DNA and DNA-Surfactant Complexes at Solid Surfaces

DNA Interactions with Polymers and Surfactants

Volumn , Issue , 2007, Pages 291-315

  Cárdenas, Marité ^a   Nylander, Tommy ^b  

^a MALMÖ UNIVERSITY   (Sweden)

^b LUND UNIVERSITY   (Sweden)

Author keywords

DNA and DNA surfactant complexes and solid surface; DNA microarrays and nanostamping; DNA structure on surfaces

Indexed keywords

EID: 84889316070     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470286364.ch11     Document Type: Chapter

References (87)

1. A. Bertin, A. Leforestier, D. Durand, F. Livolant. Role of histone tails in the conformation and interactions of nucleosome core particles. Biochemistry 43 (2004): 4773-4780.
2. G. Wagner, A. Bancaud, J.-P. Quivy, C. Clapier, G. Almouzni, J.-L. Viovy. Compaction kinetics on single DNAs: Purified nucleosome reconstitution systems versus crude extract. Biophys. J. 89 (2005): 3647-3659.
3. K. Matsubara, N. Sano, T. Umehara, M. Horikoshi. Global analysis of functional surfaces of core histones with comprehensive point mutants. Genes Cells 12 (2007): 13-33.
4. A. Elaissari, P. Cros, C. Pichot, V. Laurent, B. Mandrand. Adsorption of oligonucleotides ontoo negatively and positively charged latex particles. Coll. Surf. A, Physicochem. Eng. Aspects 83 (1994): 25-31.
5. S. A. Gani, D. C. Mukherjee, D. K. Chattoraj. Adsorption of biopolymer at solid-liquid interfaces. 1. Affinities of DNA to hydrophobic and hydrophilic solid surfaces. Langmuir 15 (1999): 7130-7138.
6. V. Balladur, A. Theretz, B. Mandrand. Determination of the main driving forces driving DNAoligonucleotide adsorption onto aminated silica wafers. J. Coll. Int. Sci. 194 (1997): 408-418.
7. R. R. Kunze, R. R. Netz. Salt induced DNA-histone complexation. Phys. Rev. Lett. 85 (2000): 4389-4392.
8. S. P. A. Fodor. DNA sequencing-Massively parallel genomics. Science 277 (1997): 393-395.
9. R. Lenigk, M. Carles, N. Y. Ip, N. J. Sucher. Surface characterization of a silicon-chipbased DNA microarray. Langmuir 17 (2001): 2497-2501.
10. K. S. Midwood, M. D. Carolus, M. P. Danahy, J. E. Schwarzbauer, J. Schwartz. Easy and efficient bonding of biomolecules to an oxide surface of silicon. Langmuir 20 (2004): 5501-5505.
11. A. L. M. Le Ny, C. T. Lee. Photoreversible DNA condensation using light-responsive surfactants. J. Am. Chem. Soc. 128 (2006): 6400-6408.
12. P. Gong, C.-Y. Lee, L. J. Gamble, D. G. Castner, D.W. Grainger. Hybridization behavior of mixed DNA/alkylthiol monolayers on gold: Characterization by surface plasmon resonance and 32P radiometric assay. Anal. Chem. 78 (2006): 3326-3334.
13. I. Pfeiffer, F. Höök. Bivalent cholesterol-based coupling of oligonucletided to lipid membrane assemblies. J. Am. Chem. Soc. 126 (2004): 10224-10225.
14. I. Pfeiffer, F. Höök. Quantification of oligonucleotide modifications of small unilamellar lipid vesicles. Anal. Chem. 78 (2006): 7493-7498.
15. R. M. Stoltenberg, A. T. Woolley. DNA-templated nanowire fabrication. Biomed. Microdev. 6 (2004): 105-111.
16. I. M. Verma, N. Somia. Gene therapy-Promises, problems and prospects. Nature 389 (1997): 239-242.
17. N. S. Templeton, D. D. Lasic. Newdirections in liposome gene delivery. Mol. Biotechn. 11 (1999): 175-180.
18. C. R. Cantor, P. R. Schimmel. Biophysical Chemistry. Freeman, San Francisco, 1980.
19. L. Stryer. Biochemistry. Freeman, New York, 1995.
20. B. Tinland, A. Pluen, J. Sturm, G. Weill. Persistence length of single-stranded DNA. Macromolecules 30 (1997): 5763-5765.
21. A. M. van Oijen. Honey., I shrunk the DNA: DNA length as a probe for nucleic-acid enzyme activity. Biopolymers 85 (2007): 144.
22. D. K. Chattoraj, P. Chowrashi, K. Chakravarti. Electrophoresis of adsorbed DNA. Biopolymers 5 (1967): 173-184.
23. K. Eskilsson, C. Leal, B. Lindman, M. Miguel, T. Nylander. DNA-surfactant complexes at solid surfaces. Langmuir 17 (2001): 1666-1669.
24. M. Cárdenas, A. Braem, T. Nylander, B. Lindman. DNA compaction at hydrophobic surfaces induced by a cationic amphiphile. Langmuir 19 (2003): 7712-7718.
25. M. Cardenas, K. Schillen, T. Nylander, J. Jansson, B. Lindman. DNA compaction by cationic surfactant in solution and at polystyrene particle solution interfaces: A dynamic light scattering study. Phys. Chem. Chem. Phys. 6 (2004): 1603-1607.
26. M. I. Pividori, S. Alegret. DNA adsorption on carbonaceous materials. Topics Curr. Chem. 260 (2005): 1-36.
27. A.-M. Chiorcea Paquim, T. S. Oretskaya, A. M. Oliveira Brett. Adsorption of synthetic homo-and hetero-oligodeoxynucleotides onto highly oriented pyrolytic graphite: Atomic force microscopy characterisation. Biophys. Chem. 121 (2006): 131-141.
28. G. J. Fleer, M. A. Cohen Stuart, J. M. H. M. Scheutjens, T. Cosgrove, B. Vincent. Polymer at Interfaces. Chapman & Hall, London, 1993.
29. M. Cárdenas, K. Schillén, T. Nylander, J. Jansson, B. Lindman. DNA compaction by cationic surfactant in solution and at polystyrene particle solution interfaces: A dynamic light scattering study. Phys. Chem. Chem. Phys. 6 (2004): 1603-1607.
30. S. Sowerby, C. A. Cohn, W. M. Heckl, N. G. Holm. Differential adsorption of nucleic acid bases: relevance to the origin of life. Proc. Natl. Sci. USA. 98 (2001): 820-822.
31. J. J. Storhoff, R. Elghanian, C. A. Mirkin, R. L. Letsinger. Sequence-dependent stability of DNA-modified gold nanoparticles. Langmuir 18 (2002): 6666-6670.
32. P. Cai, Q. Haung, X. Zhang, H. Chen. Adsorption of DNA on clay mineral and various colloidal particles from an alfisol. Soil Biol. Biochem. 38 (2006): 471-476.
33. M. J. Allen, E. M. Bradbury, R. Balhorn. AFM analysis of DNA-protamine complexes bound to mica. Nucl. Acids Res. 25 (1997): 2221-2226.
34. H. G. Hansma, M. Bezanilla, F. Zenhausern, M. Adrian, R. L. Sinsheimer. Atomic force microsopy of DNA in aqueous solutions. Nucl. Acids Res. 21 (1993): 505-512.
35. K. Umemura, F. Nagami, T. Okada, R. Kuroda. AFM characterization of single strand specific endonuclease activity on linear DNA. Nucl. Acids Res. 28 (2000): e38-e42.
36. M. Cárdenas, K. Schillén, D. Pebalk, T. Nylander, B. Lindman. Interaction between DNA and amino functionalized particles could be hydrophobically driven. Biomacromolecules 6 (2005): 832-836.
37. S. J. Oh, S. J. Cho, C. O. Kim, J.W. Park. Characteristics of DNA microarrays fabricated on various aminosilane layers. Langmuir 18 (2002): 1764-1769.
38. E. Metwalli, D. Haines, O. Becker, S. Conzone, C. G. Pantano. Surface characterizations of mono, di and tri aminosilane treated glass substrates. J Coll. Interface Sci. 298 (2006): 825-831.
39. R. K. Iler. The Chemistry of Silica. Wiley, New York, 1979.
40. M. E. McGovern, K. M. R. Kallury, M. Thompson. Role of solvent on the silanization of glass with octadecyltrichlorosilane. Langmuir 10 (1994): 3607-3614.
41. K. Saal, T. Töatte, I. Tulp, I. Kink, A. Kurg, U. Möaeorg, A. Rinken, A. Lõhmus. Sol-gel films for DNA microarray applications. Mat. Lett. 60 (2006): 1833-1838.
42. A. P. R. Johnston, H. Mitomo, E. S. Read, F. Caruso. Compositional and structural engineering of DNA multilayer films. Langmuir 22 (2006): 3251-3258.
43. H. Wackerbarth, M. Grubb, J. Zhang, A. G. Hansen, J. Ulstrup. Long-range order of organized oligonucleotide monolayers on Au (111) electrodes. Langmuir 20 (2004): 1647.
44. L. M. Demers, C. A. Mirkin, R. C. Mucic, R. A. Reynolds, R. L. Letsinger, R. Elghanian, G.Viswanadham. Afluorescence-based method for determining the surface coverage and hybridization efficiency of thiol-capped oligonucleotides bound to gold thin films and nanoparticles. Anal. Chem. 72 (2000): 5535-5541.
45. C.-Y. Lee, P. Gong, G. M. Harbers, D.W. Grainger, D. G. Castner, L. J. Gamble. Surface coverage and structure of mixed DNA/alkylthiol monolayers on gold: Characterization by XPS, NEXAFS, and Fluorescence Intensity Measurements. Anal. Chem. 78 (2006): 3316-3325.
46. R. Levicky, T. M. Herne, M. J. Tarlov, S. K. Satija. Using self-assembly to control the structure ofDNAmonolayers on gold:Aneutron reflectivity study. J. Am. Chem. Soc. 120 (1998): 9787-9792.
47. D. Zanchet, C. M. Michel, W. J. Parak, D. Gerion, A. P. Alivisatos. Electrophoretic isolation of discrete Au nanocrystal/DNA conjugates. Nanoletters 1 (2001): 32-35.
48. S. Moses, S. H. Brewer, L.B. Lowe, S. E. Lappi, L. B. G. Gilvey, M. Sauthier, R.C. Tenent, D. L. Feldheim, S. Franzen. Characterization of single-and double-strandedDNAon gold surfaces. Langmuir 20 (2004): 11134-11140.
49. L. Olofsson, T. Rindzevicius, I. Pfeiffer, M. Käll, F. Höök. Surface-based gold-nanoparticlec sensor for specific and quantitative DNA hybridization detection. Langmuir 19 (2003): 10414-10419.
50. S. J. Park, A. A. Lazarides, J. J. Storhoff, L. Pesce, C. A. Mirkin. The structural characterization of oligonucleotide-modified gold nanoparticle networks formed by DNA hybridization. J. Phys. Chem. B 108 (2004): 12375-12380.
51. T. M. Herne, M. J. Tarlov. Characterization ofDNA probes immobilized on gold surfaces. J. Am. Chem. Soc. 119 (1997): 8916-8920.
52. M. Cárdenas, J. Barauskas, K. Schillen, J. Brennan, M. Brust, T. Nylander. Thiol-specific and non-specific interactions between DNA and gold nanoparticles. Biomacromolecules 22 (2006): 3294-3299.
53. P. Sandström, M. Boncheva, B.Å kerman. Nonspecific and thiol-specific binding of DNA to gold nanoparticles. Langmuir 19 (2003): 7537-7543.
54. U. Rant, K. Arinaga, S. Fujita, N. Yokoyama, G. Abstreiter, M. Tornow. Structural properties of oligonucleotide monolayers on gold surfaces probed by fluorescence investigations. Langmuir 20 (2004): 10086-10092.
55. S. Svenson, D. A. Tomalia. Dendrimers in biomedical applications-Reflections on the field. Adv. Drug Deliv. Rev. 57 (2005): 2106-2129.
56. M.-L. Örberg, K. Schillen, T. Nylander. Dynamic light scattering and fluorescence study of the interaction between double-stranded DNA and poly(amido amine), dendrimers. Biomacromolecules 8 (2007): 1557-1563.
57. A. Dèdinaité, M. Ernstsson. Chitosan-SDS interactions at a solid-liquid interface: Effects of surfactant concentration and ionic stength. J. Phys. Chem. B 107 (2003): 8181-8188.
58. O. Anthony, C. M. Marques, P. Richetti. Bulk and surface behavior of cationic guars in solutions of oppositely charged surfactants. Langmuir 14 (1998): 6086-6095.
59. A. Dèdinaité, P. M. Claesson, M. Bergström. Polyelectrolyte-surfactant layers: adsorption of preformed aggregates versus adsorption of surfactant to preadsorbed polyelectrolyte. Langmuir 16 (2000): 5257-5266.
60. E. Terada, Y. Samoshina, T. Nylander, B. Lindman. Adsorption of cationic cellulose derivatives/anionic surfactant complexes onto solid surfaces. I. Silica surfaces. Langmuir 20 (2004): 1753-1762.
61. B. Jönsson, B. Lindman, K. Holmberg, B. Kronberg. Surfactants and Polymers in Aqueous Solution. Wiley, West Sussex, 1998.
62. S. Manne. Visualizing self-assembly: Force microscopy of ionic surfactant aggregates at solid-liquid interfaces. Prog. Coll. Polym. Sci. 103 (1997): 226-233.
63. R. Atkin, V. S. J. Craig, E. J. Wanless, S. Biggs. Adsorption of 12-s-12 gemini surfactants at the silica-aqueous solution interface. J. Phys. Chem. B 107 (2003): 2978-2985.
64. A. D. Braem, J. Campos-Teran, B. Lindman. Influence of DNA adsorption and DNA/cationic surfactant coadsorption on the interaction forces between hydrophobic surface. Langmuir 20 (2004): 6407-6413.
65. B. T. Ingram, R. H. Ottewill. Adsorption of cationic surfactants at interfaces. In: D. N. Rugingh, P. M. Holland (Ed.). Cationic Surfactants. Dekker, New York, 1991, pp. 88-140.
66. R. Atkins, V. S. J. Craig, S. Biggs. Adsorption kinetics and structural arrangements of cationic surfactants on silica surfaces. Langmuir 16 (2000): 9374-9380.
67. C. Ström. Adsorption and self-assembly of cationic surfactants at silica surfaces. PhD thesis. Lund University, Lund, Sweden (1999).
68. A. D. Braem, D. C. Prieve, R. D. Tilton. Electrostatically tunable coadsorption of sodium dodecyl sulfate and poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide), triblock copolymer to silica. Langmuir 17 (2001): 883-890.
69. M. Cárdenas, T. Nylander, R. K. Thomas, B. Lindman. DNA compaction at hydrophobic surfaces by different cationic surfactants. Langmuir 21 (2005): 6495-6500.
70. R. Dias, S. Mel'nikov, B. Lindman, M. G. Miguel. DNA phase behaviour in the presence of oppositely charged surfacants. Langmuir 16 (2000): 9577-9583.
71. S. M. Mel'nikov, V. G. Sergeyev, K. Yoshikawa. Transition of D-S DNA chains between random coil and compact globule states induced by cooperative binding of cationic surfactant. J. Am. Chem. Soc. 117 (1995): 9951-9956.
72. C. Leal, L. Wadsö, G. Olofsson, M. Miguel, H. Wennerström. The hydration of a DNA-amphiphile complex. J. Phys. Chem. B 108 (2004): 3044-3050.
73. R. Chatterej, D. K. Chattoraj. Hydrophobic interactions of DNAwith long chain amines. Biopolymers 18 (1979): 147-166.
74. S. Bhattacharya, S. S. Mandal. Evidence of interlipidic ion-pairing in anion-inducedDNA release from cationic amphiphile-DNA complexes. Biochemistry 37 (1998): 7764-7777.
75. R. S. Dias, B. Lindman, M. G. Miguel. Compaction and decompaction of DNA in the presence of catanionic amphiphile mixtures. J. Phys. Chem. B 106 (2002): 12608-12612.
76. M. Cárdenas, J. Campos-Téran, T. Nylander, B. Lindman. DNA and cationic surfactant complexes at hydrophilic surfaces: An ellipsometry and surface force study. Langmuir 20 (2004): 8597-8603.
77. M. Cárdenas, T. Nylander, C. Dreiss, T. Cosgrove, B. Lindman. A SANS study of the interactions between DNA, a cationic surfactant and latex particles. Langmuir 21 (2005): 3578-3583.
78. M. Cárdenas, H. Vacklin, R. Campbell, P. Vandoolaeghe, R. K. Thomas, T. Nylander. On the structure of DNAcompaction with cationic surfactants at the solid liquid interface. Forthcoming.
79. R. Bruinsma. Electrostatics of DNA-cationic lipid complexes: Isoelectric stability. Eur. Phys. J. B 4 (1998): 75-88.
80. W. Michel, T. Mai, T. Naiser, A. Ott. Optical study of DNA surface hybridization reveals DNAsurface density as a key parameter for microarray hybridization kinetics. Biophys. J. 92 (2007): 999-1004.
81. R. Levicky, A. Horgan. Physicochemical perspectives on DNA microarray and biosensor technologies. Trends in Biotechnol. 23 (2005): 143-149.
82. A. Vainrub, B. M. Pettitt. Sensitive quantitative nucleic acid detection using oligonucleotide microarrays. J. Am. Chem. Soc. 125 (2003): 7798-7799.
83. B. J. Hong, V. Sunkara, J. W. Park. DNA microarrays on nanoscale-controlled surface. Nucl. Acids Res. 33 (2005): e106.
84. N. C. Seeman, P. S. Lukeman. Nucleic acid nanostructures: bottom-up control of geometry on the nanoscale. Rep. Prog. Phys. 68 (2005): 237-270.
85. J. Zheng, P. E. Constantinou, C. Micheel, A. P. Alivisatos, R. A. Kiehl, N. C. Seeman. Two-dimensional nanoparticle arrays show the organizational power of robust DNA motifs. Nanoletters 6 (2006): 1502-1504.
86. L. Jaeger, A. Chworos. The architectonics of programmable RNA and DNA nanostructures. Curr. Opin. Struct. Biol. 16 (2006): 531-543.
87. A. A. Yu, T. A. Savas, G. S. Taylor, A. Guiseppe-Elie, H. I. Smith, F. Stellacci. Supramolecular nanostamping: Using DNA as movable type. Nanoletters 5 (2005): 1061-1064.