Jove
Visualize
Contact Us

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Engineering plasmids with synthetic origins of replication.

Nature communications·2026
Same author

On Degradation-Induced Leak in Heterochiral DNA Strand Displacement Cascades.

ACS synthetic biology·2026
Same author

Smart Nucleic Acid Chaperones: Phase-Separating Intrinsically Disordered Proteins for Accelerating DNA Hybridization Reactions.

ACS synthetic biology·2026
Same author

A Study of CRISPR Ribonucleoprotein Displacement in Cell-Free Systems.

ACS omega·2025
Same author

Engineering Plasmids with Synthetic Origins of Replication.

bioRxiv : the preprint server for biology·2025
Same author

Isolation of nucleic acids using liquid-liquid phase separation of pH-sensitive elastin-like polypeptides.

Scientific reports·2024
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 Experiment Video

Updated: Nov 2, 2025

Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage
06:51

Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage

Published on: May 6, 2020

4.1K

Structure sampling for computational estimation of localized DNA interaction rates.

Sarika Kumar1, Julian M Weisburd1, Matthew R Lakin2,3,4

  • 1Department of Computer Science, University of New Mexico, Albuquerque, NM, 87131, USA.

Scientific Reports
|June 17, 2021
PubMed
Summary

This study introduces an automated method to estimate reaction rates in tethered molecular circuits, considering molecular geometry. This approach enhances the design and modeling of localized molecular systems for diagnostics and therapeutics.

More Related Videos

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA
12:05

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Published on: October 1, 2017

8.4K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.3K

Related Experiment Videos

Last Updated: Nov 2, 2025

Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage
06:51

Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage

Published on: May 6, 2020

4.1K
A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA
12:05

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Published on: October 1, 2017

8.4K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.3K

Area of Science:

  • Biophysics
  • Molecular Biology
  • Nanotechnology

Background:

  • Molecular circuits offer advantages over solution-phase circuits due to increased reaction speed and scalability.
  • Tethering molecular components to DNA nanostructures enables precise spatial arrangement for enhanced functionality.
  • Accurate modeling of these systems requires consideration of molecular geometry, which influences interaction rates.

Purpose of the Study:

  • To develop an automated method for estimating reaction rates in tethered molecular circuits.
  • To incorporate the influence of molecular geometry on reaction kinetics into computational models.
  • To provide a foundation for advanced modeling and design tools for localized molecular circuits.

Main Methods:

  • Probabilistically generating samples of structure distributions based on biophysical models.
  • Estimating key parameters for kinetic models using these generated structure distributions.
  • Developing an automated computational approach to account for molecular geometry in reaction rate estimations.

Main Results:

  • The developed method successfully estimates reaction rates in tethered molecular circuits.
  • The approach accounts for the geometric constraints of tethered molecular components.
  • Provides a quantitative link between molecular structure and reaction kinetics.

Conclusions:

  • The automated method offers a significant advancement in modeling tethered molecular circuits.
  • Geometric considerations are crucial for accurate prediction of reaction rates in these systems.
  • This work facilitates the future design and optimization of localized molecular circuits for various applications.