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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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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
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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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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
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Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline
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Structure-function analysis of DEAD-box helicase DDX43.

Ravi Shankar Singh1, Ananna Bhadra Arna1, He Dong1

  • 1Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada.

Methods (San Diego, Calif.)
|March 8, 2022
PubMed
Summary
This summary is machine-generated.

DEAD-box helicase 43 (DDX43) is overexpressed in tumors and acts as an RNA/DNA helicase. Its KH domain binds DNA/RNA, offering a therapeutic target for cancers.

Keywords:
DDX43DEAD-box helicaseFunctionHAGEKH domainStructure

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Cancer Research

Background:

  • DDX43 (DEAD-box helicase 43), also known as HAGE, is a DEAD-box protein.
  • It is overexpressed in various tumors but not in normal tissues, making it a potential cancer therapeutic target.
  • DDX43 possesses both RNA and DNA helicase activity, crucial for its cellular functions.

Purpose of the Study:

  • To investigate the structural and functional properties of DDX43, particularly its K homology (KH) domain.
  • To explore the substrate binding preferences and helicase activity of DDX43.
  • To assess the potential of DDX43 as a therapeutic target in cancer treatment.

Main Methods:

  • Electrophoretic mobility shift assay (EMSA)
  • Systematic evolution of ligands by exponential enrichment (SELEX)
  • Chromatin immunoprecipitation (ChIP)-seq
  • Crosslinking immunoprecipitation (CLIP)-seq
  • Nuclear magnetic resonance (NMR)

Main Results:

  • The KH domain of DDX43 is essential for its ATPase and unwinding activities.
  • DDX43's KH domain preferentially binds pyrimidine-rich single-stranded DNA and RNA (e.g., TTGT) in gene promoter regions.
  • The KH domain enhances the substrate specificity and processivity of the DDX43 helicase.
  • Cellular studies indicate DDX43's involvement in piRNA amplification, tumorigenesis, RAS signaling, and innate immunity.

Conclusions:

  • DDX43 is an ATP-dependent RNA/DNA helicase with a KH domain crucial for its function.
  • Understanding DDX43's structure and function can lead to targeted small molecule therapies for DDX43-overexpressing cancers.
  • DDX43 represents a promising therapeutic target for various cancers due to its overexpression and essential roles in tumorigenesis.