Sensing with electro-switchable biosurfaces

Bioanalytical Reviews

Volumn 4, Issue 2-4, 2012, Pages 97-114

  Rant, Ulrich ^a,b  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b WALTER SCHOTTKY INSTITUT   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALKANETHIOL DERIVATIVE; DNA; DNA MONOLAYER; DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; OLIGOPEPTIDE; THIOL DERIVATIVE; UNCLASSIFIED DRUG;

ATOMIC FORCE MICROSCOPY; BIOSENSOR; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; DENSITY; DNA CONFORMATION; DNA DENATURATION; DNA DETERMINATION; DNA HYBRIDIZATION; ELECTRIC POTENTIAL; ELECTRICALLY SWITCHABLE BIOSENSOR; ELECTROCHEMICAL ANALYSIS; ELECTRON TRANSPORT; HUMAN; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NANOTECHNOLOGY; NONHUMAN; PARTICLE SIZE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; REVIEW; SIGNAL TRANSDUCTION; SURFACE CHARGE;

EID: 84870824540     PISSN: 18672086     EISSN: 18672094     Source Type: Book Series    
DOI: 10.1007/s12566-012-0030-0     Document Type: Review

References (91)

1. Nandivada H, Ross AM, Lahann J (2010) Stimuli-responsive monolayers for biotechnology. Prog Polym Sci 35(1-2): 141-154. doi: 10. 1016/j. progpolymsci. 2009. 11. 001.
2. Mendes PM (2008) Stimuli-responsive surfaces for bio-applications. Chem Soc Rev 37(11): 2512-2529. doi: 10. 1039/b714635n.
3. Wong IY, Almquist BD, Melosh NA (2010) Dynamic actuation using nano-bio interfaces. Materials Today 13(6): 14-22.
4. Hook AL, Voelcker NH, Thissen H (2009) Patterned and switchable surfaces for biomolecular manipulation. Acta Biomaterialia 5(7): 2350-2370. doi: 10. 1016/j. actbio. 2009. 03. 040.
5. Liu Y, Mu L, Liu BH, Kong JL (2005) Controlled switchable surface. Chem Eur J 11(9): 2622-2631. doi: 10. 1002/chem. 200400931.
6. Lahann J, Mitragotri S, Tran TN, Kaido H, Sundaram J, Choi IS et al (2003) A reversibly switching surface. Science 299(5605): 371-374.
7. Kimura-Suda H, Petrovykh DY, Tarlov MJ, Whitman LJ (2003) Base-dependent competitive adsorption of single-stranded DNA on gold. J Am Chem Soc 125: 9014-9015.
8. Herne TM, Tarlov MJ (1997) Characterization of DNA probes immobilized on gold surfaces. J Am Chem Soc 119: 8916-8920.
9. Petrovykh DY, Kimura-Suda H, Whitman LJ, Tarlov MJ (2003) Quantitative analysis and characterization of DNA immobilized on gold. J Am Chem Soc 125: 5219-5226.
10. Lee C-Y, Gong P, Harbers GM, Grainger DW, Castner DG, Gamble LJ (2006) Surface coverage and structure of mixed DNA/alkylthiol monolayers on gold: characterization by XPS, NEXAFS, and fluorescence intensity measurements. Anal Chem 78: 3316-3325.
11. Lee CY, Nguyen PCT, Grainger DW, Gamble LJ, Castner DG (2007) Structure and DNA hybridization properties of mixed nucleic acid/maleimide-ethylene glycol monolayers. Anal Chem 79(12): 4390-4400. doi: 10. 1021/ac0703395.
12. Petrovykh DY, Kimura-Suda H, Tarlov MJ, Whitman LJ (2004) Quantitative characterization of DNA films by X-ray photoelectron spectroscopy. Langmuir 20: 429-440.
13. Levicky R, Herne TM, Tarlov MJ, Satija SK (1998) Using self-assembly to control the structure of DNA monolayers on gold: a neutron reflectivity study. J Am Chem Soc 120: 9787-9792.
14. Peterlinz KA, Georgiadis RM, Herne TM, Tarlov MJ (1997) Observation of hybridization and dehybridization of thiol-tethered DNA using two-color surface plasmon resonance spectroscopy. J Am Chem Soc 119(14): 3401-3402.
15. Georgiadis R, Peterlinz KP, Peterson AW (2000) Quantitative measurements and modeling of kinetics in nucleic acid monolayer films using SPR spectroscopy. J Am Chem Soc 122: 3166-3173.
16. Peterlinz KA, Georgiadis R (1996) In situ kinetics of self-assembly by surface plasmon resonance spectroscopy. Langmuir 12(20): 4731-4740.
17. Wolf LK, Gao Y, Georgiadis RM (2004) Sequence-dependent DNA immobilization: specific versus nonspecific contributions. Langmuir 20(8): 3357-3361. doi: 10. 1021/la036125.
18. Rant U, Arinaga K, Fujita S, Yokoyama N, Abstreiter G, Tornow M (2004) Structural properties of oligonucleotide monolayers on gold surfaces probed by fluorescence investigations. Langmuir 20(23): 10086-10092.
19. Murphy JN, Cheng AKH, Yu HZ, Bizzotto D (2009) On the nature of DNA self-assembled monolayers on Au: measuring surface heterogeneity with electrochemical in situ fluorescence microscopy. J Am Chem Soc 131(11): 4042-4050. doi: 10. 1021/ja808696p.
20. Arinaga K, Rant U, Tornow M, Fujita S, Abstreiter G, Yokoyama N (2006) The role of surface charging during the coadsorption of mercaptohexanol to DNA layers on gold: direct observation of desorption and layer reorientation. Langmuir 22(13): 5560-5562. doi: 10. 1021/la060324m.
21. Kaiser W, Rant U (2010) Conformations of end-tethered DNA molecules on gold surfaces: influences of applied electric potential, electrolyte screening, and temperature. Journal of the American Chemical Society 132(23): 7935-7945. doi: 10. 1021/ja908727d.
22. Moiseev L, Ünlü MS, Swan AK, Goldberg BB, Cantor CR (2006) DNA conformation on surfaces measured by fluorescence self-interference. Proc Nat Acad Sci 103(8): 2623-2628.
23. Wang K, Zangmeister RA, Levicky R (2009) Equilibrium electrostatics of responsive polyelectrolyte monolayers. J Am Chem Soc 131(1): 318-326. doi: 10. 1021/ja807435q.
24. Steel AB, Herne TM, Tarlov MJ (1998) Electrochemical quantitation of DNA immobilized on gold. Anal Chem 70: 4670-4677.
25. Carrascosa LG, Martinez L, Huttel Y, Roman E, Lechuga LM (2010) Understanding the role of thiol and disulfide self-assembled DNA receptor monolayers for biosensing applications. Eur Biophys J Biophys Lett 39(10): 1433-1444. doi: 10. 1007/s00249- 010-0599-6.
26. Su XD, Wu YJ, Robelek R, Knoll W (2005) Surface plasmon resonance spectroscopy and quartz crystal microbalance study of streptavidin film structure effects on biotinylated DNA assembly and target DNA hybridization. Langmuir 21(1): 348-353. doi: 10. 1021/la047997u.
27. Nelson BP, Grimsrud TE, Liles MR, Goodman RM, Corn RM (2001) Surface plasmon resonance imaging measurements of DNA and RNA hybridization adsorption onto DNA microarrays. Anal Chem 73(1): 1-7.
28. Rant U, Arinaga K, Fujita S, Yokoyama N, Abstreiter G, Tornow M (2004) Dynamic electrical switching of DNA layers on a metal surface. Nano Letters 4(12): 2441-2445.
29. Ricci F, Lai RY, Heeger AJ, Plaxco KW, Sumner JJ (2007) Effect of molecular crowding on the response of an electrochemical DNA sensor. Langmuir 23(12): 6827-6834. doi: 10. 1021/la0700328r.
30. Opdahl A, Petrovykh DY, Kimura-Suda H, Tarlov MJ, Whitman LJ (2007) Independent control of grafting density and conformation of single-stranded DNA brushes. Proc Natl Acad Sci India USA 104(1): 9-14. doi: 10. 1073/pnas. 0608568103.
31. Wang J, Rivas G, Jiang MA, Zhang XJ (1999) Electrochemically induced release of DNA from gold ultramicroelectrodes. Langmuir 15(19): 6541-6545.
32. Arinaga K, Rant U, Knezevic J, Pringsheim E, Tornow M, Fujita S et al (2007) Controlling the surface density of DNA on gold by electrically induced desorption. Biosens Bioelectron 23(3): 326-331. doi: 10. 1016/j. bios. 2007. 04. 012.
33. Takeishi S, Rant U, Fujiwara T, Buchholz K, Usuki T, Arinaga K et al (2004) Observation of electrostatically released DNA from gold electrodes with controlled threshold voltages. J Chem Phys 120(12): 5501-5504.
34. Biagiotti V, Porchetta A, Desiderati S, Plaxco KW, Palleschi G, Ricci F (2012) Probe accessibility effects on the performance of electrochemical biosensors employing DNA monolayers. Analytical and Bioanalytical Chemistry 402(1): 413-421. doi: 10. 1007/s00216-011-5361-0.
35. Gong P, Lee CY, Gamble LJ, Castner DG, Grainger DW (2006) Hybridization behavior ofmixed DNA/alkylthiol monolayers on gold: characterization by surface plasmon resonance and P-32 radiometric assay. Anal Chem 78: 3326-3334. doi: 10. 1021/ac052138b.
36. Wong IY, Melosh NA (2010) An electrostatic model for DNA surface hybridization. Biophys J 98(12): 2954-2963. doi: 10. 1016/j. bpj. 2010. 03. 017.
37. Yu F, Yao DF, Knoll W (2004) Oligonucleotide hybridization studied by a surface plasmon diffraction sensor (SPDS). Nucleic Acids Res 32(9): doi: 10. 1093/nar/gnh067.
38. Gong P, Levicky R (2008) DNA surface hybridization regimes. Proc Natl Acad Sci U S A 105(14): 5301-5306. doi: 10. 1073/pnas. 0709416105.
39. Irving D, Gong P, Levicky R (2010) DNA surface hybridization: comparison of theory and experiment. J Phys Chem B 114(22): 7631-7640. doi: 10. 1021/jp100860z.
40. Kelley SO, Barton JK, Jackson NM, McPherson LD, Potter AB, Spain EM et al (1998) Orienting DNA helices on gold using applied electric fields. Langmuir 14(24): 6781-6784.
41. Zhang Z-L, Pang D-W, Zhang R-Y (2002) Investigation of DNA orientation on gold by EC-STM. Bioconjugate Chem 13: 104-109.
42. Wackerbarth H, Grubb M, Zhang J, Hansen AG, Ulstrup J (2004) Dynamics of ordered-domain formation of DNA fragments on Au(111) with molecluar resolution. Angew Chem Int Ed 43: 198-203.
43. Grubb M, Wackerbarth H, Ulstrup J (2006) Identification of single-strand DNA by in situ scanning tunneling microscopy. J Am Chem Soc 128(24): 7734-7735. doi: 10. 1021/ja061747d.
44. Li YC, Li PCH, Parameswaran M, Yu HZ (2008) Inkjet printed electrode arrays for potential modulation of DNA self-assembled monolayers on gold. Anal Chem 80(22): 8814-8821. doi: 10. 1021/ac801420h.
45. Huang SX, Chen Y (2008) Ultrasensitive fluorescence detection of single protein molecules manipulated electrically on Au nanowire. Nano Lett 8(9): 2829-2833. doi: 10. 1021/nl801429p.
46. Chance RR, Prock A, Silbey R (1978) Molecular fluorescence and energy transfer near interfaces. Adv Chem Phys 37: 1-65.
47. Yang XH, Wang Q, Wang KM, Tan WH, Yao J, Li HM (2006) Electrical switching of DNA monolayers investigated by surface plasmon resonance. Langmuir 22(13): 5654-5659. doi: 10. 1021/la052907m.
48. Mahajan S, Richardson J, Brown T, Bartlett PN (2008) SERS-melting: a new method for discriminating mutations in DNA sequences. J Am Chem Soc 130(46): 15589-15601. doi: 10. 1021/ja805517q.
49. Rant U, Arinaga K, Fujita S, Yokoyama N, Abstreiter G, Tornow M (2006) Electrical manipulation of oligonucleotides grafted to charged surfaces. Org Biomol Chem 4(18): 3448-3455. doi: 10. 1039/b605712h.
50. Erdmann M, David R, Fornof A, Gaub HE (2010) Electrically controlled DNA adhesion. Nat Nanotechnol 5(2): 154-159. doi: 10. 1038/nnano. 2009. 377.
51. Zhou F, Biesheuvel PM, Chol EY, Shu W, Poetes R, Steiner U et al (2008) Polyelectrolyte brush amplified electroactuation of microcantilevers. Nano Letters 8(2): 725-730. doi: 10. 1021/nl073157z.
52. Meng FB, Liu YX, Liu L, Li GX (2009) Conformational transitions of immobilized DNA chains driven by pH with electrochemical output. J Phys Chem B 113(4): 894-896. doi: 10. 1021/jp806268z.
53. Germishuizen WA, Walti C, Wirtz R, Johnston MB, Pepper M, Davies AG et al (2003) Selective dielectrophoretic manipulation of surface-immobilized DNA molecules. Nanotechnology 14(8): 896-902.
54. Germishuizen WA, Tosch P, Middelberg APJ, Walti C, Davies AG, Wirtz R et al (2005) Influence of alternating current electrokinetic forces and torque on the elongation of immobilized DNA. J Appl Phys 97(1): doi: 10. 1063/1. 1825627.
55. Wang J (2001) On-demand electrochemical release of nucleic acids. Electroanalysis 13(8-9): 635-638.
56. 2)(6)-poly(dT)(18)-fluorescein at gold electrodes under cyclic voltammetric conditions. J Electroanal Chem 621(1): 75-82. doi: 10. 1016/j. jelechem. 2008. 04. 028.
57. Netz RR, Andelman D (2003) Neutral and charged polymers at interfaces. Phys Rep 380: 1-95, and references therein.
58. Dobrynin AV, Rubinstein M (2005) Theory of polyelectrolytes in solutions and at surfaces. Prog Polym Sci 30: 1049-1118. doi: 10. 1016/j. progpolymsci. 2005. 07. 006.
59. Rant U, Arinaga K, Tornow M, Kim YW, Netz RR, Fujita S et al (2006) Dissimilar kinetic behavior of electrically manipulated single- and double-stranded DNA tethered to a gold surface. Biophys J 90(10): 3666-3671. doi: 10. 1529/biophysj. 105. 078857.
60. Wong KY, Pettitt BM (2004) Orientation of DNA on a surface from simulation. Biopolymers 73(5): 570-578. doi: 10. 1002/bip. 20004.
61. Crozier PS, Stevens MJ (2003) Simulations of single grafted polyelectrolyte chains: ssDNA and dsDNA. J Chem Phys 118(8): 3855-3860. doi: 10. 1063/1. 1540098.
62. Sendner C, Kim YW, Rant U, Arinaga K, Tornow M, Netz RR (2006) Dynamics of end grafted DNA molecules and possible biosensor applications. Physica Status Solidi a-Applications and Materials Science 203(14): 3476-3491. doi: 10. 1002/pssa. 200622444.
63. Vainrub A, Pettitt BM (2000) Thermodynamics of association to a molecule immobilized in an electric double layer. Chem Phys Lett 323(1-2): 160-166.
64. Vainrub A, Pettitt BM (2003) Surface electrostatic effects in oligonucleotide microarrays: control and optimization of binding thermodynamics. Biopolymers 68(2): 265-270. doi: 10. 1002/bip. 10271.
65. Pei Y, Ma J (2005) Electric field induced switching behaviors of monolayer-modified silicon surfaces: surface designs and molecular dynamics simulations. J Am Chem Soc 127(18): 6802-6813. doi: 10. 1021/ja045506m.
66. Rant U, Arinaga K, Scherer S, Pringsheim E, Fujita S, Yokoyama N et al (2007) Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets. Proc Natl Acad Sci U S A 104(44): 17364-17369. doi: 10. 1073/pnas. 0703974104.
67. Rant U, Pringsheim E, Kaiser W, Arinaga K, Knezevic J, Tornow M et al (2009) Detection and size analysis of proteins with switchable DNA layers. Nano Lett 9(4): 1290-1295. doi: 10. 1021/nl8026789.
68. Wang Y, Zocchi G (2010) Elasticity of globular proteins measured from the ac susceptibility. Phys Rev Lett 105(23): doi: 10. 1103/PhysRevLett. 105. 238104.
69. Genereux JC, Barton JK (2010) Mechanisms for DNA charge transport. Chem Rev 110(3): 1642-1662. doi: 10. 1021/cr900228f.
70. Kelley SO, Boon EM, Barton JK, Jackson NM, Hill MG (1999) Single-base mismatch detection based on charge transduction through DNA. Nucleic Acids Res 27(24): 4830-4837. doi: 10. 1093/nar/27. 24. 4830.
71. Gorodetsky AA, Buzzeo MC, Barton JK (2008) DNA-mediated electrochemistry. Bioconjugate Chem 19(12): 2285-2296. doi: 10. 1021/bc8003149.
72. Wierzbinski E, Arndt J, Hammond W, Slowinski K (2006) In situ electrochemical distance tunneling spectroscopy of ds-DNA molecules. Langmuir 22(6): 2426-2429. doi: 10. 1021/la053224+.
73. Anne A, Bouchardon A, Moiroux J (2003) 3′-ferrocene-labeled oligonucleotide chains end- tethered to gold electrode surfaces: novel model systems for exploring flexibility of short DNA using cyclic voltammetry. J Am Chem Soc 125(5): 1112-1113.
74. Fan C, Plaxco KW, Heeger AJ (2003) Electrochemical interrogation of conformational changes as a reagentless method for the sequence-specific detection of DNA. Proc Nat Acad Sci 100(16): 9134-9137.
75. Farjami E, Clima L, Gothelf K, Ferapontova EE (2011) "Off On" electrochemical hairpin-DNA-based genosensor for cancer diagnostics. Anal Chem 83(5): 1594-1602. doi: 10. 1021/ac1032929.
76. Lubin AA, Plaxco KW (2010) Folding-based electrochemical biosensors: the case for responsive nucleic acid architectures. Accounts Chem Res 43(4): 496-505. doi: 10. 1021/ar900165x.
77. Anne A, Demaille C (2006) Dynamics of electron transport by elastic bending of short DNA duplexes. Experimental study and quantitative modeling of the cyclic voltammetric behavior of 3′-ferrocenyl DNA end-grafted on gold. J Am Chem Soc 128(2): 542-557. doi: 10. 1021/ja055112a.
78. Huesken N, Gebala M, La Mantia F, Schuhmann W, Metzler-Nolte N (2011) Mechanistic studies of Fc-PNA(. DNA) surface dynamics based on the kinetics of electron-transfer processes. Chem Eur J 17(35): 9678-9690. doi: 10. 1002/chem. 201003764.
79. Wang K, Goyer C, Anne A, Demaille C (2007) Exploring the motional dynamics of end-grafted DNA oligonucleotides by in situ electrochemical atomic force microscopy. J Phys Chem B 111(21): 6051-6058. doi: 10. 1021/jp070432x.
80. Anne A, Demaille C (2008) Electron transport by molecular motion of redox-DNA strands: unexpectedly slow rotational dynamics of 20-mer ds-DNA chains end-grafted onto surfaces via C-6 linkers. J Am Chem Soc 130(30): 9812-9823. doi: 10. 1021/ja801074m.
81. Uzawa T, Cheng RR, White RJ, Makarov DE, Plaxco KW (2010) A mechanistic study of electron transfer from the distal termini of electrode-bound, single-stranded DNAs. J Am Chem Soc 132(45): 16120-16126. doi: 10. 1021/ja106345d.
82. Edman CF, Raymond DE, Wu DJ, Tu E, Sosnowski RG, Butler WF et al (1997) Electric field directed nucleic acid hybridization on microchips. Nucl Acids Res 25(24): 4907-4914.
83. Heaton RJ, Peterson AW, Georgiadis RM (2001) Electrostatic surface plasmon resonance: direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches. Proc Natl Acad Sci U S A 98(7): 3701-3704.
84. Wong IY, Melosh NA (2009) Directed hybridization and melting of DNA linkers using counterion-screened electric fields. Nano Lett 9(10): 3521-3526. doi: 10. 1021/nl901710n.
85. Sosnowski RG, Tu E, Butler WF, O'Connell JP, Heller MJ (1997) Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc Nat Acad Sci 94: 1119-1123.
86. Gurtner C, Tu E, Jamshidi N, Haigis RW, Onofrey TJ, Edman CF et al (2002) Microelectronic array devices and techniques for electric field enhanced DNA hybridization in low-conductance buffers. Electrophoresis 23(10): 1543-1550. doi: 10. 1002/1522-2683(200205)23: 10< 1543:: aid-elps1543> 3. 0. co; 2-#.
87. Rant U, Arinaga K, Fujita S, Yokoyama N, Abstreiter G, Tornow M (2004) Dynamic electrical switching of DNA layers on a metal surface. Nano Letters 4(12): 2441-2445. doi: 10. 1021/nl0484494.
88. Spuhler PS, Knezevic J, Yalcin A, Bao QY, Pringsheim E, Droge P et al (2010) Platform for in situ real-time measurement of protein-induced conformational changes of DNA. Proc Natl Acad Sci U S A 107(4): 1397-1401. doi: 10. 1073/pnas. 0912182107.
89. Yeung CL, Iqbal P, Allan M, Lashkor M, Preece JA, Mendes PM (2010) Tuning specific biomolecular interactions using electro-switchable oligopeptide surfaces. Adv Funct Mater 20(16): 2657-2663. doi: 10. 1002/adfm. 201000411.
90. Liu Y, Mu L, Liu BH, Zhang S, Yang PY, Kong JL (2004) Controlled protein assembly on a switchable surface. Chem Commun 10: 1194-1195. doi: 10. 1039/b400776j.
91. Wackerbarth H, Grubb M, Zhang J, Hansen AG, Ulstrup J (2004) Long-range order of organized oligonucleotide monolayers on Au(111) electrodes. Langmuir 20: 1647-1655.