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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...
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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,...
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Updated: Jul 8, 2025

Design and Synthesis of a Reconfigurable DNA Accordion Rack
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pH-Controlled Resettable Modular DNA Strand-Displacement Circuits.

Xiaoyun Sun1, Dongbao Yao1, Haojun Liang1

  • 1Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China.

Nano Letters
|December 12, 2023
PubMed
Summary
This summary is machine-generated.

Researchers developed a new proton-driven method to reset dynamic DNA circuits. This strategy enables repeated operation of DNA nanotechnology systems without waste, advancing molecular computing and diagnostics.

Keywords:
detachable substratei-motifpH-responsive intermolecular triplexresettable modular DNA circuittoehold-mediated strand displacement

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Area of Science:

  • Molecular nanotechnology
  • Biochemistry
  • Synthetic biology

Background:

  • Dynamic DNA nanotechnology relies on toehold-mediated strand displacement (TMSD) for molecular systems.
  • Existing TMSD systems lack simple resetting mechanisms due to challenges in backward reaction kinetics.

Purpose of the Study:

  • To develop a facile and efficient strategy for resetting TMSD-based dynamic DNA circuits.
  • To enable repeated operation of modular DNA circuits at constant temperature without waste generation.

Main Methods:

  • Integration of pH-responsive intermolecular CG-C+ triplex DNA and i-motif DNA into DNA substrates.
  • Utilizing a pH-programmed strategy to control association/dissociation of DNA components.
  • Facilitating forward and backward TMSD reactions via pH-induced structural changes.

Main Results:

  • A proton-driven strategy for complete resetting of modular DNA circuits was successfully developed.
  • The system demonstrated repeated operation at constant temperature without producing DNA waste.
  • Resettable DNA logic gates for computation and catalytic DNA systems for signal transduction were constructed.

Conclusions:

  • The developed pH-programmed strategy offers a tractable approach for resetting TMSD-based dynamic DNA systems.
  • This method enhances the reusability and sustainability of DNA nanotechnology applications.
  • The constructed resettable logic gates and catalytic systems show promise for advanced molecular computing and diagnostics.