://doi.org/10.1021/ar200313h
[13]
Wu, J., Fu, Y., He, Z., Han, Y., Zheng, L., Zhang, J. and Li, W. (2012) Growth Mechanisms of Fluorescent Silver Clusters Regulated by Polymorphic DNA Templates: A DFT Study. The Journal of Physical Chemistry B, 116, 1655-1665.
https://doi.org/10.1021/jp206251v
[14]
Müller, A., Talbot, F. and Leutwyler, S. (2002) Hydrogen Bond Vibrations of 2-Aminopyridinea2-Pyridone, Watson-Crick Analogue of Adenine Uracil. Journal of the American Chemical Society, 124, 14486-14494.
https://doi.org/10.1021/ja0209969
[15]
Brown, G.J. (2004) Encyclopedia of Supramolecular Chemistry. In: Atwood, J.L. and Steed, J.W., Eds., Encyclopedia of Supramolecular Chemistry, CRC Press, Taylor and Francis Group, New York, 893.
[16]
Kubo, K. (2005) PET Sensors. In: Geddes, C.D. and Lakowicz, J.R., Eds., Topics in Fluorescence Spectroscopy: Advanced Concepts in Fluorescence Sensing, Springer Science Business Media, New York, 241.
[17]
Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J.A., Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, O., Foresman, J.B., Ortiz, J.V., Cioslowski, J. and Fox, D.J. (2009) Gaussian 09, Revision E.01. Gaussian Inc., Wallingford.
[18]
Dennington, R., Keith, T. and Millam, J. (2009) Gauss View.
[19]
Zhang, B., Ma, P., Gao, D., Wang, Z., Sun, Y., Song, D. and Li, X. (2016) A FRET-Based Fluorescent Probe Formercury Ions in Water and Living Cells. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 165, 99-105.
[20]
Sicilia, V., Borja, P., Bayab, M. and Casasb, J. (2015) Selective Turn-Off Phosphorescent and Colorimetric Detection of Mercury (II) in Water ByhalfLantern Platinum(II) Complexes. Dalton Transactions, 44, 6936-6943.
https://doi.org/10.1039/C5DT00087D
[21]
Karhu, A., Rautiainen, M., Oilunkaniemi, R., Chivers, T. and Laitinen, R. (2015) Mercury- and Cadmium-Assisted [2 + 2] Cyclodimerization of Tert-Butylselenium Diimide. Inorganic Chemistry, 54, 9499-9508.
https://doi.org/10.1021/acs.inorgchem.5b01434
[22]
Zhao, Y. and Truhlar, D.G. (2006) The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals. Theoretical Chemistry Accounts, 120, 215-241. https://doi.org/10.1007/s00214-007-0310-x
[23]
Rives, J.T. and Jorgensen, W.L. (2008) Performance of B3LYP Density Functional Methods for a Large Set of Organic Molecules. Journal of Chemical Theory and Computation, 4, 297-306. https://doi.org/10.1021/ct700248k
[24]
Adamo, C. and Barone, V. (1999) Toward Reliable Density Functional Methods without Adjustable Parameters: The PBE0 Model. The Journal of Chemical Physics, 113, 6158-6170. https://doi.org/10.1063/1.478522
[25]
Chiodo, S., Russo, N. and Sicilia, E. (2006) LANL2DZ Basis Sets Recontracted in the Framework Of Density Functional Theory. The Journal of Chemical Physics, 125, 104-107. https://doi.org/10.1063/1.2345197
[26]
Klamt, A. (1994) Conductor-Like Screening Model for Real Solvents: A New Approach to the Quantitative Calculation of Solvation Phenomena. The Journal of Physical Chemistry, 99, 2224-2235. https://doi.org/10.1021/j100007a062
