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Related Concept Videos

DNA Topoisomerases02:02

DNA Topoisomerases

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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.
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
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Co-activators and Co-repressors02:04

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Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
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Eukaryotic Transcription Activators02:42

Eukaryotic Transcription Activators

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Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These...
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tRNA Activation02:26

tRNA Activation

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Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...
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Activation Energy01:26

Activation Energy

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Activation energy is the minimum amount of energy necessary for a chemical reaction to move forward. The higher the activation energy, the slower the rate of the reaction. However, adding heat to the reaction will increase the rate, since it causes molecules to move faster and increase the likelihood that molecules will collide. The collision and breaking of bonds represents the uphill phase of a reaction and generates the transition state. The transition state is an unstable high-energy state...
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Prokaryotic Transcriptional Activators and Repressors01:58

Prokaryotic Transcriptional Activators and Repressors

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The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...
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Simple and Fast Rolling Circle Amplification-Based Detection of Topoisomerase 1 Activity in Crude Biological Samples
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Active DNA Olympic Hydrogels Driven by Topoisomerase Activity.

Brad A Krajina1, Audrey Zhu1, Sarah C Heilshorn2

  • 1Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA.

Physical Review Letters
|October 20, 2018
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Scientists created novel DNA-based Olympic hydrogels using topoisomerases. These active materials can switch between liquid and solid states, offering new possibilities for topological materials research.

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Area of Science:

  • Biochemistry
  • Polymer Chemistry
  • Materials Science

Background:

  • Biological systems utilize proteins like topoisomerases to precisely manage DNA topology.
  • Conventional polymer chemistry faces limitations in replicating this topological control.
  • Understanding DNA topology is crucial for chromosome physics and advanced materials.

Purpose of the Study:

  • To synthesize novel DNA topological materials using enzymatic methods.
  • To engineer switchable hydrogels with tunable viscoelastic properties.
  • To explore the potential of DNA topological networks in materials science.

Main Methods:

  • Enzymatic synthesis of topologically interlinked DNA rings using topoisomerases.
  • Dynamic light scattering microrheology to analyze viscoelastic properties.
  • Characterization of adenosine triphosphate-driven (ATP-driven) hydrogel behavior.

Main Results:

  • Successful synthesis of Olympic hydrogels composed of interlinked DNA rings.
  • Demonstration of ATP-driven switchable behavior, transitioning between liquid and solid states.
  • Quantification of viscoelasticity in DNA topological networks.

Conclusions:

  • Topoisomerase II facilitates the creation of active, switchable Olympic hydrogels.
  • These engineered materials offer a versatile platform for studying topological constraints.
  • The system provides a model for active dynamics in biological and synthetic polymers.