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

Translesion DNA Polymerases02:10

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...

You might also read

Related Articles

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

Sort by
Same author

Force Reveals Hidden Conformations and Dissociation Pathways in Individual π-Interacting Dimers.

Angewandte Chemie (International ed. in English)·2026
Same author

Microbiota-gut-brain axis and treatment resistance in epilepsy: a multicentre prospective study protocol (CARE).

BMJ open·2026
Same author

On the Design of Steep Optical Absorbers for Vacuum-Processed Organic Solar Cells: One Isopropyl Group Makes the Difference.

Small science·2026
Same author

Mechanistic insights into azo compound back-isomerization from spin-flip time-dependent DFT combined with Marcus theory.

Chemical science·2026
Same author

Molecular Dynamics Workflows to Compute Large-Scale Sets of Absolute Binding Free Energies Aiding Drug Candidate and Binding Pose Selection.

Journal of chemical theory and computation·2026
Same author

Wavelength-steered directional rotation in an autonomous light-driven molecular motor.

Nature chemistry·2026

Related Experiment Video

Updated: May 12, 2026

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

11.7K

Simulating the Lyotropic Phase Behavior of a Partially Self-Complementary DNA Tetramer.

Silvia Cristofaro1, Lara Querciagrossa2,1, Lorenzo Soprani1

  • 1Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy.

Biomacromolecules
|June 3, 2024
PubMed
Summary

Short DNA strands self-assemble into liquid crystal phases. Molecular dynamics simulations accurately predict the phase behavior and aggregation of DNA tetramers, revealing cooperative assembly into larger structures.

More Related Videos

Author Spotlight: Developing Synthetic Cells from Programmable Amphiphilic DNA Nanostructures
08:02

Author Spotlight: Developing Synthetic Cells from Programmable Amphiphilic DNA Nanostructures

Published on: May 31, 2024

744
Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

533

Related Experiment Videos

Last Updated: May 12, 2026

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

11.7K
Author Spotlight: Developing Synthetic Cells from Programmable Amphiphilic DNA Nanostructures
08:02

Author Spotlight: Developing Synthetic Cells from Programmable Amphiphilic DNA Nanostructures

Published on: May 31, 2024

744
Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

533

Area of Science:

  • Biophysics
  • Materials Science
  • Computational Chemistry

Background:

  • DNA oligomers in solution can form liquid crystal phases through hierarchical self-assembly.
  • The multiscale nature of DNA assembly complicates quantitative analysis, especially for short strands.

Purpose of the Study:

  • To quantitatively model the assembly processes and phase behavior of short DNA oligomers.
  • To investigate the liquid crystal phase formation in solutions of GCCG tetramers using molecular dynamics.

Main Methods:

  • Coarse-grained molecular dynamics simulations using the oxDNA model.
  • Analysis of molecular association (thermal melting) and collective ordering (phase diagram).
  • Characterization of isotropic, nematic, and columnar liquid crystal phases.

Main Results:

  • Simulations showed good quantitative agreement with experimental data for thermal melting and phase diagrams.
  • Characterized different liquid crystal phases (isotropic, nematic, columnar) by molecular order, aggregate size, and structure.
  • Observed a cooperative aggregation mechanism favoring longer DNA aggregates over dimers.

Conclusions:

  • The oxDNA model accurately captures the assembly and phase behavior of short DNA oligomers.
  • Cooperative assembly drives the formation of liquid crystal phases in DNA tetramer solutions.
  • Understanding DNA self-assembly is crucial for designing novel DNA-based materials.