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Sequence dependent interaction of single stranded DNA with graphitic flakes: atomistic molecular dynamics simulations

Published online by Cambridge University Press:  05 February 2016

Ho Shin Kim ,
Sabrina M. Huang  and
Yaroslava G. Yingling
Ho Shin Kim
Affiliation:
Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, U.S.A.
Sabrina M. Huang
Affiliation:
Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, U.S.A.
Yaroslava G. Yingling*
Affiliation:
Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, U.S.A.
*
*(Email: [email protected])
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Abstract

In an attempt to understand the structure and dynamics of ssDNA on graphene based surfaces, we performed all-atom implicit solvent molecular dynamics simulations of ssDNA on graphene and graphene oxide (GO) surfaces. Simulations indicate that adsorption of poly(A), poly(T) and poly (AT) have similar mechanisms of adsorption to free standing graphitic flakes, which are governed by a surface oxygen content. Specifically, higher oxygen content of a surface leads to decrease in persistence length of ssDNA. However, the role of DNA sequence on the physisorption mechanism is minimal.

Keywords

simulationsensorbiomaterial
Type
Articles
Information
MRS Advances , Volume 1 , Issue 25: Theory, Characterization, and Modeling , 2016 , pp. 1883 - 1889
Copyright
Copyright © Materials Research Society 2016 

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References

REFERENCES

Hogan, M.E., Austin, R.H., “Importance of DNA Stiffness in Protein DNA-Binding Specificity” Nature 1987, 329, 263–266.Google Scholar
Gooding, J.J., King, G.C., “Nucleic acid biosensors based upon surface-assembled monolayers: exploiting and enhancing materials properties” Journal of Materials Chemistry 2005, 15, 4876–4880.Google Scholar
Lozano, M.M., Starkel, C.D., Longo, M.L., “Vesicles Tethered to Microbubbles by Hybridized DNA Oligonucleotides: Flow Cytometry Analysis of This New Drug Delivery Vehicle Design” Langmuir 2010, 26, 8517–8524.Google Scholar
Li, N.K., Kim, H.S., Nash, J.A., Lim, M., Yingling, Y.G., “Progress in molecular modelling of DNA materials” Molecular Simulation 2014, 40, 777–783.Google Scholar
Singh, A., Eksiri, H., Yingling, Y.G., “Theoretical Perspective on Properties of DNA-Functionalized Surfaces” Journal of Polymer Science Part B-Polymer Physics 2011, 49, 1563–1568.Google Scholar
He, Y., Jiao, B.N., Tang, H.W., “Interaction of single-stranded DNA with graphene oxide: fluorescence study and its application for S1 nuclease detection” Rsc Advances 2014, 4, 18294–18300.Google Scholar
Singh, A., Snyder, S., Lee, L., Johnston, A.P.R., Caruso, F., Yingling, Y.G., “Effect of Oligonucleotide Length on the Assembly of DNA Materials: Molecular Dynamics Simulations of Layer-by-Layer DNA Films” Langmuir 2010, 26, 17339–17347.Google Scholar
Zhu, Y.W., Murali, S., Cai, W.W., Li, X.S., Suk, J.W., Potts, J.R., Ruoff, R.S., “Graphene and Graphene Oxide: Synthesis, Properties, and Applications” Advanced Materials 2010, 22, 3906–3924.CrossRefGoogle Scholar
Chen, J.L., Wang, X.G., Dai, C.Q., Chen, S.D., Tu, Y.S., “Adsorption of GA module onto graphene and graphene oxide: A molecular dynamics simulation study” Physica E-Low-Dimensional Systems & Nanostructures 2014, 62, 59–63.Google Scholar
Baweja, L., Balamurugan, K., Subramanian, V., Dhawan, A., “Hydration Patterns of Graphene-Based Nanomaterials (GBNMs) Play a Major Role in the Stability of a Helical Protein: A Molecular Dynamics Simulation Study” Langmuir 2013, 29, 14230–14238.CrossRefGoogle Scholar
Sun, X.T., Feng, Z.W., Hou, T.J., Li, Y.Y., “Mechanism of Graphene Oxide as an Enzyme Inhibitor from Molecular Dynamics Simulations” Acs Applied Materials & Interfaces 2014, 6, 7153–7163.Google Scholar
Macke, T.J., Case, D.A., “Modeling unusual nucleic acid structures” Molecular Modeling of Nucleic Acids 1998, 682, 379–393.Google Scholar
Case, D., Darden, T., Cheatham, T. III, Simmerling, C, Wang, J., Duke, R., Luo, R., Walker, R., Zhang, W., Merz, K., “AMBER 12” University of California, San Francisco 2012.Google Scholar
Range, K., Mayaan, E., Maher, L.J., York, D.M., “The contribution of phosphate-phosphate repulsions to the free energy of DNA bending” Nucleic Acids Research 2005, 33, 1257–1268.Google Scholar
Wang, J.M., Cieplak, P., Kollman, P.A., “How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?” Journal of Computational Chemistry 2000, 21, 1049–1074.Google Scholar
Humphrey, W., Dalke, A., Schulten, K., “VMD: Visual molecular dynamics” Journal of Molecular Graphics & Modelling 1996, 14, 33–38.CrossRefGoogle ScholarPubMed
Wang, J.M., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Case, D.A., “Development and testing of a general amber force field” Journal of Computational Chemistry 2004, 25, 1157–1174.Google Scholar
Stauffer, D., Dragneva, N., Floriano, W.B., Mawhinney, R.C., Fanchini, G., French, S., Rubel, O., “An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water” Journal of Chemical Physics 2014, 141.CrossRefGoogle Scholar
Berendsen, H.J.C., Postma, J.P.M., Vangunsteren, W.F., Dinola, A., Haak, J.R., “Molecular-Dynamics with Coupling to an External Bath” Journal of Chemical Physics 1984, 81, 3684–3690.Google Scholar
Rubinstein, M., Colby, R., Polymers Physics. Oxford: 2003.Google Scholar
Bashford, D., Case, D.A., “Generalized born models of macromolecular solvation effects” Annual Review of Physical Chemistry 2000, 51, 129–152.Google Scholar
Manna, A.K., Pati, S.K., “Theoretical understanding of single-stranded DNA assisted dispersion of graphene” Journal of Materials Chemistry B 2013, 1, 91–100.CrossRefGoogle Scholar
Kim, H.S., Ha, S.H., Sethaphong, L., Koo, Y.M., Yingling, Y.G., “The relationship between enhanced enzyme activity and structural dynamics in ionic liquids: a combined computational and experimental study” Physical Chemistry Chemical Physics 2014, 16, 2944–2953.Google Scholar
Kim, H.S., Pani, R., Ha, S.H., Koo, Y.M., Yingling, Y.G., “The role of hydrogen bonding in water-mediated glucose solubility in ionic liquids” Journal of Molecular Liquids 2012, 166, 25–30.Google Scholar
Roe, D.R., Cheatham, T.E., “PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data” Journal of Chemical Theory and Computation 2013, 9, 3084–3095.Google Scholar
McGaughey, G.B., Gagne, M., Rappe, A.K., “pi-stacking interactions - Alive and well in proteins” Journal of Biological Chemistry 1998, 273, 15458–15463.CrossRefGoogle Scholar
Hunter, C.A., Singh, J., Thornton, J.M., “Pi-Pi-Interactions - the Geometry and Energetics of Phenylalanine Phenylalanine Interactions in Proteins” Journal of Molecular Biology 1991, 218, 837–846.Google Scholar
Round, A.N., Berry, M., McMaster, T.J., Stoll, S., Gowers, D., Corfield, A.P., Miles, M.J., “Heterogeneity and persistence length in human ocular mucins” Biophysical Journal 2002, 83, 1661–1670.Google Scholar