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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...
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

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, a...
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...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

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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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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DEAD-box proteins unwind duplexes by local strand separation.

Quansheng Yang1, Mark Del Campo, Alan M Lambowitz

  • 1Department of Biochemistry, Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.

Molecular Cell
|October 30, 2007
PubMed
Summary

DEAD-box proteins unwind RNA duplexes locally, acting as "strand separators" rather than processive helicases. This mechanism facilitates structural changes in complex RNA and RNA-protein complexes (RNPs).

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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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11:42

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes

Published on: November 1, 2012

Area of Science:

  • Molecular Biology
  • Biochemistry
  • RNA Biology

Background:

  • DEAD-box proteins are ATP-dependent enzymes involved in RNA structural rearrangements.
  • Canonical helicases unwind nucleic acids via directional, processive translocation.
  • The specific unwinding mechanism of DEAD-box proteins remains poorly understood.

Purpose of the Study:

  • To elucidate the unwinding mechanism of DEAD-box proteins.
  • To compare the unwinding activity of DEAD-box proteins with canonical helicases.
  • To investigate the role of DEAD-box proteins in RNA structural dynamics.

Main Methods:

  • In vitro biochemical assays using DEAD-box proteins (Ded1p and Mss116p).
  • Analysis of RNA duplex unwinding from internal and terminal regions.
  • Testing activity on short RNA segments flanked by DNA.

Main Results:

  • DEAD-box proteins can unwind RNA duplexes from internal and terminal helical regions.
  • Unwinding occurs on short RNA segments (as small as two nucleotides).
  • Enzymes act via local destabilization, not directional translocation.

Conclusions:

  • DEAD-box proteins function as local strand separators, distinct from canonical helicases.
  • This mechanism enables localized structural changes in RNA and RNP assemblies.
  • The findings provide a new mechanistic model for DEAD-box protein function.