1887
banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
f
Exploring the mechanisms of DNA hybridization on a surface
Rent:
Rent this article for
Access full text Article
/content/aip/journal/jcp/138/3/10.1063/1.4775480
1.
1. B. Vastag, “New clinical trials policy at FDA,” Nat. Biotechnol. 24, 1043 (2006).
http://dx.doi.org/10.1038/nbt0906-1043
2.
2. F. W. Frueh, “Impact of microarray data quality on genomic data submissions to the FDA,” Nat. Biotechnol. 24, 1105 (2006).
http://dx.doi.org/10.1038/nbt0906-1105
3.
3. D. A. Casciano and J. Woodcock, “Empowering microarrays in the regulatory setting,” Nat. Biotechnol. 24, 1103 (2006).
http://dx.doi.org/10.1038/nbt0906-1103
4.
4. W. Tong, A. B. Lucas, R. Shippy, X. Fan, H. Fang, H. Hong, M. S. Orr, T.-M. Chu, X. Guo, P. J. Collins, Y. A. Sun, S.-J. Wang, W. Bao, R. D. Wolfinger, S. Shchegrova, L. Guo, J. A. Warrington, and L. Shi, “Evaluation of external RNA controls for the assessment of microarray performance,” Nat. Biotechnol. 24, 1132 (2006).
http://dx.doi.org/10.1038/nbt1237
5.
5. H. Ji and R. W. Davis, “Data quality in genomics and microarrays,” Nat. Biotechnol. 24, 1112 (2006).
http://dx.doi.org/10.1038/nbt0906-1112
6.
6. L. Guo, E. K. Lobenhofer, C. Wang, R. Shippy, S. C. Harris, L. Zhang, N. Mei, T. Chen, D. Herman, F. M. Goodsaid, P. Hurban, K. L. Phillips, J. Xu, X. Deng, Y. A. Sun, W. Tong, Y. P. Dragan, and L. Shi, “Rat toxicogenomic study reveals analytical consistency across microarray platforms,” Nat. Biotechnol. 24, 1162 (2006).
http://dx.doi.org/10.1038/nbt1238
7.
7. W. P. Kuo, F. Liu, J. Trimarchi, C. Punzo, M. Lombardi, J. Sarang, M. E. Whipple, M. Maysuria, K. Serikawa, S. Young Lee, D. McCrann, J. Kang, J. R. Shearstone, J. Burke, D. J. Park, X. Wang, T. L. Rector, P. Ricciardi-Castagnoli, S. Perrin, S. Choi, R. Bumgarner, J. H. Kim, G. F. Short, III, M. W. Freeman, B. Seed, R. Jensen, G. M. Church, E. Hovig, C. L. Cepko, P. Park, L. Ohno-Machado, and T.-K. Jenssen, “A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies,” Nat. Biotechnol. 24, 832 (2006).
http://dx.doi.org/10.1038/nbt1217
8.
8. A. C. Eklund, L. R. Turner, P. Chen, R. V. Jensen, G. deFeo, A. R. Kopf-Sill, and Z. Szallasi, “Replacing cdna targets with cDNA reduces microarray cross-hybridization,” Nat. Biotechnol. 24, 1071 (2006).
http://dx.doi.org/10.1038/nbt0906-1071
9.
9. L. Shi, L. H. Reid, W. D. Jones, R. Shippy, J. A. Warrington, S. C. Baker, P. J. Collins, F. de Longueville, E. S. Kawasaki, K. Y. Lee, Y. Luo, Y. A. Sun, J. C. Willey, R. A. Setterquist, G. M. Fischer, W. Tong, Y. P. Dragan, D. J. Dix, F. W. Frueh, F. M. Goodsaid, D. Herman, R. V. Jensen, C. D. Johnson, E. K. Lobenhofer, R. K. Puri, U. Scherf, J. Thierry-Mieg, C. Wang, M. Wilson, P. K. Wolber, L. Zhang, S. Amur, W. Bao, C. C. Barbacioru, A. B. Lucas, V. Bertholet, C. Boysen, B. Bromley, D. Brown, A. Brunner, R. Canales, X. M. Cao, T. A. Cebula, J. J. Chen, J. Cheng, T.-M. Chu, E. Chudin, J. Corson, J. C. Corton, L. J. Croner, C. Davies, T. S. Davison, G. Delenstarr, X. Deng, D. Dorris, A. C. Eklund, X.-h. Fan, H. Fang, S. Fulmer-Smentek, J. C. Fuscoe, K. Gallagher, W. Ge, L. Guo, X. Guo, J. Hager, P. K. Haje, J. Han, T. Han, H. C. Harbottle, S. C. Harris, E. Hatchwell, C. A. Hauser, S. Hester, H. Hong, P. Hurban, S. A. Jackson, H. Ji, C. R. Knight, W. P. Kuo, J. E. LeClerc, S. Levy, Q.-Z. Li, C. Liu, Y. Liu, M. J. Lombardi, Y. Ma, S. R. Magnuson, B. Maqsodi, T. McDaniel, N. Mei, O. Myklebost, B. Ning, N. Novoradovskaya, M. S. Orr, T. W. Osborn, A. Papallo, T. A. Patterson, R. G. Perkins, E. H. Peters, R. Peterson, K. L. Philips, P. S. Pine, L. Pusztai, F. Qian, H. Ren, M. Rosen, B. A. Rosenzweig, R. R. Samaha, M. Schena, G. P. Schroth, S. Shchegrova, D. D. Smith, F. Staedtler, Z. Su, H. Sun, Z. Szallasi, Z. Tezak, D. Thierry-Mieg, K. L. Thompson, I. Tikhonova, Y. Turpaz, B. Vallanat, C. Van, S. J. Walker, S. J. Wang, Y. Wang, R. Wolfinger, A. Wong, J. Wu, C. Xiao, Q. Xie, J. Xu, W. Yang, L. Zhang, S. Zhong, Y. Zong, W. Slikker, Jr., and M. Consortium, “The microarray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements,” Nat. Biotechnol. 24, 1151 (2006).
http://dx.doi.org/10.1038/nbt1239
10.
10. T. A. Knotts, N. Rathore, D. C. Schwartz, and J. J. de Pablo, “A coarse grain model for DNA,” J. Chem. Phys. 126, 084901 (2007).
http://dx.doi.org/10.1063/1.2431804
11.
11. K.-Y. Wong and B. M. Pettitt, “The pathway of oligomeric DNA melting investigated by molecular dynamics simulations,” Biophys. J. 95, 5618 (2008).
http://dx.doi.org/10.1529/biophysj.108.141010
12.
12. E. J. Sambriski, D. C. Schwartz, and J. J. de Pablo, “A mesoscale model of DNA and its renaturation,” Biophys. J. 96, 1675 (2009).
http://dx.doi.org/10.1016/j.bpj.2008.09.061
13.
13. E. J. Sambriski, D. C. Schwartz, and J. J. de Pablo, “Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis,” Proc. Natl. Acad. Sci. U.S.A. 106, 18125 (2009).
http://dx.doi.org/10.1073/pnas.0904721106
14.
14. E. J. Sambriski, V. Ortiz, and J. J. de Pablo, “Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways,” J. Phys.: Condes. Matter 21, 034105 (2009).
http://dx.doi.org/10.1088/0953-8984/21/3/034105
15.
15. M. C. Linak and K. D. Dorfman, “Analysis of a DNA simulation model through hairpin melting experiments,” J. Chem. Phys. 133, 125101 (2010).
http://dx.doi.org/10.1063/1.3480685
16.
16. T. R. Prytkova, I. Eryazici, B. Stepp, S.-B. Nguyen, and G. C. Schatz, “DNA melting in small-molecule-DNA-hybrid dimer structures: Experimental characterization and coarse-grained molecular dynamics simulations,” J. Phys. Chem. B 114, 2627 (2010).
http://dx.doi.org/10.1021/jp910395k
17.
17. Y. Wang, D. R. Tree, and K. D. Dorfman, “Simulation of DNA extension in nanochannels,” Macromolecules 44, 6594 (2011).
http://dx.doi.org/10.1021/ma201277e
18.
18. M. C. Linak, R. Tourdot, and K. D. Dorfman, “Moving beyond Watson–Crick models of coarse grained DNA dynamics,” J. Chem. Phys. 135, 205102 (2011).
http://dx.doi.org/10.1063/1.3662137
19.
19. G. S. Freeman, D. M. Hinckley, and J. J. de Pablo, “A coarse-grain three-site-per-nucleotide model for DNA with explicit ions,” J. Chem. Phys. 135, 165104 (2011).
http://dx.doi.org/10.1063/1.3652956
20.
20. A.-M. Florescu and M. Joyeux, “Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide,” J. Chem. Phys. 135, 085105 (2011).
http://dx.doi.org/10.1063/1.3626870
21.
21. T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, “Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model,” J. Chem. Phys. 134, 085101 (2011).
http://dx.doi.org/10.1063/1.3552946
22.
22. M. R. Machado, P. D. Dans, and S. Pantano, “A hybrid all-atom/coarse grain model for multiscale simulations of DNA,” Phys. Chem. Chem. Phys. 13, 18134 (2011).
http://dx.doi.org/10.1039/c1cp21248f
23.
23. R. C. DeMille, T. E. Cheatham, and V. Molinero, “A coarse-grained model of DNA with explicit solvation by water and ions,” J. Phys. Chem. B 115, 132 (2011).
http://dx.doi.org/10.1021/jp107028n
24.
24. K.-Y. Wong and B. M. Pettitt, “A study of DNA tethered to surface by an all-atom molecular dynamics simulation,” Theor. Chem. Acc. 106, 233 (2001).
http://dx.doi.org/10.1007/s002140100269
25.
25. K.-Y. Wong and B. M. Pettitt, “Orientation of DNA on a surface from simulation,” Biopolymers 73, 570 (2004).
http://dx.doi.org/10.1002/bip.20004
26.
26. A. Jayaraman, C. K. Hall, and J. Genzer, “Computer simulation study of molecular recognition in model dna microarrays,” Biophys. J. 91, 2227 (2006).
http://dx.doi.org/10.1529/biophysj.106.086173
27.
27. N. B. Tito and J. M. Stubbs, “Application of a coarse-grained model for DNA to homo- and heterogeneous melting equilibria,” Chem. Phys. Lett. 485, 354 (2010).
http://dx.doi.org/10.1016/j.cplett.2009.12.079
28.
28. K. Drukker, G. Wu, and G. C. Schatz, “Model simulations of DNA denaturation dynamics,” J. Chem. Phys. 114, 579 (2001).
http://dx.doi.org/10.1063/1.1329137
29.
29. J. H. Allen, E. T. Schoch, and J. M. Stubbs, “Effect of surface binding on heterogeneous dna melting equilibria: A monte carlo simulation study,” J. Phys. Chem. B 115, 1720 (2011).
http://dx.doi.org/10.1021/jp111347p
30.
30. M. J. Hoefert, E. J. Sambriski, and J. J. de Pablo, “Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides,” Soft Matter 7, 560 (2011).
http://dx.doi.org/10.1039/c0sm00729c
31.
31. T. J. Schmitt and T. A. Knotts, “Thermodynamics of DNA hybridization on surfaces,” J. Chem. Phys. 134, 205105 (2011).
http://dx.doi.org/10.1063/1.3592557
32.
32. J. G. Mulle, V. C. Patel, S. T. Warren, M. R. Hegde, D. J. Cutler, and M. E. Zwick, “Empirical evaluation of oligonucleotide probe selection for DNA microarrays,” PLoS ONE 5, e9921 (2010).
http://dx.doi.org/10.1371/journal.pone.0009921
33.
33. S. Suzuki, N. Ono, C. Furusawa, A. Kashiwagi, and T. Yomo, “Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays,” BMC Genomics 8, 373 (2007).
http://dx.doi.org/10.1186/1471-2164-8-373
34.
34. G. Bell, R. Pictet, W. Rutter, B. Cordell, E. Tischer, and H. Goodman, “Sequence of the human insulin gene,” Nature (London) 284, 26 (1980).
http://dx.doi.org/10.1038/284026a0
35.
35. G. Martyna, M. Klein, and M. Tuckerman, “Nosé-Hoover chains - the canonical ensemble via continuous dynamics,” J. Chem. Phys. 97, 2635 (1992).
http://dx.doi.org/10.1063/1.463940
36.
36. S. Kumar, D. Bouzida, R. Swendsen, P. Kollman, and J. Rosenberg, “The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method,” J. Comput. Chem. 13, 1011 (1992).
http://dx.doi.org/10.1002/jcc.540130812
37.
37. S. Kumar, J. Rosenberg, D. Bouzida, R. Swendsen, and P. Kollman, “Multidimensional free-energy calculations using the weighted histogram analysis method,” J. Comput. Chem. 16, 1339 (1995).
http://dx.doi.org/10.1002/jcc.540161104
38.
38. T. A. Knotts IV, N. Rathore, and J. J. de Pablo, “Structure and stability of a model three-helix-bundle protein on tailored surfaces,” Proteins 61, 385 (2005).
http://dx.doi.org/10.1002/prot.20581
39.
39. S. Wei and T. A. Knotts IV, “Predicting stability of alpha-helical, orthogonal-bundle proteins on surfaces,” J. Chem. Phys. 133, 115102 (2010).
http://dx.doi.org/10.1063/1.3479039
40.
40. S. Wei and T. A. Knotts IV, “Effects of tethering a multistate folding protein to a surface,” J. Chem. Phys. 134, 185101 (2011).
http://dx.doi.org/10.1063/1.3589863
41.
41. J. D. Weeks, D. Chandler, and H. C. Andersen, “Role of repulsive forces in determining the equilibrium structure of simple liquids,” J. Chem. Phys. 54, 5237 (1971).
http://dx.doi.org/10.1063/1.1674820
42.
42. N. Rathore, T. A. Knotts IV, and J. J. de Pablo, “Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations,” Biophys. J. 90, 17671773 (2006).
http://dx.doi.org/10.1529/biophysj.105.071076
43.
43. T. A. Knotts IV, N. Rathore, and J. J. de Pablo, “An entropic perspective of protein stability on surfaces,” Biophys. J. 94, 4473 (2008).
http://dx.doi.org/10.1529/biophysj.107.123158
44.
44. K. M. Guckian, B. A. Schweitzer, R. X.-F. Ren, C. J. Sheils, D. C. Tahmassebi, and E. T. Kool, “Factors contributing to aromatic stacking in water: Evaluation in the context of DNA,” J. Am. Chem. Soc. 122, 2213 (2000).
http://dx.doi.org/10.1021/ja9934854
45.
45. S. Bommarito, N. Peyret, and J. SantaLucia, Jr., “Thermodynamic parameters for dna sequences with dangling ends,” Nucleic Acids Res. 28, 1929 (2000).
http://dx.doi.org/10.1093/nar/28.9.1929
46.
46. J. Isaksson and J. Chattopadhyaya, “A uniform mechanism correlating dangling-end stabilization and stacking geometry,” Biochemistry 44, 5390 (2005).
http://dx.doi.org/10.1021/bi047414f
47.
47. B. G. Moreira, Y. You, M. A. Behlke, and R. Owczarzy, “Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability,” Biochem. Biophys. Res. Commun. 327, 473 (2005).
http://dx.doi.org/10.1016/j.bbrc.2004.12.035
48.
48. J. I. Lewis, D. J. Moss, and T. A. Knotts IV, “Multiple molecule effects on the cooperativity of protein folding transitions in simulations,” J. Chem. Phys. 136, 245101 (2012).
http://dx.doi.org/10.1063/1.4729604
49.
49. O.-S. Lee and G. C. Schatz, “Interaction between DNAs on a gold surface,” J. Phys. Chem. C 113, 15941 (2009).
http://dx.doi.org/10.1021/jp905469q
50.
journal-id:
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/3/10.1063/1.4775480
Loading
/content/aip/journal/jcp/138/3/10.1063/1.4775480
Loading

Data & Media loading...

Loading

Article metrics loading...

/content/aip/journal/jcp/138/3/10.1063/1.4775480
2013-01-16
2014-07-23

Abstract

DNA microarrays are a potentially disruptive technology in the medical field, but their use in such settings is limited by poor reliability. Microarrays work on the principle of hybridization and can only be as reliable as this process is robust, yet little is known at the molecular level about how the surface affects the hybridization process. This work uses advanced molecular simulation techniques and an experimentally parameterized coarse-grain model to determine the mechanism by which hybridization occurs on surfaces. The results show that hybridization proceeds through a mechanism where the untethered (target) strand often flips orientation. For evenly lengthed strands, the surface stabilizes hybridization (compared to the bulk system) by reducing the barriers involved in the flipping event. For unevenly lengthed strands, the surface destabilizes hybridization compared to the bulk, but the degree of destabilization is dependent on the location of the matching sequence. Taken as a whole, the results offer an unprecedented view into the hybridization process on surfaces and provide some insights as to the poor reproducibility exhibited by microarrays.

Loading

Full text loading...

/deliver/fulltext/aip/journal/jcp/138/3/1.4775480.html;jsessionid=208vu4tnq6vke.x-aip-live-03?itemId=/content/aip/journal/jcp/138/3/10.1063/1.4775480&mimeType=html&fmt=ahah&containerItemId=content/aip/journal/jcp
true
true
This is a required field
Please enter a valid email address
This feature is disabled while Scitation upgrades its access control system.
This feature is disabled while Scitation upgrades its access control system.
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Exploring the mechanisms of DNA hybridization on a surface
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/3/10.1063/1.4775480
10.1063/1.4775480
SEARCH_EXPAND_ITEM