Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block
The DNA double helix is a versatile building block used in DNA nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base-Ag+-base bonding rather than by Watson-Crick pairing. In this work, we study the class...
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- 2017
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- Universidad de Medellín
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- Repositorio UDEM
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Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block |
| title |
Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block |
| spellingShingle |
Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block |
| title_short |
Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block |
| title_full |
Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block |
| title_fullStr |
Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block |
| title_full_unstemmed |
Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block |
| title_sort |
Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block |
| dc.contributor.affiliation.spa.fl_str_mv |
Chen, X., Department of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, Aalto, Finland Karpenko, A., Department of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, Aalto, Finland Lopez-Acevedo, O., Department of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, Aalto, Finland, Facultad de Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, Medellín, Colombia |
| description |
The DNA double helix is a versatile building block used in DNA nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base-Ag+-base bonding rather than by Watson-Crick pairing. In this work, we study the classical dynamics of a parallel silver-mediated homobase double helix and compare it to the dynamics of the antiparallel double helix. Our classical simulations show that only the parallel double helix is highly stable through the 100 ns simulation time. A new type of H-bond previously proposed by our collaboration and recently observed in crystal-determined helices drives the physicochemical stabilization. Compared to the natural B-DNA form, the metal-mediated helix has a contracted axial base pair rise and smaller numbers of base pairs per turn. These results open the path for the inclusion of this robust metal-mediated building block into new nanoscale DNA assemblies. © 2017 American Chemical Society. |
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2017 |
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2017-12-19T19:36:41Z |
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2017-12-19T19:36:41Z |
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2017 |
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Article |
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http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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http://purl.org/coar/resource_type/c_6501 http://purl.org/coar/resource_type/c_2df8fbb1 |
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info:eu-repo/semantics/article |
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24701343 |
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http://hdl.handle.net/11407/4251 |
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10.1021/acsomega.7b01089 |
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reponame:Repositorio Institucional Universidad de Medellín |
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24701343 10.1021/acsomega.7b01089 reponame:Repositorio Institucional Universidad de Medellín instname:Universidad de Medellín |
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http://hdl.handle.net/11407/4251 |
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eng |
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eng |
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https://www.scopus.com/inward/record.uri?eid=2-s2.0-85032582170&doi=10.1021%2facsomega.7b01089&partnerID=40&md5=4fc49f30d5400640857d887ac8dc953f |
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ACS Omega ACS Omega Volume 2, Issue 10, 2017, Pages 7343-7348 |
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Bath, J., & Turberfield, A. J. (2007). DNA nanomachines. Nature Nanotechnology, 2(5), 275-284. doi:10.1038/nnano.2007.104 Bayly, C. I., Cieplak, P., Cornell, W. D., & Kollman, P. A. (1993). A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. Journal of Physical Chemistry, 97(40), 10269-10280. Bayly, C. I., Merz, K. M., Jr., Ferguson, D. M., Cornell, W. D., Fox, T., Caldwell, J. W., . . . Spellmeyer, D. C. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, 117(19), 5179-5197. doi:10.1021/ja00124a002 Berdakin, M., Taccone, M. I., Pino, G. A., & Sánchez, C. G. (2017). DNA-protected silver emitters: Charge dependent switching of fluorescence. Physical Chemistry Chemical Physics, 19(8), 5721-5726. doi:10.1039/c6cp08345e Case, D. A., Cheatham III, T. E., Darden, T., Gohlke, H., Luo, R., Merz Jr., K. M., . . . Woods, R. J. (2005). The amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668-1688. doi:10.1002/jcc.20290 Chu, X., & Dalgarno, A. (2004). Linear response time-dependent density functional theory for van der waals coefficients. Journal of Chemical Physics, 121(9), 4083-4088. doi:10.1063/1.1779576 Clever, G. H., & Shionoya, M. (2010). Metal-base pairing in DNA. Coordination Chemistry Reviews, 254(19-20), 2391-2402. doi:10.1016/j.ccr.2010.04.014 Douglas, S. M., Dietz, H., Liedl, T., Högberg, B., Graf, F., & Shih, W. M. (2009). Self-assembly of DNA into nanoscale three-dimensional shapes. Nature, 459(7245), 414-418. doi:10.1038/nature08016 Douglas, S. M., Marblestone, A. H., Teerapittayanon, S., Vazquez, A., Church, G. M., & Shih, W. M. (2009). Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Research, 37(15), 5001-5006. doi:10.1093/nar/gkp436 Enkovaara, J., Rostgaard, C., Mortensen, J. J., Chen, J., Dułak, M., Ferrighi, L., . . . Jacobsen, K. W. (2010). Electronic structure calculations with GPAW: A real-space implementation of the projector augmented-wave method. Journal of Physics Condensed Matter, 22(25) doi:10.1088/0953-8984/22/25/253202 Espinosa Leal, L. A., Karpenko, A., Swasey, S., Gwinn, E. G., Rojas-Cervellera, V., Rovira, C., & Lopez-Acevedo, O. (2015). The role of hydrogen bonds in the stabilization of silver-mediated cytosine tetramers.Journal of Physical Chemistry Letters, 6(20), 4061-4066. doi:10.1021/acs.jpclett.5b01864 Frisch, M. J. (2009). Gaussian 09. Funke, J. J., & Dietz, H. (2016). Placing molecules with bohr radius resolution using DNA origami. Nature Nanotechnology, 11(1), 47-52. doi:10.1038/nnano.2015.240 Gehring, K., Leroy, J. -., & Guéron, M. (1993). A tetrameric DNA structure with protonated cytosine-cytosine base pairs. Nature, 363(6429), 561-565. Germann, M. W., Kalisch, B. W., & Van De Sande, J. H. (1988). Relative stability of parallel- and antiparallel-stranded duplex DNA. Biochemistry, 27(22), 8302-8306. doi:10.1021/bi00422a002 Hazel, P., Huppert, J., Balasubramanian, S., & Neidle, S. (2004). Loop-length-dependent folding of G-quadruplexes. Journal of the American Chemical Society, 126(50), 16405-16415. doi:10.1021/ja045154j Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463-1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463 Hess, B., Kutzner, C., Van Der Spoel, D., & Lindahl, E. (2008). GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435-447. doi:10.1021/ct700301q Hohenberg, P., & Kohn, W. (1964). Inhomogeneous electron gas. Physical Review, 136(3B), B864-B871. doi:10.1103/PhysRev.136.B864 Johannsen, S., Megger, N., Böhme, D., Sigel, R. K. O., & Müller, J. (2010). Solution structure of a DNA double helix with consecutive metal-mediated base pairs. Nature Chemistry, 2(3), 229-234. doi:10.1038/nchem.512 Kabsch, W., Sander, C., & Trifonov, E. N. (1982). The ten helical twist angles of B-DNA. Nucleic Acids Research, 10(3), 1097-1104. doi:10.1093/nar/10.3.1097 Kondo, J., Tada, Y., Dairaku, T., Hattori, Y., Saneyoshi, H., Ono, A., & Tanaka, Y. (2017). A metallo-DNA nanowire with uninterrupted one-dimensional silver array. Nature Chemistry, 9(10), 956-960. doi:10.1038/nchem.2808 Lavery, R., Moakher, M., Maddocks, J. H., Petkeviciute, D., & Zakrzewska, K. (2009). Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Research, 37(17), 5917-5929. doi:10.1093/nar/gkp608 Li, J., Correia, J. J., Wang, L., Trent, J. O., & Chaires, J. B. (2005). Not so crystal clear: The structure of the human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic Acids Research, 33(14), 4649-4659. doi:10.1093/nar/gki782 Li, P., Song, L. F., & Merz, K. M. (2015). Systematic parameterization of monovalent ions employing the nonbonded model. Journal of Chemical Theory and Computation, 11(4), 1645-1657. doi:10.1021/ct500918t Lu, X. -., & Olson, W. K. (2003). 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Research, 31(17), 5108-5121. doi:10.1093/nar/gkg680 Luzar, A., & Chandler, D. (1996). Hydrogen-bond kinetics in liquid water. Nature, 379(6560), 55-57. Mandal, S., Hepp, A., & Müller, J. (2015). Unprecedented dinuclear silver(i)-mediated base pair involving the DNA lesion 1,N6-ethenoadenine. Dalton Transactions, 44(8), 3540-3543. doi:10.1039/c4dt02663b Megger, D. A., & Müller, J. (2010). Silver(I)-mediated cytosine self-pairing is preferred over hoogsteen-type base pairs with the artificial nucleobase 1,3-dideaza-6-nitropurine. Nucleosides, Nucleotides and Nucleic Acids, 29(1), 27-38. doi:10.1080/15257770903451579 Mergny, J. -., Lacroix, L., Hélène, C., Han, X., & Leroy, J. -. (1995). Intramolecular folding of pyrimidine oligodeoxynucleotides into an i-DNA motif. Journal of the American Chemical Society, 117(35), 8887-8898. doi:10.1021/ja00140a001 Ono, A., Cao, S., Togashi, H., Tashiro, M., Fujimoto, T., MacHinami, T., . . . Tanaka, Y. (2008). Specific interactions between silver(i) ions and cytosine-cytosine pairs in DNA duplexes. Chemical Communications, (39), 4825-4827. doi:10.1039/b808686a Park, K. S., & Park, H. G. (2014). Technological applications arising from the interactions of DNA bases with metal ions. Current Opinion in Biotechnology, 28, 17-24. doi:10.1016/j.copbio.2013.10.013 Pérez, A., Marchán, I., Svozil, D., Sponer, J., Cheatham III, T. E., Laughton, C. A., & Orozco, M. (2007). Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers.Biophysical Journal, 92(11), 3817-3829. doi:10.1529/biophysj.106.097782 Polonius, F. -., & Müller, J. (2007). An artificial base pair, mediated by hydrogen bonding and metal-ion binding. Angewandte Chemie - International Edition, 46(29), 5602-5604. doi:10.1002/anie.200700315 Ramazanov, R. R., Sych, T. S., Reveguk, Z. V., Maksimov, D. A., Vdovichev, A. A., & Kononov, A. I. (2016). Ag-DNA emitter: Metal nanorod or supramolecular complex? Journal of Physical Chemistry Letters, 7(18), 3560-3566. doi:10.1021/acs.jpclett.6b01672 Rangnekar, A., & Labean, T. H. (2014). Building DNA nanostructures for molecular computation, templated assembly, and biological applications. Accounts of Chemical Research, 47(6), 1778-1788. doi:10.1021/ar500023b Rippe, K., & Jovin, T. M. (1992). Parallel-stranded duplex DNA doi:10.1016/0076-6879(92)11013-9 Rothemund, P. W. K. (2006). Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082), 297-302. doi:10.1038/nature04586 Sa-Ardyen, P., Vologodskii, A. V., & Seeman, N. C. (2003). The flexibility of DNA double crossover molecules. Biophysical Journal, 84(6), 3829-3837. doi:10.1016/S0006-3495(03)75110-8 Scharf, P., & Müller, J. (2013). Nucleic acids with metal-mediated base pairs and their applications. ChemPlusChem, 78(1), 20-34. doi:10.1002/cplu.201200256 Sinha, I., Fonsecaguerra, C., & Müller, J. (2015). A highly stabilizing silver(I)-mediated base pair in parallel-stranded DNA. Angewandte Chemie - International Edition, 54(12), 3603-3606. doi:10.1002/anie.201411931 Swasey, S. M., & Gwinn, E. G. (2016). Silver-mediated base pairings: Towards dynamic DNA nanostructures with enhanced chemical and thermal stability. New Journal of Physics, 18(4) doi:10.1088/1367-2630/18/4/045008 Swasey, S. M., Leal, L. E., Lopez-Acevedo, O., Pavlovich, J., & Gwinn, E. G. (2015). Silver (I) as DNA glue: Ag+-mediated guanine pairing revealed by removing watson-crick constraints. Scientific Reports, 5doi:10.1038/srep10163 Terrón, A., Moreno-Vachiano, B., Bauzá, A., García-Raso, A., Fiol, J. J., Barceló-Oliver, M., . . . Frontera, A. (2017). X-ray crystal structure of a metalled double-helix generated by infinite and consecutive C*-AgI-C* (C*:N1-hexylcytosine) base pairs through argentophilic and hydrogen bond interactions. Chemistry - A European Journal, 23(9), 2103-2108. doi:10.1002/chem.201604331 Tkatchenko, A., & Scheffler, M. (2009). Accurate molecular van der waals interactions from ground-state electron density and free-atom reference data. Physical Review Letters, 102(7) doi:10.1103/PhysRevLett.102.073005 Ussery, D. W. (2002). DNA structure: A-, B- and Z-DNA helix families. Encyclopedia of Life Sciences. Wei, B., Ong, L. L., Chen, J., Jaffe, A. S., & Yin, P. (2014). Complex reconfiguration of DNA nanostructures. Angewandte Chemie - International Edition, 53(29), 7475-7479. doi:10.1002/anie.201402437 Yang, H., Metera, K. L., & Sleiman, H. F. (2010). DNA modified with metal complexes: Applications in the construction of higher order metal-DNA nanostructures. Coordination Chemistry Reviews, 254(19-20), 2403-2415. doi:10.1016/j.ccr.2010.02.026 Zhang, D. Y., & Winfree, E. (2009). Control of DNA strand displacement kinetics using toehold exchange. Journal of the American Chemical Society, 131(47), 17303-17314. doi:10.1021/ja906987s |
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2017-12-19T19:36:41Z2017-12-19T19:36:41Z201724701343http://hdl.handle.net/11407/425110.1021/acsomega.7b01089reponame:Repositorio Institucional Universidad de Medellíninstname:Universidad de MedellínThe DNA double helix is a versatile building block used in DNA nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base-Ag+-base bonding rather than by Watson-Crick pairing. In this work, we study the classical dynamics of a parallel silver-mediated homobase double helix and compare it to the dynamics of the antiparallel double helix. Our classical simulations show that only the parallel double helix is highly stable through the 100 ns simulation time. A new type of H-bond previously proposed by our collaboration and recently observed in crystal-determined helices drives the physicochemical stabilization. Compared to the natural B-DNA form, the metal-mediated helix has a contracted axial base pair rise and smaller numbers of base pairs per turn. These results open the path for the inclusion of this robust metal-mediated building block into new nanoscale DNA assemblies. © 2017 American Chemical Society.engAmerican Chemical SocietyFacultad de Ciencias Básicashttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85032582170&doi=10.1021%2facsomega.7b01089&partnerID=40&md5=4fc49f30d5400640857d887ac8dc953fACS OmegaACS Omega Volume 2, Issue 10, 2017, Pages 7343-7348Bath, J., & Turberfield, A. J. (2007). DNA nanomachines. Nature Nanotechnology, 2(5), 275-284. doi:10.1038/nnano.2007.104Bayly, C. I., Cieplak, P., Cornell, W. D., & Kollman, P. A. (1993). A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. Journal of Physical Chemistry, 97(40), 10269-10280.Bayly, C. I., Merz, K. M., Jr., Ferguson, D. M., Cornell, W. D., Fox, T., Caldwell, J. W., . . . Spellmeyer, D. C. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, 117(19), 5179-5197. doi:10.1021/ja00124a002Berdakin, M., Taccone, M. I., Pino, G. A., & Sánchez, C. G. (2017). DNA-protected silver emitters: Charge dependent switching of fluorescence. Physical Chemistry Chemical Physics, 19(8), 5721-5726. doi:10.1039/c6cp08345eCase, D. A., Cheatham III, T. E., Darden, T., Gohlke, H., Luo, R., Merz Jr., K. M., . . . Woods, R. J. (2005). The amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668-1688. doi:10.1002/jcc.20290Chu, X., & Dalgarno, A. (2004). Linear response time-dependent density functional theory for van der waals coefficients. Journal of Chemical Physics, 121(9), 4083-4088. doi:10.1063/1.1779576Clever, G. H., & Shionoya, M. (2010). Metal-base pairing in DNA. Coordination Chemistry Reviews, 254(19-20), 2391-2402. doi:10.1016/j.ccr.2010.04.014Douglas, S. M., Dietz, H., Liedl, T., Högberg, B., Graf, F., & Shih, W. M. (2009). Self-assembly of DNA into nanoscale three-dimensional shapes. Nature, 459(7245), 414-418. doi:10.1038/nature08016Douglas, S. M., Marblestone, A. H., Teerapittayanon, S., Vazquez, A., Church, G. M., & Shih, W. M. (2009). Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Research, 37(15), 5001-5006. doi:10.1093/nar/gkp436Enkovaara, J., Rostgaard, C., Mortensen, J. J., Chen, J., Dułak, M., Ferrighi, L., . . . Jacobsen, K. W. (2010). Electronic structure calculations with GPAW: A real-space implementation of the projector augmented-wave method. Journal of Physics Condensed Matter, 22(25) doi:10.1088/0953-8984/22/25/253202Espinosa Leal, L. A., Karpenko, A., Swasey, S., Gwinn, E. G., Rojas-Cervellera, V., Rovira, C., & Lopez-Acevedo, O. (2015). The role of hydrogen bonds in the stabilization of silver-mediated cytosine tetramers.Journal of Physical Chemistry Letters, 6(20), 4061-4066. doi:10.1021/acs.jpclett.5b01864Frisch, M. J. (2009). Gaussian 09.Funke, J. J., & Dietz, H. (2016). Placing molecules with bohr radius resolution using DNA origami. Nature Nanotechnology, 11(1), 47-52. doi:10.1038/nnano.2015.240Gehring, K., Leroy, J. -., & Guéron, M. (1993). A tetrameric DNA structure with protonated cytosine-cytosine base pairs. Nature, 363(6429), 561-565.Germann, M. W., Kalisch, B. W., & Van De Sande, J. H. (1988). Relative stability of parallel- and antiparallel-stranded duplex DNA. Biochemistry, 27(22), 8302-8306. doi:10.1021/bi00422a002Hazel, P., Huppert, J., Balasubramanian, S., & Neidle, S. (2004). Loop-length-dependent folding of G-quadruplexes. Journal of the American Chemical Society, 126(50), 16405-16415. doi:10.1021/ja045154jHess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463-1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463Hess, B., Kutzner, C., Van Der Spoel, D., & Lindahl, E. (2008). GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435-447. doi:10.1021/ct700301qHohenberg, P., & Kohn, W. (1964). Inhomogeneous electron gas. Physical Review, 136(3B), B864-B871. doi:10.1103/PhysRev.136.B864Johannsen, S., Megger, N., Böhme, D., Sigel, R. K. O., & Müller, J. (2010). Solution structure of a DNA double helix with consecutive metal-mediated base pairs. Nature Chemistry, 2(3), 229-234. doi:10.1038/nchem.512Kabsch, W., Sander, C., & Trifonov, E. N. (1982). The ten helical twist angles of B-DNA. Nucleic Acids Research, 10(3), 1097-1104. doi:10.1093/nar/10.3.1097Kondo, J., Tada, Y., Dairaku, T., Hattori, Y., Saneyoshi, H., Ono, A., & Tanaka, Y. (2017). A metallo-DNA nanowire with uninterrupted one-dimensional silver array. Nature Chemistry, 9(10), 956-960. doi:10.1038/nchem.2808Lavery, R., Moakher, M., Maddocks, J. H., Petkeviciute, D., & Zakrzewska, K. (2009). Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Research, 37(17), 5917-5929. doi:10.1093/nar/gkp608Li, J., Correia, J. J., Wang, L., Trent, J. O., & Chaires, J. B. (2005). Not so crystal clear: The structure of the human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic Acids Research, 33(14), 4649-4659. doi:10.1093/nar/gki782Li, P., Song, L. F., & Merz, K. M. (2015). Systematic parameterization of monovalent ions employing the nonbonded model. Journal of Chemical Theory and Computation, 11(4), 1645-1657. doi:10.1021/ct500918tLu, X. -., & Olson, W. K. (2003). 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Research, 31(17), 5108-5121. doi:10.1093/nar/gkg680Luzar, A., & Chandler, D. (1996). Hydrogen-bond kinetics in liquid water. Nature, 379(6560), 55-57.Mandal, S., Hepp, A., & Müller, J. (2015). Unprecedented dinuclear silver(i)-mediated base pair involving the DNA lesion 1,N6-ethenoadenine. Dalton Transactions, 44(8), 3540-3543. doi:10.1039/c4dt02663bMegger, D. A., & Müller, J. (2010). Silver(I)-mediated cytosine self-pairing is preferred over hoogsteen-type base pairs with the artificial nucleobase 1,3-dideaza-6-nitropurine. Nucleosides, Nucleotides and Nucleic Acids, 29(1), 27-38. doi:10.1080/15257770903451579Mergny, J. -., Lacroix, L., Hélène, C., Han, X., & Leroy, J. -. (1995). Intramolecular folding of pyrimidine oligodeoxynucleotides into an i-DNA motif. Journal of the American Chemical Society, 117(35), 8887-8898. doi:10.1021/ja00140a001Ono, A., Cao, S., Togashi, H., Tashiro, M., Fujimoto, T., MacHinami, T., . . . Tanaka, Y. (2008). 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Journal of the American Chemical Society, 131(47), 17303-17314. doi:10.1021/ja906987sScopusSilver-Mediated Double Helix: Structural Parameters for a Robust DNA Building BlockArticleinfo:eu-repo/semantics/articlehttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1Chen, X., Department of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, Aalto, FinlandKarpenko, A., Department of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, Aalto, FinlandLopez-Acevedo, O., Department of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, Aalto, Finland, Facultad de Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, Medellín, ColombiaChen X.Karpenko A.Lopez-Acevedo O.Department of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, Aalto, FinlandFacultad de Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, Medellín, ColombiaThe DNA double helix is a versatile building block used in DNA nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base-Ag+-base bonding rather than by Watson-Crick pairing. In this work, we study the classical dynamics of a parallel silver-mediated homobase double helix and compare it to the dynamics of the antiparallel double helix. Our classical simulations show that only the parallel double helix is highly stable through the 100 ns simulation time. A new type of H-bond previously proposed by our collaboration and recently observed in crystal-determined helices drives the physicochemical stabilization. Compared to the natural B-DNA form, the metal-mediated helix has a contracted axial base pair rise and smaller numbers of base pairs per turn. These results open the path for the inclusion of this robust metal-mediated building block into new nanoscale DNA assemblies. © 2017 American Chemical Society.http://purl.org/coar/access_right/c_16ec11407/4251oai:repository.udem.edu.co:11407/42512020-05-27 19:08:13.43Repositorio Institucional Universidad de Medellinrepositorio@udem.edu.co |