Optimal hybridization efficiency upon immobilization of oligonucleotide double helices

Journal of Physical Chemistry B

Volumn 113, Issue 24, 2009, Pages 8383-8390

  Razumovitch, Julia ^a   De França, Kelnner ^b   Kehl, Florian ^a   Wiki, Max ^c   Meier, Wolfgang ^a   Vebert, Corinne ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

^b CSEM   (Switzerland)

^c DYNETIX AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ADSORPTION; OLIGONUCLEOTIDES; OXIDE MINERALS; QUARTZ;

COIL CONFORMATIONS; COVALENT IMMOBILIZATION; DOUBLE HELIX; HYBRIDIZATION EFFICIENCY; IN-SITU; INDIRECT METHODS; NUCLEOTIDE SEQUENCES; POLYMER THEORY; QUARTZ CRYSTAL MICROBALANCE WITH DISSIPATION MONITORING; RE-HYBRIDIZATION;

QUARTZ CRYSTAL MICROBALANCES;

EID: 67149133372     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp902383m     Document Type: Article

References (23)

1. Watson, J. D.; Crick, F. H. C. Molecular Structure of Nucleic Acids - a Structure for Deoxyribose Nucleic Acid. Nature 1953, 171(4356), 737-738.
2. Sassolas, A.; Leca-Bouvier, B. D.; Blum, L. J. DNA biosensors and microarrays. Chem. Rev. 2008, 108(1), 109-139.
3. Niemeyer, C. M.; Boldt, L.; Ceyhan, B.; Blohm, D. DNA-Directed Immobilization: Efficient, Reversible, and Site-Selective Surface Binding of Proteins by Means of Covalent DNA-Streptavidin Conjugates. Anal. Biochem. 1999, 268(1), 54-63.
4. Wacker, R.; Schröder, H.; Niemeyer, C. M. Performance of antibody microarrays fabricated by either DNA-directed immobilization, direct spotting, or streptavidin-biotin attachment: a comparative study. Anal. Biochem. 2004, 330(2), 281-287.
5. Lucarelli, F.; Tombelli, S.; Minunni, M.; Marrazza, G.; Mascini, M. Electrochemical and piezoelectric DNA biosensors for hybridisation detection. Anal. Chim. Acta 2008, 609(2), 139-159.
6. Gong, P.; Levicky, R. DNA surface hybridization regimes. Proc. Natl. Acad. Sci. U.S.A. 2008, 105(14), 5301-5306.
7. Chan, V.; Graves, D. J.; McKenzie, S. E. The biophysics of DNA hybridization with immobilized oligonucleotide probes. Biophys. J. 1995, 69(6), 2243-55.
8. Opdahl, A.; Petrovykh, D. Y.; Kimura-Suda, H.; Tarlov, M. J.; Whitman, L. J. Independent control of grafting density and conformation of single-stranded DNA brushes. Proc. Natl. Acad. Sci. U.S.A. 2007, 104(1), 9-14.
9. Halperin, A.; Buhot, A.; Zhulina, E. B. On the hybridization isotherms of DNA microarrays: the Langmuir model and its extensions. J. Phys.: Condens. Matter 2006, 18(18), S463-S490.
10. Halperin, A.; Buhot, A.; Zhulina, E. B. Hybridization isotherms of DNA microarrays and the quantification of mutation studies. Clin. Chem. 2004, 50(12), 2254-2262.
11. Smith, S. B.; Finzi, L.; Bustamante, C. Direct Mechanical Measurements of the Elasticity of Single DNA-Molecules by Using Magnetic Beads. Science 1992, 258(5085), 1122-1126.
12. Perkins, T. T.; Quake, S. R.; Smith, D. E.; Chu, S. Relaxation of a Single DNA Molecule Observed by Optical Microscopy. Science 1994, 264(5160), 822-826.
13. Kratky, O.; Porod, G. Rontgenuntersuchung Geloster Fadenmole-kule. Rec. Trav. Chim. Pavs-Bas 1949, 68(12), 1106-1122.
14. Schallhorn, K. A.; Freedman, K. O.; Moore, J. M.; Lin, J.; Ke, P. C. Single-molecule DNA flexibility in the presence of base-pair mismatch. Appl. Phys. Lett. 2005, 87(3),-.
15. Bustamante, C.; Smith, S. B.; Liphardt, J.; Smith, D. Single-molecule studies of DNA mechanics. Curr. Opin. Struct. Biol. 2000, 10(3), 279-285.
16. Larsson, C.; Rodahl, M.; Hook, F. Characterization of DNA immobilization and subsequent hybridization on a 2D arrangement of streptavidin on a biotin-modified lipid bilayer supported on SiO2. Anal. Chem. 2003, 75(19), 5080-5087.
17. Wang, G.; Rodahl, M.; Edvardsson, M.; Svedhem, S.; Ohlsson, G.; Hook, F.; Kasemo, B. A combined reflectometry and quartz crystal microbalance with dissipation setup for surface interaction studies. Rev. Sci. Instrum. 2008, 79(7), 7.
18. Voinova, M. V.; Rodahl, M.; Jonson, M.; Kasemo, B. Viscoelastic acoustic response of layered polymer films at fluid-solid interfaces: Continuum mechanics approach. Phys. Scr. 1999, 59(5), 391-396.
19. Cottier, K.; Wiki, M.; Voirin, G.; Gao, H.; Kunz, R. E. Label-free highly sensitive detection of (small) molecules by wavelength interrogation of integrated optical chips. Sens. Actuators. B 2003, 91(1-3), 241-251.
20. Kunz, R. E.; Cottier, K. Optimizing integrated optical chips for label-free (bio-)chemical sensing. Anal. Bioanal. Chem. 2006, 384(1), 180-190.
21. Razumovitch, J.; Meier, W.; Vebert, C. A microcontact printing approach to the immobilization of oligonucleotide brushes. Biophys. Chem. 2009, 139(1), 70-74.
22. Halperin, A.; Buhot, A.; Zhulina, E. B. Brash effects on DNA chips: thermodynamics, kinetics, and design guidelines. Biophys. J. 2005, 89(2), 796-811.
23. Mills, J. B.; Vacano, E.; Hagerman, P. J. Flexibility of single-stranded DNA: Use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA). J. Mol. Biol. 1999, 285 (1), 245-257.