Surface enzyme kinetics for biopolymer microarrays: a combination of Langmuir and Michaelis-Menten concepts

H.J. Lee, A.W. Wark, T.T. Goodrich, S. Fang, R.M. Corn

Research output: Contribution to journalArticle

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Abstract

Real-time surface plasmon resonance (SPR) imaging measurements of surface enzymatic reactions on DNA microarrays are analyzed using a kinetics model that couples the contributions of both enzyme adsorption and surface enzyme reaction kinetics. For the case of a 1:1 binding of an enzyme molecule (E) to a surface-immobilized substrate (S), the overall enzymatic reaction can be described in terms of classical Langmuir adsorption and Michaelis−Menten concepts and three rate constants:  enzyme adsorption (ka), enzyme desorption (kd) and enzyme catalysis (kcat). In contrast to solution enzyme kinetics, the amount of enzyme in solution is in excess as compared to the amount of substrate on the surface. Moreover, the surface concentration of the intermediary enzyme−substrate complex (ES) is not constant with time, but goes to zero as the reaction is completed. However, kinetic simulations show that the fractional surface coverage of ES on the remaining unreacted sites does reach a steady-state value throughout the course of the surface reaction. This steady-state value approaches the Langmuir equilibrium value for cases where ka[E] kcat. Experiments using the 3‘ → 5‘ exodeoxyribonuclease activity of Exonuclease III on double-stranded DNA microarrays as a function of temperature and enzyme concentration are used to demonstrate how this model can be applied to quantitatively analyze the SPR imaging data.
LanguageEnglish
Pages4050-4057
Number of pages8
JournalLangmuir
Volume21
Issue number9
Early online date22 Mar 2005
DOIs
Publication statusPublished - 2005

Fingerprint

Enzyme kinetics
Biopolymers
biopolymers
Microarrays
enzymes
Enzymes
kinetics
Adsorption
Surface plasmon resonance
Surface Plasmon Resonance
Substrates
Oligonucleotide Array Sequence Analysis
Catalysis
surface plasmon resonance
surface reactions
adsorption
catalysis
DNA
Exodeoxyribonucleases
deoxyribonucleic acid

Keywords

  • surface enzyme kinetics
  • biopolymer microarrays
  • Langmuir and Michaelis-Menten concepts

Cite this

Lee, H.J. ; Wark, A.W. ; Goodrich, T.T. ; Fang, S. ; Corn, R.M. / Surface enzyme kinetics for biopolymer microarrays : a combination of Langmuir and Michaelis-Menten concepts. In: Langmuir. 2005 ; Vol. 21, No. 9. pp. 4050-4057.
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abstract = "Real-time surface plasmon resonance (SPR) imaging measurements of surface enzymatic reactions on DNA microarrays are analyzed using a kinetics model that couples the contributions of both enzyme adsorption and surface enzyme reaction kinetics. For the case of a 1:1 binding of an enzyme molecule (E) to a surface-immobilized substrate (S), the overall enzymatic reaction can be described in terms of classical Langmuir adsorption and Michaelis−Menten concepts and three rate constants:  enzyme adsorption (ka), enzyme desorption (kd) and enzyme catalysis (kcat). In contrast to solution enzyme kinetics, the amount of enzyme in solution is in excess as compared to the amount of substrate on the surface. Moreover, the surface concentration of the intermediary enzyme−substrate complex (ES) is not constant with time, but goes to zero as the reaction is completed. However, kinetic simulations show that the fractional surface coverage of ES on the remaining unreacted sites does reach a steady-state value throughout the course of the surface reaction. This steady-state value approaches the Langmuir equilibrium value for cases where ka[E] kcat. Experiments using the 3‘ → 5‘ exodeoxyribonuclease activity of Exonuclease III on double-stranded DNA microarrays as a function of temperature and enzyme concentration are used to demonstrate how this model can be applied to quantitatively analyze the SPR imaging data.",
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Surface enzyme kinetics for biopolymer microarrays : a combination of Langmuir and Michaelis-Menten concepts. / Lee, H.J.; Wark, A.W.; Goodrich, T.T.; Fang, S.; Corn, R.M.

In: Langmuir, Vol. 21, No. 9, 2005, p. 4050-4057.

Research output: Contribution to journalArticle

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AB - Real-time surface plasmon resonance (SPR) imaging measurements of surface enzymatic reactions on DNA microarrays are analyzed using a kinetics model that couples the contributions of both enzyme adsorption and surface enzyme reaction kinetics. For the case of a 1:1 binding of an enzyme molecule (E) to a surface-immobilized substrate (S), the overall enzymatic reaction can be described in terms of classical Langmuir adsorption and Michaelis−Menten concepts and three rate constants:  enzyme adsorption (ka), enzyme desorption (kd) and enzyme catalysis (kcat). In contrast to solution enzyme kinetics, the amount of enzyme in solution is in excess as compared to the amount of substrate on the surface. Moreover, the surface concentration of the intermediary enzyme−substrate complex (ES) is not constant with time, but goes to zero as the reaction is completed. However, kinetic simulations show that the fractional surface coverage of ES on the remaining unreacted sites does reach a steady-state value throughout the course of the surface reaction. This steady-state value approaches the Langmuir equilibrium value for cases where ka[E] kcat. Experiments using the 3‘ → 5‘ exodeoxyribonuclease activity of Exonuclease III on double-stranded DNA microarrays as a function of temperature and enzyme concentration are used to demonstrate how this model can be applied to quantitatively analyze the SPR imaging data.

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