Dna2 is a structure-specific nuclease, with affinity for 5′-flap intermediates

Dna2 is a nuclease/helicase with proposed roles in DNA replication, double-strand break repair and telomere maintenance. For each role Dna2 is proposed to process DNA substrates with a 5′-flap. To date, however, Dna2 has not revealed a preference for binding or cleavage of flaps over single-stranded DNA. Using DNA binding competition assays we found that Dna2 has substrate structure specificity. The nuclease displayed a strong preference for binding substrates with a 5′-flap or some variations of flap structure. Further analysis revealed that Dna2 recognized and bound both the single-stranded flap and portions of the duplex region immediately downstream of the flap. A model is proposed in which Dna2 first binds to a flap base, and then the flap threads through the protein with periodic cleavage, to a terminal flap length of ∼5 nt. This resembles the mechanism of flap endonuclease 1, consistent with cooperation of these two proteins in flap processing.

• Publication year

  2009

• Venue

  Nucleic Acids Research

• Publication date

  2009-11-24

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1093/nar/gkp1055PMID 19934252PMCID 2817469
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Human Dna2 Is a Nuclear and Mitochondrial DNA Maintenance Protein

  2009cited by this paper
• Significance of the Dissociation of Dna2 by Flap Endonuclease 1 to Okazaki Fragment Processing in Saccharomyces cerevisiae*

  2009influential reference
• Supplemental information Differential arrival of leading and lagging strand DNA polymerases at fission yeast telomeres

  2009cited by this paper
• Multiple pathways regulate 3' overhang generation at S. cerevisiae telomeres.

  2009cited by this paper
• Interplay of Mre11 Nuclease with Dna2 plus Sgs1 in Rad51-Dependent Recombinational Repair

  2009cited by this paper
• DNA Repair in Mammalian Cells

  2009cited by this paper
• Long Patch Base Excision Repair Proceeds via Coordinated Stimulation of the Multienzyme DNA Repair Complex*

  2009cited by this paper
• Long Patch Base Excision Repair in Mammalian Mitochondrial Genomes*

  2008cited by this paper
• Human DNA2 is a mitochondrial nuclease/helicase for efficient processing of DNA replication and repair intermediates and defective in myopathy

  2008cited by this paper
• Identification of the Xenopus DNA2 protein as a major nuclease for the 5′→3′ strand-specific processing of DNA ends

  2008cited by this paper
• Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends.

  2008cited by this paper
• Genome instability: a mechanistic view of its causes and consequences

  2008cited by this paper
• Dynamic Removal of Replication Protein A by Dna2 Facilitates Primer Cleavage during Okazaki Fragment Processing in Saccharomyces cerevisiae*

  2008cited by this paper
• Domain swapping between FEN-1 and XPG defines regions in XPG that mediate nucleotide excision repair activity and substrate specificity

  2007cited by this paper
• Comparison of the catalytic parameters and reaction specificities of a phage and an archaeal flap endonuclease.

  2007cited by this paper
• Crystal Structure of Bacteriophage T4 5′ Nuclease in Complex with a Branched DNA Reveals How Flap Endonuclease-1 Family Nucleases Bind Their Substrates*

  2007cited by this paper
• Isolation of human Dna2 endonuclease and characterization of its enzymatic properties

  2006cited by this paper
• The DNA–protein interaction modes of FEN-1 with gap substrates and their implication in preventing duplication mutations

  2006cited by this paper
• Single Strand Annealing and ATP-independent Strand Exchange Activities of Yeast and Human DNA2

  2006cited by this paper
• Flap Endonuclease Disengages Dna2 Helicase/Nuclease from Okazaki Fragment Flaps*

  2006influential reference
• Biochemical analysis of human Dna2

  2006cited by this paper
• A Network of Multi-Tasking Proteins at the DNA Replication Fork Preserves Genome Stability

  2005cited by this paper
• Idling by DNA polymerase delta maintains a ligatable nick during lagging-strand DNA replication.

  2004cited by this paper
• On the Roles of Saccharomyces cerevisiae Dna2p and Flap Endonuclease 1 in Okazaki Fragment Processing*

  2004cited by this paper
• Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair.

  2004cited by this paper
• Flap endonuclease 1: a central component of DNA metabolism.

  2004influential reference
• Dna2p Helicase/Nuclease Is a Tracking Protein, Like FEN1, for Flap Cleavage during Okazaki Fragment Maturation*

  2004cited by this paper
• Interaction Interface of Human Flap Endonuclease-1 with Its DNA Substrates*

  2004cited by this paper
• Faculty Opinions recommendation of Okazaki fragment maturation in yeast. I. Distribution of functions between FEN1 AND DNA2.

  2003cited by this paper
• Okazaki Fragment Maturation in Yeast

  2003cited by this paper
• Dna2 Helicase/Nuclease Causes Replicative Fork Stalling and Double-strand Breaks in the Ribosomal DNA of Saccharomyces cerevisiae*

  2003cited by this paper
• Okazaki Fragment Maturation in Yeast

  2003cited by this paper
• Mfold web server for nucleic acid folding and hybridization prediction

  2003cited by this paper
• Interactions of mutant and wild-type flap endonucleases with oligonucleotide substrates suggest an alternative model of DNA binding

  2002cited by this paper
• DNA replication in eukaryotic cells.

  2002cited by this paper
• Cleavage Specificity of Saccharomyces cerevisiae Flap Endonuclease 1 Suggests a Double-Flap Structure as the Cellular Substrate*

  2002cited by this paper
• RPA governs endonuclease switching during processing of Okazaki fragments in eukaryotes

  2001influential reference
• Contacts between the 5′ Nuclease of DNA Polymerase I and Its DNA Substrate*

  2001cited by this paper
• The endonuclease activity of the yeast Dna2 enzyme is essential in vivo.

  2000cited by this paper
• The Nuclease Activity of the Yeast Dna2 Protein, Which Is Related to the RecB-like Nucleases, Is Essential in Vivo *

  2000influential reference
• Characterization of the Enzymatic Properties of the Yeast Dna2 Helicase/Endonuclease Suggests a New Model for Okazaki Fragment Processing*

  2000cited by this paper
• Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

  1999cited by this paper
• Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity.

  1998cited by this paper
• Dna2 of Saccharomyces cerevisiae Possesses a Single-stranded DNA-specific Endonuclease Activity That Is Able to Act on Double-stranded DNA in the Presence of ATP*

  1998cited by this paper
• A yeast replicative helicase, Dna2 helicase, interacts with yeast FEN-1 nuclease in carrying out its essential function

  1997influential reference
• A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease

  1996cited by this paper
• Structure of bacteriophage T4 RNase H, a 5' to 3' RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins.

  1996cited by this paper
• Calf 5′ to 3′ Exo/Endonuclease Must Slide from a 5′ End of the Substrate to Perform Structure-specific Cleavage (*)

  1995cited by this paper
• Crystal structure of Thermus aquaticus DNA polymerase

  1995cited by this paper
• A yeast gene required for DNA replication encodes a protein with homology to DNA helicases.

  1995cited by this paper
• DNA2 Encodes a DNA Helicase Essential for Replication of Eukaryotic Chromosomes (*)

  1995cited by this paper
• The characterization of a mammalian DNA structure‐specific endonuclease.

  1994cited by this paper
• Artificial nucleosome positioning sequences.

  1989cited by this paper

• Mitochondrial exonuclease EXOG supports DNA integrity by the removal of single-stranded DNA flaps

  2025cites this paper
• Biochemical impact of p300-mediated acetylation of replication protein A: Implications for DNA metabolic pathway choice

  2024cites this paper
• Synthesis of Pyrimidine Modified Seleno‐DNA as a Novel Approach to Antisense Candidate

  2023cites this paper
• Syntheses of Pyrimidine-Modified Seleno-DNAs as Stable Antisense Molecules

  2023cites this paper
• Phosphoproteomics reveals a distinctive Mec1/ATR signaling response upon DNA end hyper‐resection

  2021cites this paper
• Mapping the Genetic Landscape of DNA Double-strand Break Repair

  2021cites this paper
• Congenital Diseases of DNA Replication: Clinical Phenotypes and Molecular Mechanisms

  2021cites this paper
• A model for the formation of the duplicated enhancers found in polyomavirus regulatory regions.

  2020cites this paper
• Phosphoproteomics Reveals a Distinct Mode of Mec1/ATR Signaling in Response to DNA End Hyper-Resection

  2020cites this paper
• Checkpoint Responses to DNA Double-Strand Breaks.

  2020cites this paper
• A single molecule view of FEN1 remarkable substrate recognition, perfect catalysis and regulation

  2019influential citation
• Bulk and single-molecule analysis of a bacterial DNA2-like helicase–nuclease reveals a single-stranded DNA looping motor

  2019cites this paper
• Elucidating the role of the iron-sulfur cluster in the nuclease/helicase Dna2

  2019cites this paper
• Multiple roles of DNA2 nuclease/helicase in DNA metabolism, genome stability and human diseases

  2019cites this paper
• hDNA2 nuclease/helicase promotes centromeric DNA replication and genome stability

  2018cites this paper
• Structural insights into DNA degradation by human mitochondrial nuclease MGME1

  2018cites this paper
• Human mitochondrial nucleases

  2017cites this paper
• Mechanism of Lagging-Strand DNA Replication in Eukaryotes.

  2017cites this paper
• Endonuclease EEPD1 Is a Gatekeeper for Repair of Stressed Replication Forks*

  2017cites this paper
• Genetic Separation of Sae2 Nuclease Activity from Mre11 Nuclease Functions in Budding Yeast

  2017cites this paper
• Inhibition of DNA2 nuclease as a therapeutic strategy targeting replication stress in cancer cells

  2017cites this paper
• Role of human DNA2 (hDNA2) as a potential target for cancer and other diseases: A systematic review.

  2017cites this paper
• Metnase Mediates Loading of Exonuclease 1 onto Single Strand Overhang DNA for End Resection at Stalled Replication Forks*

  2016cites this paper
• Cdc24 Is Essential for Long-range End Resection in the Repair of Double-stranded DNA Breaks*

  2016cites this paper
• A Selective Small Molecule DNA2 Inhibitor for Sensitization of Human Cancer Cells to Chemotherapy

  2016cites this paper
• MGME1 processes flaps into ligatable nicks in concert with DNA polymerase γ during mtDNA replication

  2016cites this paper
• Dynamics of replication proteins during lagging strand synthesis: A crossroads for genomic instability and cancer.

  2016cites this paper
• Yet another job for Dna2: Checkpoint activation.

  2015cites this paper
• EEPD1 Rescues Stressed Replication Forks and Maintains Genome Stability by Promoting End Resection and Homologous Recombination Repair

  2015cites this paper
• Exonuclease of human DNA polymerase gamma disengages its strand displacement function.

  2013cites this paper
• Flap endonuclease 1.

  2013cites this paper
• Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels

  2013cites this paper
• Okazaki fragment metabolism.

  2013cites this paper
• Okazaki Fragment Processing-independent Role for Human Dna2 Enzyme during DNA Replication*

  2012cites this paper
• Genome instability induced by structured DNA and replication fork restart

  2012cites this paper
• Structure and Function Studies of Selenium Substituted Nucleic Acids

  2012cites this paper
• Cross talk between the nuclease and helicase activities of Dna2: role of an essential iron–sulfur cluster domain

  2012cites this paper
• Biochemical analyses indicate that binding and cleavage specificities define the ordered processing of human Okazaki fragments by Dna2 and FEN1

  2012cites this paper
• The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes.

  2011cites this paper
• Biochemical and genetic studies of genomic stability

  2011cites this paper
• The Pathways of Double-Strand Break Repair

  2011cites this paper
• Characterization of the Endonuclease and ATP-dependent Flap Endo/Exonuclease of Dna2*

  2011cites this paper
• Dna2 Exhibits a Unique Strand End-dependent Helicase Function*

  2010cites this paper
• Functional regulation of FEN1 nuclease and its link to cancer

  2010cites this paper
• Complementary non-radioactive assays for investigation of human flap endonuclease 1 activity

  2010cites this paper