Complex Thermodynamic Behavior of Single-Stranded Nucleic Acid Adsorption to Graphene Surfaces

Langmuir

Volumn 32, Issue 24, 2016, Pages 6028-6034

  Ranganathan, Srivathsan V ^a   Halvorsen, Ken ^a   Myers, Chris A ^a   Robertson, Neil M ^a   Yigit, Mehmet V ^a   Chen, Alan A ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BINS; BIOMOLECULES; BIOSENSORS; MOLECULAR MODELING; NUCLEIC ACIDS; OLIGONUCLEOTIDES; QUENCHING; THERMODYNAMICS; WATER ABSORPTION;

BINDING THERMODYNAMICS; COMPLEX THERMODYNAMICS; COMPUTATIONAL RESULTS; FLUORESCENCE QUENCHING; ISOTHERMAL TITRATION CALORIMETRY; PREDICTIVE MODELING; SINGLE STRANDED NUCLEIC ACIDS; WATER-SOLUBLE FORM;

GRAPHENE;

EID: 84975818481     PISSN: 07437463     EISSN: 15205827     Source Type: Journal    
DOI: 10.1021/acs.langmuir.6b00456     Document Type: Article

References (43)

1. Geim, A. K.; Novoselov, K. S. The rise of graphene Nat. Mater. 2007, 6 (3) 183-91 10.1038/nmat1849
2. Novoselov, K. S.; Geim, A. K.; Morozov, S. V.; Jiang, D.; Zhang, Y.; Dubonos, S. V.; Grigorieva, I. V.; Firsov, A. A. Electric field effect in atomically thin carbon films Science 2004, 306 (5696) 666-9 10.1126/science.1102896
3. Balci, O.; Polat, E. O.; Kakenov, N.; Kocabas, C. Graphene-enabled electrically switchable radar-absorbing surfaces Nat. Commun. 2015, 6, 6628 10.1038/ncomms7628
4. Sydlik, S. A.; Jhunjhunwala, S.; Webber, M. J.; Anderson, D. G.; Langer, R. In vivo compatibility of graphene oxide with differing oxidation states ACS Nano 2015, 9 (4) 3866-74 10.1021/acsnano.5b01290
5. Zhu, A. Y.; Yi, F.; Reed, J. C.; Zhu, H.; Cubukcu, E. Optoelectromechanical multimodal biosensor with graphene active region Nano Lett. 2014, 14 (10) 5641-9 10.1021/nl502279c
6. Reed, J. C.; Zhu, A. Y.; Zhu, H.; Yi, F.; Cubukcu, E. Wavelength tunable microdisk cavity light source with a chemically enhanced MoS2 emitter Nano Lett. 2015, 15 (3) 1967-71 10.1021/nl5048303
7. Guo, Q.; Zhu, H.; Liu, F.; Zhu, A. Y.; Reed, J. C.; Yi, F.; Cubukcu, E. Silicon-on-Glass Graphene-Functionalized Leaky Cavity Mode Nanophotonic Biosensor ACS Photonics 2014, 1 (3) 221-227 10.1021/ph400073w
8. Chung, C.; Kim, Y. K.; Shin, D.; Ryoo, S. R.; Hong, B. H.; Min, D. H. Biomedical applications of graphene and graphene oxide Acc. Chem. Res. 2013, 46 (10) 2211-24 10.1021/ar300159f
9. Zhang, Y.; Nayak, T. R.; Hong, H.; Cai, W. Graphene: a versatile nanoplatform for biomedical applications Nanoscale 2012, 4 (13) 3833-42 10.1039/c2nr31040f
10. Song, Y.; Qu, K.; Zhao, C.; Ren, J.; Qu, X. Graphene oxide: intrinsic peroxidase catalytic activity and its application to glucose detection Adv. Mater. 2010, 22 (19) 2206-10 10.1002/adma.200903783
11. Wang, Y.; Li, Z.; Hu, D.; Lin, C. T.; Li, J.; Lin, Y. Aptamer/graphene oxide nanocomplex for in situ molecular probing in living cells J. Am. Chem. Soc. 2010, 132 (27) 9274-6 10.1021/ja103169v
12. Lu, C. H.; Yang, H. H.; Zhu, C. L.; Chen, X.; Chen, G. N. A graphene platform for sensing biomolecules Angew. Chem., Int. Ed. 2009, 48 (26) 4785-7 10.1002/anie.200901479
13. Hizir, M. S.; Balcioglu, M.; Rana, M.; Robertson, N. M.; Yigit, M. V. Simultaneous detection of circulating oncomiRs from body fluids for prostate cancer staging using nanographene oxide ACS Appl. Mater. Interfaces 2014, 6 (17) 14772-8 10.1021/am504190a
14. Huang, P. J.; Liu, J. Molecular beacon lighting up on graphene oxide Anal. Chem. 2012, 84 (9) 4192-8 10.1021/ac300778s
15. Balcioglu, M.; Buyukbekar, B. Z.; Yavuz, M. S.; Yigit, M. V. Smart-polymer-functionalized graphene nanodevices for thermo-switch-controlled biodetection ACS Biomater. Sci. Eng. 2014, 1 (1) 27-36 10.1021/ab500029h
16. Liu, J. Adsorption of DNA onto gold nanoparticles and graphene oxide: surface science and applications Phys. Chem. Chem. Phys. 2012, 14 (30) 10485-96 10.1039/c2cp41186e
17. Robertson, N. M.; Salih Hizir, M.; Balcioglu, M.; Wang, R.; Yavuz, M. S.; Yumak, H.; Ozturk, B.; Sheng, J.; Yigit, M. V. Discriminating a Single Nucleotide Difference for Enhanced miRNA Detection Using Tunable Graphene and Oligonucleotide Nanodevices Langmuir 2015, 31 (36) 9943-52 10.1021/acs.langmuir.5b02026
18. Robertson, N. M.; Hizir, M. S.; Balcioglu, M.; Rana, M.; Yumak, H.; Ecevit, O.; Yigit, M. V. Monitoring the multitask mechanism of DNase I activity using graphene nanoassemblies Bioconjugate Chem. 2015, 26 (4) 735-45 10.1021/acs.bioconjchem.5b00067
19. Rana, M.; Balcioglu, M.; Robertson, N.; Yigit, M. V. Nano-graphene oxide as a novel platform for monitoring the effect of LNA modification on nucleic acid interactions Analyst 2014, 139 (4) 714-20 10.1039/C3AN02066E
20. Chehel Amirani, M.; Tang, T. Binding of nucleobases with graphene and carbon nanotube: a review of computational studies J. Biomol. Struct. Dyn. 2015, 33 (7) 1567-1597 10.1080/07391102.2014.954315
21. Varghese, N.; Mogera, U.; Govindaraj, A.; Das, A.; Maiti, P. K.; Sood, A. K.; Rao, C. N. Binding of DNA nucleobases and nucleosides with graphene ChemPhysChem 2009, 10 (1) 206-10 10.1002/cphc.200800459
22. Das, A.; Sood, A. K.; Maiti, P. K.; Das, M.; Varadarajan, R.; Rao, C. N. R. Binding of nucleobases with single-walled carbon nanotubes: Theory and experiment Chem. Phys. Lett. 2008, 453 (4) 266-273 10.1016/j.cplett.2008.01.057
23. Cavaluzzi, M. J.; Borer, P. N. Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA Nucleic Acids Res. 2004, 32 (1) 13e 10.1093/nar/gnh015
24. Tellinghuisen, J. Calibration in isothermal titration calorimetry: heat and cell volume from heat of dilution of NaCl(aq) Anal. Biochem. 2007, 360, 47-55 10.1016/j.ab.2006.10.015
25. Demarse, N. A.; Quinn, C. F.; Eggett, D. L.; Russell, D. J.; Hansen, L. D. Calibration of nanowatt isothermal titration calorimeters with overflow reaction vessels Anal. Biochem. 2011, 417, 247-255 10.1016/j.ab.2011.06.014
26. Kallansrud, G.; Ward, B. A comparison of measured and calculated single- and double-stranded oligodeoxynucleotide extinction coefficients Anal. Biochem. 1996, 236 (1) 134-138 10.1006/abio.1996.0141
27. Antony, J.; Grimme, S. Structures and interaction energies of stacked graphene-nucleobase complexes Phys. Chem. Chem. Phys. 2008, 10 (19) 2722-2729 10.1039/b718788b
28. Kong, J.; White, C. A.; Krylov, A. I.; Sherrill, D.; Adamson, R. D.; Furlani, T. R.; Lee, M. S.; Lee, A. M.; Gwaltney, S. R.; Adams, T. R.; Ochsenfeld, C.; Gilbert, A. T. B.; Kedziora, G. S.; Rassolov, V. A.; Maurice, D. R.; Nair, N.; Shao, Y.; Besley, N. A.; Maslen, P. E.; Dombroski, J. P.; Daschel, H.; Zhang, W.; Korambath, P. P.; Baker, J.; Byrd, E. F. C.; Van Voorhis, T.; Oumi, M.; Hirata, S.; Hsu, C.-P.; Ishikawa, N.; Florian, J.; Warshel, A.; Johnson, B. G.; Gill, P. M. W.; Head-Gordon, M.; Pople, J. A. Q-Chem 2.0: A high-performance ab initio electronic structure program package J. Comput. Chem. 2000, 21, 1532-1548 10.1002/1096-987X(200012)21:16<1532::AID-JCC10>3.0.CO;2-W
29. Rezác, J.; Kevin, E. R.; Pavel, H. S66: A well-balanced database of benchmark interaction energies relevant to biomolecular structures J. Chem. Theory Comput. 2011, 7 (8) 2427-2438 10.1021/ct2002946
30. Goerigk, L.; Holger, K.; Grimme, S. Benchmarking Density Functional Methods against the S66 and S66 × 8 Datasets for Non-Covalent Interactions ChemPhysChem 2011, 12 (17) 3421-3433 10.1002/cphc.201100826
31. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4 (3) 435-447 10.1021/ct700301q
32. Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling J. Chem. Phys. 2007, 126, 014101-1-014101-7 10.1063/1.2408420
33. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald-an N.LOG(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092 10.1063/1.464397
34. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79 (2) 926-935 10.1063/1.445869
35. Hess, B.; Bekker, H.; Berendsen, H.; Fraaije, J. LINCS: a linear constraint solver for molecular simulations J. Comput. Chem. 1997, 18, 1463-1472 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
36. Rosenbergl, J. M. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 1992, 13 (8) 1011-1021 10.1002/jcc.540130812
37. Stankovich, S.; Dikin, D. A.; Piner, R. D.; Kohlhaas, K. A.; Kleinhammes, A.; Jia, Y.; Wu, Y.; Nguyen, S. T.; Ruoff, R. S. Synthesis of graphene-based nanosheets via chemical reduction of exfoliated graphite oxide Carbon 2007, 45 (7) 1558-1565 10.1016/j.carbon.2007.02.034
38. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179-5197 10.1021/ja00124a002
39. Chen, A. A.; García, A. E. High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations Proc. Natl. Acad. Sci. U. S. A. 2013, 110 (42) 16820-16825 10.1073/pnas.1309392110
40. He, Y.; Jiao, B.; Tang, H. Interaction of single-stranded DNA with graphene oxide: fluorescence study and its application for S1 nuclease detection RSC Adv. 2014, 4 (35) 18294-18300 10.1039/c4ra01102c
41. Liu, B.; Sun, Z.; Zhang, X.; Liu, J. Mechanisms of DNA sensing on graphene oxide Anal. Chem. 2013, 85 (16) 7987-7993 10.1021/ac401845p
42. Park, J. S.; Goo, N. I.; Kim, D. E. Mechanism of DNA adsorption and desorption on graphene oxide Langmuir 2014, 30 (42) 12587-12595 10.1021/la503401d
43. Wu, M.; Kempaiah, R.; Huang, P. J.; Maheshwari, V.; Liu, J. Adsorption and desorption of DNA on graphene oxide studied by fluorescently labeled oligonucleotides Langmuir 2011, 27 (6) 2731-2738 10.1021/la1037926