Nearest-neighbour transition-state analysis for nucleic acid kinetics
| Autor: | Carl T. Wittwer, Aisha M. Zuiter, Nick A Rejali, Caroline C Keller, Felix D Ye |
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| Rok vydání: | 2021 |
| Předmět: |
AcademicSubjects/SCI00010
Annealing (metallurgy) Kinetics Magnesium Chloride Oligonucleotides Ionic bonding Thermodynamics Sodium Chloride Biology Nucleic Acid Denaturation 010402 general chemistry Kinetic energy Polymerase Chain Reaction 01 natural sciences Dissociation (chemistry) 03 medical and health sciences Reaction rate constant Nucleic Acids Genetics Cluster Analysis Computer Simulation Denaturation (biochemistry) Molecular Biology 030304 developmental biology 0303 health sciences Temperature DNA 0104 chemical sciences Models Chemical Nucleic acid Nucleic Acid Conformation |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | We used stopped-flow to monitor hypochromicity for 43 oligonucleotide duplexes to study nucleic acid kinetics and extract transition-state parameters for association and dissociation. Reactions were performed in 1.0 M NaCl (for literature comparisons) and 2.2 mM MgCl2 (PCR conditions). Dissociation kinetics depended on sequence, increased exponentially with temperature, and transition-state parameters inversely correlated to thermodynamic parameters (r = −0.99). Association had no consistent enthalpic component, varied little with temperature or sequence, and poorly correlated to thermodynamic parameters (r = 0.28). Average association rates decreased 78% in MgCl2 compared to NaCl while dissociation was relatively insensitive to ionic conditions. A nearest-neighbour kinetic model for dissociation predicted rate constants within 3-fold of literature values (n = 11). However, a nearest-neighbour model for association appeared overparameterized and inadequate for predictions. Kinetic predictions were used to simulate published high-speed ( |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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