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Cooperative nonenzymic base recognition. Kinetics of the binding of a base monomer to a complementary polynucleotide template
Author(s) -
Hoffman Geoffrey W.,
Pörschke Dietmar
Publication year - 1973
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1973.360120714
Subject(s) - chemistry , monomer , trimer , temperature jump , kinetics , reaction rate constant , polynucleotide , helix (gastropod) , receptor–ligand kinetics , crystallography , polymer , thermodynamics , dimer , organic chemistry , physics , biochemistry , receptor , quantum mechanics , ecology , snail , biology
The kinetics of double‐helix formation by poly U and the complementary monomer N ‐6,9‐dimethyladenine (m 6 m 9 A) has been measured using a new fast temperature‐jump apparatus. The cooperative binding kinetics are complicated by the extensive self‐association of the monomers, but a satisfactory analysis using average relaxation times was possible in terms of three different models. Application of a model which considers only monomer binding yields the upper limit for the binding rate constant of an m 6 m 9 A monomer next to an already bound monomer on a poly U strand: (2 ± 0.4) × 10 8 M −1 sec −1 . A lower limit is found by using a model which allows for binding of all m 6 m 9 A stacks to poly U with equal rate constants: (3 ± 0.3) × 10 7 M −1 sec −1 . A third model with “weighted” rate constants consistent with the data: (7.5 ± 1.0) × 10 7 M −1 sec −1 . The rate of cooperative binding of m 6 m 9 A to the trimer UpUpU has also been measured. The rate constants obtained with the trimer agree with those obtained with the polymer for each of the three models within experimental error.