Related Experiment Video
Updated: Apr 30, 2026
08:14
Kinetics of Lagging-strand DNA Synthesis In Vitro by the Bacteriophage T7 Replication Proteins
Published on: February 25, 2017
7.1K
Sequence-dependent theory of oligonucleotide hybridization kinetics
Karthikeyan Marimuthu1, Raj Chakrabarti1
1Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.
The Journal of Chemical Physics
|May 10, 2014
Summary
A new model predicts DNA hybridization rate constants using relaxation kinetics and nearest-neighbor thermodynamics. This approach accurately estimates temperature- and sequence-dependent parameters for oligonucleotide reactions.
Area of Science:
- Biophysical Chemistry
- Molecular Biology
- Computational Biology
Background:
- Oligonucleotide hybridization is crucial in molecular biology.
- Predicting hybridization kinetics is complex due to sequence and temperature dependencies.
- Existing models may lack robustness or experimental agreement.
Purpose of the Study:
- Develop a theoretical model for predicting sequence- and temperature-dependent rate constants of oligonucleotide hybridization.
- Establish a physically consistent and robust model for DNA hybridization relaxation times.
- Integrate thermodynamic and kinetic models for enhanced predictive power.
Main Methods:
- Applied the theory of relaxation kinetics to model hybridization reactions.
- Considered and compared one-sided and two-sided melting mechanisms.
- Estimated model parameters using experimental data.
- Combined the relaxation time model with the nearest-neighbor thermodynamic model.
Main Results:
- Developed a robust model for predicting relaxation times of DNA hybridization.
- Successfully estimated temperature- and sequence-dependent model parameters.
- Model-predicted rate constants show good agreement with experimental data.
- Demonstrated the utility of the model for kinetically controlled DNA hybridization.
Conclusions:
- The developed theoretical approach provides accurate predictions for oligonucleotide hybridization rate constants.
- The integrated kinetic and thermodynamic model enhances understanding of DNA hybridization.
- The model has significant applications in areas utilizing kinetically controlled DNA hybridization.
Related Concept Videos
02:14SN2 Reaction: Kinetics
8.5K
Kinetic Studies and Significance
In a chemical reaction, a relationship exists between the concentration of reactants and the rate at which the reaction proceeds. The study to measure this relationship is known as the kinetics of a chemical reaction. Kinetic studies are used to deduce the rate law of a chemical reaction, which provides information about the species involved during the transition state of the rate-determining step. Thus, kinetic studies help to derive the mechanism of a...
In a chemical reaction, a relationship exists between the concentration of reactants and the rate at which the reaction proceeds. The study to measure this relationship is known as the kinetics of a chemical reaction. Kinetic studies are used to deduce the rate law of a chemical reaction, which provides information about the species involved during the transition state of the rate-determining step. Thus, kinetic studies help to derive the mechanism of a...
8.5K
02:05SN1 Reaction: Kinetics
8.2K
In an SN2 reaction, the reaction rate depends on both the type of nucleophile and the substrate. A hindered tertiary alkyl halide is practically inert to the SN2 mechanism despite using a strong nucleophile.
However, Sir Christopher Ingold and Edward D. Hughes, who studied the kinetics of various nucleophilic substitution reactions, noticed that a tertiary alkyl halide does undergo a nucleophilic substitution reaction in the presence of a weak nucleophile. While studying the substitution...
However, Sir Christopher Ingold and Edward D. Hughes, who studied the kinetics of various nucleophilic substitution reactions, noticed that a tertiary alkyl halide does undergo a nucleophilic substitution reaction in the presence of a weak nucleophile. While studying the substitution...
8.2K
01:59Lagging Strand Synthesis
38.1K
During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...
38.1K
03:01The Replisome
31.2K
DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
31.2K
02:27SN2 Reaction: Mechanism
13.6K
The kinetic studies of SN2 reactions suggest an essential feature of its mechanism: it is a single-step process without intermediates. Here, both the nucleophile and the substrate participate in the rate-determining step.
The presence of the more electronegative halogen in the substrate creates a polarized carbon-halide bond. The halide pulls the electron cloud generating an electrophilic center at the carbon atom. Thus, the carbon atom carries a partial positive charge while the halide has a...
The presence of the more electronegative halogen in the substrate creates a polarized carbon-halide bond. The halide pulls the electron cloud generating an electrophilic center at the carbon atom. Thus, the carbon atom carries a partial positive charge while the halide has a...
13.6K
02:55Temperature Dependence on Reaction Rate
77.7K
The Collision Theory
Atoms, molecules, or ions must collide before they can react with each other. Atoms must be close together to form chemical bonds. This premise is the basis for a theory that explains many observations regarding chemical kinetics, including factors affecting reaction rates.
The collision theory is based on the postulates that (i) the reaction rate is proportional to the rate of reactant collisions, (ii) the reacting species collide in an orientation allowing contact between...
Atoms, molecules, or ions must collide before they can react with each other. Atoms must be close together to form chemical bonds. This premise is the basis for a theory that explains many observations regarding chemical kinetics, including factors affecting reaction rates.
The collision theory is based on the postulates that (i) the reaction rate is proportional to the rate of reactant collisions, (ii) the reacting species collide in an orientation allowing contact between...
77.7K