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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.
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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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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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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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DNA Helicases00:55

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DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
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When disubstituted benzenes undergo electrophilic substitution, the product distribution depends on the directing effect of both substituents. When the directing effects of both substituents reinforce each other, a single product is obtained. For example, bromination of p-nitrotoluene occurs ortho to the methyl group and meta to the nitro group, which is the same position, resulting in a single product. However, if the directing effects of the two groups oppose each other, the...
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Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks
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Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions.

Drew Lysne1, Tim Hachigian1, Chris Thachuk2

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Steric hindrance significantly impacts DNA strand displacement networks, reducing reaction rates by up to 1000-fold. This finding offers new kinetic control strategies for DNA nanotechnology and therapeutics.

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Area of Science:

  • Biochemistry
  • Nanotechnology
  • Chemical Engineering

Background:

  • DNA strand displacement networks are key in DNA nanotechnology and chemical reaction networks.
  • Kinetic control is crucial for these networks, with factors like toehold properties being well-studied.
  • The precise role of steric hindrance in these systems remains unclear.

Purpose of the Study:

  • To systematically investigate the impact of steric hindrance on DNA toehold-mediated strand displacement kinetics.
  • To quantify the effect of steric moieties on reaction rates.
  • To explore the potential of steric factors for kinetic control in DNA nanotechnology.

Main Methods:

  • Tracking kinetic reactions of reporter complexes with added steric moieties near the toehold.
  • Testing two subsets of steric moieties under varied structures and reaction conditions.
  • Employing thermodynamic and coarse-grained computational modeling.

Main Results:

  • Steric hindrance caused a decrease in reaction rate constants by up to three orders of magnitude.
  • Systematic variations helped isolate steric effects from electrostatic interactions.
  • Computational modeling provided insights into the mechanisms of steric hindrance.

Conclusions:

  • Steric moieties are a powerful tool for precise kinetic control in DNA strand displacement networks.
  • Understanding steric hindrance is vital for DNA structural assembly in therapeutics and diagnostics.
  • This research informs the design of DNA-based functional materials and applications.