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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
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Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
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An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication...
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The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
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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.
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Related Experiment Video

Updated: Mar 24, 2026

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
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Single-Stranded Tile Stoppers for Interlocked DNA Architectures.

Julián Valero1, Finn Lohmann1, Daniel Keppner1

  • 1Life and Medical Science (LIMES) Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk Strasse 1, 53121, Bonn, Germany.

Chembiochem : a European Journal of Chemical Biology
|March 15, 2016
PubMed
Summary

Researchers developed novel single-stranded tile (SST) stoppers for creating advanced DNA nanostructures. These stoppers enable the controlled movement of components within DNA rotaxanes, advancing DNA nanotechnology applications.

Keywords:
DNA rotaxanesDNA structuresinterlocked DNA structuresnanotechnologysingle-stranded tiles (SST)

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Area of Science:

  • * Nanotechnology
  • * Supramolecular Chemistry
  • * Synthetic Biology

Background:

  • * Interlocked DNA architectures offer unique mechanical properties for DNA nanotechnology.
  • * Mechanically bonded components allow relative movement without disassembly.
  • * Existing methods for creating such architectures require further refinement.

Purpose of the Study:

  • * To design, synthesize, and characterize novel single-stranded tile (SST) stoppers.
  • * To enable the self-assembly of bulky, square-shaped stoppers for DNA rotaxanes.
  • * To create asymmetric DNA rotaxanes with controllable macrocycle positioning.

Main Methods:

  • * Self-assembly of 97 oligodeoxynucleotide (ODN) strands into square-shaped SST stoppers.
  • * Design of sticky ends for hybridization with dsDNA axles.
  • * Construction of asymmetric rotaxanes with SST and ring stoppers.
  • * Demonstration of macrocycle translocation using fuel ODNs.

Main Results:

  • * Successful self-assembly of rigid, square-shaped SST stoppers.
  • * SST stoppers prevent dethreading of a 14 nm diameter macrocycle.
  • * Assembled asymmetric rotaxane exhibits controlled macrocycle movement between stations.
  • * Macrocycle position is tunable via fuel ODN triggers.

Conclusions:

  • * SST stoppers are effective components for constructing robust interlocked DNA architectures.
  • * The developed rotaxane system demonstrates precise control over molecular motion.
  • * This work advances the design principles for complex DNA-based nanomachines.