Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

PCR01:32

PCR

192.3K
Overview
192.3K
The Replisome03:01

The Replisome

30.8K
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...
30.8K
PCR - Polymerase Chain Reaction01:32

PCR - Polymerase Chain Reaction

83.1K
83.1K
Proofreading01:31

Proofreading

7.5K
Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore,  it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase...
7.5K
Proofreading01:43

Proofreading

51.7K
Overview
51.7K
Next-generation Sequencing03:00

Next-generation Sequencing

87.2K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
87.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Evolution of Organic Solvent-Resistant DNA Polymerases.

ACS synthetic biology·2023
Same author

Improving aqueous solubility of paclitaxel with polysarcosine-b-poly(γ-benzyl glutamate) nanoparticles.

International journal of pharmaceutics·2022
Same author

Identification of a novel peptide ligand for the cancer-specific receptor mutation EGFRvIII using high-throughput sequencing of phage-selected peptides.

Scientific reports·2022
Same author

Discovery of novel compounds as potent activators of Sirt3.

Bioorganic & medicinal chemistry·2022
Same author

Biophysical characterization of hit compounds for mechanism-based enzyme activation.

PloS one·2018
Same author

Molecular system identification for enzyme directed evolution and design.

The Journal of chemical physics·2017

Related Experiment Video

Updated: Apr 21, 2026

Linear Amplification Mediated PCR – Localization of Genetic Elements and Characterization of Unknown Flanking DNA
11:58

Linear Amplification Mediated PCR – Localization of Genetic Elements and Characterization of Unknown Flanking DNA

Published on: June 25, 2014

29.4K

Dynamics and control of DNA sequence amplification.

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
|November 3, 2014
PubMed
Summary

This study presents a control theory framework for optimizing DNA amplification, like Polymerase Chain Reaction. It reveals optimal temperature cycling strategies for DNA sequence amplification, differing from standard methods.

More Related Videos

Rapid, Enzymatic Methods for Amplification of Minimal, Linear Templates for Protein Prototyping using Cell-Free Systems
07:35

Rapid, Enzymatic Methods for Amplification of Minimal, Linear Templates for Protein Prototyping using Cell-Free Systems

Published on: June 14, 2021

2.2K
Polymerase Chain Reaction: Basic Protocol Plus Troubleshooting and Optimization Strategies
09:00

Polymerase Chain Reaction: Basic Protocol Plus Troubleshooting and Optimization Strategies

Published on: May 22, 2012

417.9K

Related Experiment Videos

Last Updated: Apr 21, 2026

Linear Amplification Mediated PCR – Localization of Genetic Elements and Characterization of Unknown Flanking DNA
11:58

Linear Amplification Mediated PCR – Localization of Genetic Elements and Characterization of Unknown Flanking DNA

Published on: June 25, 2014

29.4K
Rapid, Enzymatic Methods for Amplification of Minimal, Linear Templates for Protein Prototyping using Cell-Free Systems
07:35

Rapid, Enzymatic Methods for Amplification of Minimal, Linear Templates for Protein Prototyping using Cell-Free Systems

Published on: June 14, 2021

2.2K
Polymerase Chain Reaction: Basic Protocol Plus Troubleshooting and Optimization Strategies
09:00

Polymerase Chain Reaction: Basic Protocol Plus Troubleshooting and Optimization Strategies

Published on: May 22, 2012

417.9K

Area of Science:

  • Biophysics
  • Control Theory
  • Molecular Biology

Background:

  • DNA amplification is crucial for molecular biology, involving in vitro replication of specific DNA sequences.
  • Current methods for DNA amplification often lack optimal dynamic control over reaction conditions.
  • A theoretical approach is needed to determine optimal operating conditions for diverse amplification objectives.

Purpose of the Study:

  • To develop a theoretical framework for optimizing DNA amplification reactions using control theory.
  • To identify optimal dynamic operating conditions for any specified DNA amplification goal.
  • To demonstrate the application of this framework using Polymerase Chain Reaction (PCR) as a model.

Main Methods:

  • Formulating DNA amplification as a control theory problem based on first-principles biophysical modeling.
  • Developing sequence-dependent biophysical models for DNA amplification, treating them as control systems.
  • Applying optimal control theory to derive optimal temperature cycling profiles for geometric DNA amplification.

Main Results:

  • Demonstrated the existence of an optimal temperature cycling strategy for geometric amplification of any DNA sequence.
  • Formulated optimal control problems to derive specific optimal temperature profiles.
  • Proposed strategies for synthesizing optimal DNA amplification control trajectories.

Conclusions:

  • Optimal control theory provides a powerful approach to DNA amplification, yielding strategies that may outperform conventional methods.
  • The framework can be extended to design novel DNA amplification reactions and optimize advanced amplification objectives.
  • This work offers a new perspective on controlling and optimizing DNA synthesis and replication in vitro.