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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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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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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 Helicases00:55

DNA Helicases

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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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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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Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein
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Intra-strand phosphate-mediated pathways in microsolvated double-stranded DNA.

Georgia Polycarpou1, Spiros S Skourtis1

  • 1Department of Physics, University of Cyprus, Nicosia 1678, Cyprus.

Journal of Physics. Condensed Matter : an Institute of Physics Journal
|June 7, 2024
PubMed
Summary
This summary is machine-generated.

Charge transport in dry DNA over nanometer distances occurs through phosphate groups on independent intra-strand pathways. This mechanism explains experimental results in intact versus nicked DNA molecules.

Keywords:
DNA transportdynamic disordersingle-molecule junction

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Area of Science:

  • Molecular electronics
  • Biophysics
  • Materials science

Background:

  • Understanding charge transport in DNA is crucial for molecular electronics and biosensing applications.
  • Previous models often focused on pi-stacking of bases, but experimental data suggests alternative mechanisms.

Purpose of the Study:

  • To investigate charge transport mechanisms in dry DNA molecular junctions.
  • To explain experimental observations of current in intact and nicked double-stranded DNA.
  • To identify factors influencing charge transport pathways.

Main Methods:

  • Theoretical computations were employed to model charge transport.
  • Analysis focused on intra-strand pathways involving phosphate groups.
  • Comparison with experimental data from single-molecule studies.

Main Results:

  • Dry DNA charge transport over tens of nanometers can occur via independent intra-strand phosphate pathways.
  • These phosphate-mediated pathways explain current differences observed in intact and nicked DNA.
  • Solvation degree influences DNA pi-stacking disorder and phosphate orbital energies, tuning transport.

Conclusions:

  • Phosphate-group mediated intra-strand transport is a viable mechanism for long-distance charge transport in dry DNA.
  • This mechanism offers an alternative to base-mediated transport and inter-strand hopping.
  • Environmental factors like solvation play a critical role in determining DNA charge transport efficiency.