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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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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 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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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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An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication...
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DNA substrate recognition and processing by the full-length human UPF1 helicase.

Saba Dehghani-Tafti1, Cyril M Sanders1

  • 1Department of Oncology & Metabolism, Academic Unit of Molecular oncology, University of Sheffield Medical School, Beech Hill Rd, Sheffield, S10 2RX, UK.

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Summary

Human UPF1 (hUPF1), a helicase regulating mRNA stability, also plays a role in DNA replication. Studies show hUPF1 unwinds DNA and RNA, with specific binding preferences that may influence its nuclear functions.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • UPF1 is a conserved helicase crucial for nonsense-mediated decay (NMD), regulating mRNA stability in the cytoplasm.
  • Human UPF1 (hUPF1) has a dual role, also being essential for nuclear DNA replication.
  • Loss of hUPF1 function triggers DNA damage responses and cell cycle arrest, highlighting its importance beyond mRNA regulation.

Purpose of the Study:

  • To investigate the nucleic acid (NA) binding and processing activities of full-length hUPF1.
  • To understand how hUPF1 interacts with different DNA and RNA structures.
  • To correlate NA binding properties with hUPF1's known functions in mRNA decay and DNA replication.

Main Methods:

  • In vitro analysis of nucleic acid binding and unwinding by full-length hUPF1.
  • Testing hUPF1's interaction with various DNA (B-form, non-B-form) and RNA substrates.
  • Assessing binding affinity and specificity towards single-stranded nucleic acids (ssNA) of different lengths and base compositions.

Main Results:

  • hUPF1 unwinds both DNA and RNA substrates, including non-B-form DNA.
  • hUPF1 shows no significant binding to DNA structures stabilized by inter-base-pair hydrogen bonding.
  • hUPF1 preferentially binds single-stranded nucleic acids (ssNA), with higher affinity for longer substrates and a bias towards poly (U) or poly (dT) over poly (dA).

Conclusions:

  • hUPF1's nucleic acid processing activities align with its role in mRNA regulation.
  • The observed binding preferences suggest that hUPF1's function in DNA replication may be influenced by base sequence and ssNA structures.
  • hUPF1's reduced affinity for stacked bases in ssNA could be a key factor in its DNA processing roles.