title: Kinetics of signaling-DNA-aptamer-ATP binding.
abstract: DNA aptamers are molecular biosensors consisting of single functionalized DNA molecules, which can bind to specific targets or complementary DNA sequences. The binding kinetics of DNA aptamers is studied by fluorescence quenching at 23 degrees C . A kinetic model for the binding reaction of DNA aptamer, antisense DNA, and ATP target is developed to describe experimental observations. The approach leads to a simple procedure to deduce relevant kinetic reactions and their rate constants. A comparison between theory and experiments indicates that the previously established bimolecular DNA-ATP binding does not provide a complete description of the experimental data. Side reactions such as trimolecular complexation are proposed. Rate constants of the model are determined by comparing the model predictions and experiments. Good agreements between the model and experiments have been obtained. Possible blocking reactions by the misfolded DNA aptamer are also discussed.
authors.affiliation: Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8. nakamur@physics.mcmaster.ca
authors.forename: Issei
authors.initials: I
authors.lastname: Nakamura
authors.forename: An-Chang
authors.initials: AC
authors.lastname: Shi
authors.forename: Razvan
authors.initials: R
authors.lastname: Nutiu
authors.forename: Jasmine M Y
authors.initials: JM
authors.lastname: Yu
authors.forename: Yingfu
authors.initials: Y
authors.lastname: Li
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism*; D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D005453:Fluorescence; D007700:Kinetics; D008958:Models, Molecular
chemical_list: D052157:Aptamers, Nucleotide; D000255:Adenosine Triphosphate