Kinetics and thermodynamics of DNA hybridization on gold nanoparticles

Nucleic Acids Research

Volumn 37, Issue 11, 2009, Pages 3756-3765

  Chen, Chunlai ^a   Wang, Wenjuan ^a   Ge, Jing ^a   Zhao, Xin Sheng ^a  

^a PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; GOLD NANOPARTICLE; SINGLE STRANDED DNA;

ARTICLE; CHEMICAL REACTION KINETICS; CONTROLLED STUDY; DISSOCIATION CONSTANT; DNA DENATURATION; DNA HYBRIDIZATION; DNA STRUCTURE; ENTHALPY; ENTROPY; FLUORESCENCE ANALYSIS; MELTING POINT; MOLECULAR INTERACTION; NUCLEIC ACID IMMOBILIZATION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SURFACE PROPERTY; THERMODYNAMICS;

DNA; DNA, SINGLE-STRANDED; GOLD; KINETICS; METAL NANOPARTICLES; NUCLEIC ACID DENATURATION; NUCLEIC ACID HYBRIDIZATION; THERMODYNAMICS;

EID: 67649872011     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp230     Document Type: Article

References (48)

1. Craig,M.E., Crothers,D.M. and Doty,P. (1971) Relaxation kinetics of dimer formation by self complementary oligonucleotides. J. Mol. Biol. 62, 383-401.
2. Eigen,M. and Porschke,D. (1970) Co-operative non-enzymic base recognition. 1. Thermodynamics of helix-coil transition of oligoriboadenylic acids at acidic pH. J. Mol. Biol., 53, 123-141.
3. Porschke,D. and Eigen,M. (1971) Co-operative non-enzymic base recognition. 3. Kinetics of helix-coil transition of oligoribouridylic oligoriboadenylic acid system and of oligoriboadenylic acid aloe at acidic pH. J. Mol. Biol., 62, 361-381.
4. Pörschke,D., Uhlenbeck,O.C. and Martin,F.H. (1973) Thermodynamics and kinetics of helix-coil transition of oligomers containing gc base pairs. Biopolymers, 12, 1313-1335.
5. Chen,C.L., Wang,W.J., Wang,Z., Wei,F. and Zhao,X.S. (2007) Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization. Nucleic Acids Res., 35, 2875-2884.
6. Morrison,L.E. and Stols,L.M. (1993) Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution. Biochemistry, 32, 3095-3104.
7. Wetmur,J.G. and Davidson,N. (1968) Kinetics of renaturation of DNA. J. Mol. Biol., 31, 349-370.
8. Blake,R.D., Klotz,L.C. and Fresco,J.R. (1968) Polynucleotides.9. Temperature dependence of kinetics of complex formation in equimolar mixtures of polyriboadenylate and polyribouridylate. J. Am. Chem. Soc., 90, 3556-3562.
9. Chan,V., Graves,D.J. and McKenzie,S.E. (1995) The biophysics of DNA hybridization with immobilized oligonucleotide probes. Biophys. J. 69, 2243-2255.
10. Axelrod,D. and Wang,M.D. (1994) Reduction-of-dimensionality kinetics at reaction-limited cell-surface receptors. Biophys. J., 66, 588-600.
11. Peterson,A.W., Heaton,R.J. and Georgiadis,R.M. (2001) The effect of surface probe density on DNA hybridization. Nucleic Acids Res., 29, 5163-5168.
12. Shchepinov,M.S., CaseGreen,S.C. and Southern,E.M. (1997) Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res., 25, 1155-1161.
13. Watterson,J.H., Piunno,P.A.E., Wust,C.C. and Krull,U.J. (2000) Effects of oligonucleotide immobilization density on selectivity of quantitative transduction of hybridization of immobilized DNA. Langmuir, 16 4984-4992.
14. Halperin,A., Buhot,A. and Zhulina,E.B. (2005) Brush effects on DNA chips: Thermodynamics, kinetics, and design guidelines. Biophys. J. 89, 796-811.
15. Vainrub,A. and Pettitt,B.M. (2003) Sensitive quantitative nucleic acid detection using oligonucleotide microarrays. J. Am. Chem. Soc., 125, 7798-7799.
16. Vainrub,A. and Pettitt,B.M. (2003) Surface electrostatic effects in oligonucleotide microarrays: Control and optimization of binding thermodynamics. Biopolymers, 68, 265-270.
17. Tawa,K. and Knoll,W. (2004) Mismatching base-pair dependence of the kinetics of DNA-DNA hybridization studied by surface plasmon fluorescence spectroscopy. Nucleic Acids Res., 32, 2372-2377.
18. Stillman,B.A. and Tonkinson,J.L. (2001) Expression microarray hybridization kinetics depend on length of the immobilized DNA but are independent of immobilization substrate. Anal. Biochem., 295 149-157.
19. Glazer,M.I., Fidanza,J.A., McGall,G.H., Trulson,M.O., Forman,J.E. and Frank,C.W. (2007) Kinetics of oligonucleotide hybridization to DNA probe Arrays on high-capacity porous silica substrates. Biophys. J., 93, 1661-1676.
20. Sips,R. (1948) On the structure of a catalyst surface. J. Chem. Phys. 16, 490-495.
21. Peterson,A.W., Wolf,L.K. and Georgiadis,R.M. (2002) Hybridization of mismatched or partially matched DNA at surfaces. J. Am. Chem. Soc. 124, 14601-14607.
22. Vijayendran,R.A. and Leckband,D.E. (2001) A quantitative assessment of heterogeneity for surface-immobilized proteins. Anal. Chem., 73 471-480.
23. Svitel,J., Balbo,A., Mariuzza,R.A., Gonzales,N.R. and Schuck,P. (2003) Combined affinity and rate constant distributions of ligand populations from experimental surface binding kinetics and equilibria. Biophys. J., 84, 4062-4077.
24. Akamatsu,K., Kimura,M., Shibata,Y., Nakano,S., Miyoshi,D., Nawafune,H. and Sugimoto,N. (2006) A DNA duplex with extremely enhanced thermal stability based on controlled immobilization on gold nanoparticles. Nano Lett., 6, 491-495.
25. Jin,R.C., Wu,G.S., Li,Z., Mirkin,C.A. and Schatz,G.C. (2003) What controls the melting properties of DNA-linked gold nanoparticle assemblies? J. Am. Chem. Soc., 125, 1643-1654.
26. Harris,N.C. and Kiang,C.H. (2006) Defects can increase the melting temperature of DNA - nanoparticle assemblies. J. Phy. Chem. B, 110, 16393-16396.
27. Hurst,S.J., Hill,H.D. and Mirkin,C.A. (2008) "Three-dimensional hybridization" with polyvalent DNA-gold nanoparticle conjugates. J. Am. Chem. Soc., 130, 12192-12200.
28. Xu,J. and Craig,S.L. (2005) Thermodynamics of DNA hybridization on gold nanoparticles. J. Am. Chem. Soc., 127, 13227-13231.
29. Lytton-Jean,A.K.R. and Mirkin,C.A. (2005) A thermodynamic investigation into the binding properties of DNA functionalized gold nanoparticle probes and molecular fluorophore probes. J. Am. Chem. Soc., 127 12754-12755.
30. Wei,F., Chen,C.L., Zhai,L., Zhang,N. and Zhao,X.S. (2005) Recognition of single nucleotide polyrnorphisms using scanning potential hairpin denaturation. J. Am. Chem. Soc., 127, 5306-5307.
31. Wei,F., Qu,P., Zhai,L., Chen,C.L., Wang,H.F. and Zhao,X.S. (2006) Electric potential induced dissociation of hybridized DNA with hairpin motif immobilized on silicon surface. Langmuir, 22, 6280-6285.
32. Demers,L.M., Mirkin,C.A., Mucic,R.C., Reynolds,R.A., Letsinger,R.L., Elghanian,R. and Viswanadham,G. (2000) A fluorescence-based method for determining the surface coverage and hybridization efficiency of thiol-capped oligonucleotides bound to gold thin films and nanoparticles. Anal. Chem., 72, 5535-5541.
33. Wong,E.L.S., Chow,E. and Gooding,J.J. (2005) DNA recognition interfaces: the influence of interfacial design on the efficiency and kinetics of hybridization. Langmuir, 21, 6957-6965.
34. Park,S., Brown,K.A. and Hamad-Schifferli,K. (2004) Changes in oligonucleotide conformation on nanoparticle surfaces by modification with mercaptohexanol. Nano Lett., 4, 1925-1929.
35. Herne,T.M. and Tarlov,M.J. (1997) Characterization of DNA probes immobilized on gold surfaces. J. Am. Chem. Soc., 119, 8916-8920.
36. Levicky,R., Herne,T.M., Tarlov,M.J. and Satija,S.K. (1998) Using self-assembly to control the structure of DNA monolayers on gold: A neutron reflectivity study. J. Am. Chem. Soc., 120, 9787-9792.
37. Maxwell,D.J., Taylor,J.R. and Nie,S.M. (2002) Self-assembled nanoparticle probes for recognition and detection of biomolecules. J. Am. Chem. Soc., 124, 9606-9612.
38. Marky,L.A. and Breslauer,K.J. (1987) Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers, 26, 1601-1620.
39. Xu,J. and Craig,S.L. (2007) Influence of the extent of hybridization on the hydrodynamic radius of DNA-functionalized gold nanoparticles. Langmuir, 23, 2015-2020.
40. Eyring,H. (1935) The activated complex in chemical reactions. J. Chem. Phys., 3, 107.
41. Glasstone,S., Laidler,K.J. and Eyring,H. (1941) The Theory of Rate Processes: The Kinetics of Chemical Reactions, Viscosity, Diffusion and Electrochemical Phenomena. McGraw-Hill, New York.
42. Foltastogniew,E. and Russu,I.M. (1994) Sequence dependence of base-pair opening in a DNA dodecamer containing the Caca/Gtgt sequence motif. Biochemistry, 33, 11016-11024.
43. Dewey,T.G. and Turner,D.H. (1980) Laser temperature jump study of solvent effects on poly(adenylic acid) stacking. Biochemistry, 19, 1681-1685.
44. Stevens,P.W., Henry,M.R. and Kelso,D.M. (1999) DNA hybridization on microparticles: Determining capture-probe density and equilibrium dissociation constants. Nucleic Acids Res., 27, 1719-1727.
45. Storhoff,J.J., Elghanian,R., Mirkin,C.A. and Letsinger,R.L. (2002) Sequence-dependent stability of DNA-modified gold nanoparticles. Langmuir, 18, 6666-6670.
46. Fiche,J.B., Buhot,A., Calemczuk,R. and Livache,T. (2007) Temperature effects on DNA chip experiments from surface plasmon resonance imaging: Isotherms and melting curves. Biophys. J., 92, 935-946.
47. Gao,Y., Wolf,L.K. and Georgiadis,R.M. (2006) Secondary structure effects on DNA hybridization kinetics: A solution versus surface comparison. Nucleic Acids Res., 34, 3370-3377.
48. Henry,M.R., Stevens,P.W., Sun,J. and Kelso,D.M. (1999) Realtime measurements of DNA hybridization on microparticles with fluorescence resonance energy transfer. Anal. Biochem., 276, 204-214.