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Topologically switchable and gated transcription machinery.

Pu Zhang1, Amit Fischer1, Yu Ouyang1

  • 1Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel itamar.willner@mail.huji.ac.il.

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Summary

Synthetically designed DNA templates with topological barriers enable switchable RNA aptamer transcription. These novel systems offer precise control over gene expression, mimicking natural processes for advanced applications.

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Area of Science:

  • Synthetic biology
  • Molecular engineering
  • Biochemistry

Background:

  • Topological barriers naturally regulate gene expression by controlling transcription machinery.
  • Developing synthetic systems to mimic and control these natural processes is crucial for advancing biotechnology.

Purpose of the Study:

  • To design synthetic DNA templates with switchable topological barriers for triggered RNA aptamer transcription.
  • To demonstrate controlled and reversible transcription of specific RNA aptamers using these novel templates.

Main Methods:

  • Utilized Sr2+-ion-stabilized G-quadruplex and kryptofix [2.2.2] (KP) as reversible topological barriers.
  • Employed T-A·T triplex barriers separated by fuel strands for cyclic transcription.
  • Incorporated photoactivated azobenzene-modified nucleic acid barriers for "ON"/"OFF" transcription control.
  • Integrated DNA tetrahedra scaffolds and T7 RNA polymerase within hydrogel microcapsules for cell-like assemblies.

Main Results:

  • Demonstrated switchable transcription of malachite green (MG) RNA aptamer using G-quadruplex/KP barriers.
  • Achieved cyclic triggered transcription of a DFHBI-binding aptamer using T-A·T triplex barriers.
  • Showcased "ON"/"OFF" control of MG aptamer transcription with photoresponsive barriers.
  • Successfully gated transcription of MG or DFHBI aptamers using a mixture of topological triggers.
  • Established reversible transcription of MG aptamer within DNA hydrogel microcapsules.

Conclusions:

  • Developed versatile synthetic DNA topological barriers for precise control over RNA aptamer transcription.
  • These systems offer a powerful platform for switchable and triggered gene expression.
  • The cell-like microcapsule assemblies demonstrate potential for in vitro synthetic biology applications.