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

Protein Complex Assembly02:41

Protein Complex Assembly

16.9K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
16.9K
Protein Complex Assembly02:41

Protein Complex Assembly

2.6K
2.6K
Spindle Assembly02:50

Spindle Assembly

4.3K
Spindle assembly occurs through three, often coexisting, pathways – the centrosome-mediated pathway, the chromatin-mediated pathway, and the microtubule-mediated pathway – collectively contributing to form a robust spindle apparatus.
In most cells, centrosomes are the primary microtubule nucleation centers. In the centrosome-mediated pathway, the G2-prophase transition triggers centrosome maturation and increased microtubule nucleation. Progressive nucleation results in a...
4.3K
Oligosaccharide Assembly01:24

Oligosaccharide Assembly

3.7K
Protein glycosylation starts in the ER lumen and continues in the Golgi apparatus. Glycosyltransferases catalyze the addition of sugar molecules or glycosylation of proteins. Usually, these enzymes add sugars to the hydroxyl groups of selected serine or threonine residues to form O-linked glycans or the amino groups of asparagine residues to form N-linked glycans. Different positions on the same polypeptide chain can contain differently linked glycans.
Multiple sugar molecules that may or may...
3.7K
Assembly of Cytoskeletal Filaments01:18

Assembly of Cytoskeletal Filaments

28.0K
Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
28.0K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

21.1K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
21.1K

You might also read

Related Articles

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

Sort by
Same author

Estimation of Total Sleep Time From Respiratory Event Intervals in Sleep Disordered Breathing.

Journal of sleep research·2026
Same author

Assessment of out-of-field doses in pediatric radiotherapy.

Radiological physics and technology·2026
Same author

Papilledema and related clinical and paraclinical visual assessment in cerebral venous and sinus thrombosis versus idiopathic intracranial hypertension.

Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology·2026
Same author

Reference Values and Accuracy-Influencing Factors for Knee Joint-Position Sense Assessments: A Cross-Sectional Study.

Journal of motor behavior·2026
Same author

Lower-limb joint moments during gait in individuals with diabetes with and without peripheral neuropathy - A systematic review with meta-analysis.

Clinical biomechanics (Bristol, Avon)·2026
Same author

Relationship Between Decomposition of Surface Electromyography Signals and Force Production: Analyzing Recovery From Intense Exercise.

Journal of applied biomechanics·2026

Related Experiment Video

Updated: Feb 12, 2026

Protocols for C-Brick DNA Standard Assembly Using Cpf1
12:03

Protocols for C-Brick DNA Standard Assembly Using Cpf1

Published on: June 15, 2017

8.7K

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly.

Pedro Fonseca1, Flavio Romano2, John S Schreck3

  • 1Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom.

The Journal of Chemical Physics
|April 9, 2018
PubMed
Summary

We developed a coarse-grained kinetic model using DNA (deoxyribonucleic acid) tiles to simulate complex structure assembly. This model accurately predicts assembly temperatures and nucleation barriers, aiding in understanding DNA self-assembly mechanisms.

More Related Videos

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

3.6K
Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning
08:31

Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning

Published on: February 5, 2021

15.0K

Related Experiment Videos

Last Updated: Feb 12, 2026

Protocols for C-Brick DNA Standard Assembly Using Cpf1
12:03

Protocols for C-Brick DNA Standard Assembly Using Cpf1

Published on: June 15, 2017

8.7K
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

3.6K
Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning
08:31

Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning

Published on: February 5, 2021

15.0K

Area of Science:

  • Biophysics
  • Materials Science
  • Computational Chemistry

Background:

  • Single-stranded DNA tiles enable the creation of intricate nanoscale structures.
  • Studying the assembly mechanisms of these structures requires models that operate at relevant time and length scales.

Purpose of the Study:

  • To develop a coarse-grained kinetic model for simulating DNA tile assembly.
  • To accurately predict critical assembly parameters like temperature and nucleation barriers.
  • To investigate the assembly pathways and intermediate structures of DNA assemblies.

Main Methods:

  • A two-step coarse-graining approach was employed, utilizing detailed thermodynamic calculations from the oxDNA (nucleotide-based DNA model) to parameterize a coarser kinetic model.
  • The model was tested by simulating the assembly of a 2D target structure composed of 334 unique 42-nucleotide DNA strands.
  • The simulation was performed without adjustable parameters.

Main Results:

  • The model accurately reproduced the critical assembly temperature observed in experiments.
  • Detailed analysis of nucleation barriers and critical nucleus shapes was performed.
  • Assembly intermediates were found to be compact and highly connected.

Conclusions:

  • The developed coarse-grained model effectively simulates DNA tile assembly at relevant scales.
  • Classical nucleation theory accurately describes the nucleation barrier near the critical assembly temperature.
  • The model provides insights into the fundamental mechanisms governing DNA self-assembly.