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

9.7K
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...
9.7K
The Replisome03:01

The Replisome

32.8K
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...
32.8K
Lagging Strand Synthesis01:59

Lagging Strand Synthesis

48.9K
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...
48.9K
Homologous Recombination02:31

Homologous Recombination

50.0K
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
50.0K
DNA-only Transposons02:57

DNA-only Transposons

14.3K
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
14.3K
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

5.7K
DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
5.7K

You might also read

Related Articles

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

Sort by
Same author

DNAzyme-based kinetic regulators enable stimulus-responsive and programmable time delays in DNA strand displacement.

Chemical communications (Cambridge, England)·2025
Same author

Interpretable molecular decision-making with DNA-based scalable and memory-efficient tree computation.

Nature communications·2025
Same author

Accelerating Toehold-Mediated DNA Strand Displacement Reaction using Polyquaternium.

Chemistry (Weinheim an der Bergstrasse, Germany)·2025
Same author

Toward 95.5% Efficient Red Emissive Carbon Dots: Oxidation State Enhancing Radiative Electron-Transition of Indole Fluorophore.

Nano letters·2024
Same author

Activating One/Two-Photon Excited Red Fluorescence on Carbon Dots: Emerging n→π Photon Transition Induced by Amino Protonation.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2023
Same author

Photoluminescence mechanism of carbon dots: triggering high-color-purity red fluorescence emission through edge amino protonation.

Nature communications·2021

Related Experiment Video

Updated: May 26, 2025

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks
07:50

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

Published on: November 25, 2015

14.3K

DNA Logic Circuit Based on a Toehold-Independent Strand Displacement Reaction Network.

Junlan Liu1, Qing Zhang2

  • 1Department of Laboratory Medicine and Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.

Nano Letters
|February 21, 2025
PubMed
Summary
This summary is machine-generated.

Researchers developed a novel toehold-independent DNA strand displacement (TISD) system for DNA logic circuits. This new method uses configurational entropy, advancing DNA nanotechnology and molecular programming.

Keywords:
DNA computationDynamic DNA reaction networkMolecular programmingToehold-independent DNA strand displacement

More Related Videos

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation
09:26

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

4.1K
Design and Synthesis of a Reconfigurable DNA Accordion Rack
07:44

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

7.0K

Related Experiment Videos

Last Updated: May 26, 2025

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks
07:50

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

Published on: November 25, 2015

14.3K
DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation
09:26

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

4.1K
Design and Synthesis of a Reconfigurable DNA Accordion Rack
07:44

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

7.0K

Area of Science:

  • Molecular Biology
  • Nanotechnology
  • Biochemistry

Background:

  • DNA strand displacement is a cornerstone of DNA nanotechnology for creating functional DNA circuits.
  • Current systems predominantly rely on toehold-mediated strand displacement, limiting circuit complexity and practicality.
  • Eliminating the toehold requirement is crucial for advancing DNA-based molecular programming.

Purpose of the Study:

  • To develop and investigate a toehold-independent DNA strand displacement (TISD) reaction network.
  • To establish a design framework and assess the practical functionality of TISD for DNA logic circuits.
  • To explore TISD as a viable alternative to toehold-dependent systems in DNA nanotechnology.

Main Methods:

  • Developed a TISD reaction network that utilizes configurational entropy instead of toehold enthalpic energy.
  • Investigated the working principle and design framework of the TISD system.
  • Evaluated the performance of TISD-based DNA logic circuits in signal transduction and digital computing tasks.

Main Results:

  • TISD-based circuits demonstrated effective cascaded, fan-in, and fan-out signal transduction.
  • Achieved comparable performance to toehold-dependent systems in Boolean logic gates, multilayer circuits, and square root computation.
  • Validated the use of configurational entropy as a driving force for DNA strand displacement reactions.

Conclusions:

  • The TISD reaction network offers a promising alternative to conventional toehold-dependent DNA strand displacement systems.
  • TISD significantly expands the design possibilities for DNA-based molecular programming.
  • This approach is expected to inspire the development of more versatile DNA-based functional systems.