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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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...
DNA Topoisomerases02:02

DNA Topoisomerases

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.  Type I...
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DNA Packaging00:58

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DNA Helicases00:55

DNA Helicases

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...
Homologous Recombination02:31

Homologous Recombination

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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Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Closing the lid on DNA end-to-end stacking interactions.

Li Li1, Suzette A Pabit, Jessica S Lamb

  • 1School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA.

Applied Physics Letters
|June 3, 2009
PubMed
Summary

Short DNA strands associate via end-to-end stacking, especially when uncapped. Modified DNA ends were studied using small angle x-ray scattering (SAXS) to confirm this interaction mechanism.

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14:43

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Published on: August 27, 2014

Area of Science:

  • Molecular Biology
  • Biophysics
  • Materials Science

Background:

  • Recent studies indicate short DNA strands can associate through end-to-end stacking.
  • Understanding DNA interactions is crucial for nanotechnology and biomaterials.

Purpose of the Study:

  • To investigate DNA-DNA interactions with modified ends.
  • To confirm the role of end-to-end stacking in short DNA association.

Main Methods:

  • Synthesized 20 bp DNA duplexes with varying T(4) loop caps on ends.
  • Studied DNA association in 20 mM Mg(2+) solutions.
  • Analyzed DNA-DNA interactions using small angle x-ray scattering (SAXS) and computed second virial coefficients.

Main Results:

  • DNA association was observed only in constructs with at least one uncapped end.
  • SAXS data variations at low angles indicated DNA-DNA interactions.
  • Second virial coefficients confirmed the role of end-to-end stacking.

Conclusions:

  • End-to-end stacking is a significant factor in the association of short DNA strands.
  • The presence of uncapped ends is necessary for observed DNA-DNA interactions.
  • SAXS is an effective method for characterizing these interactions.