Over the past decade it has become apparent that DNA in the human genome has considerable potential to form structures other than canonical Watson-Crick duplexes. Among the motifs most prone to form structures in vitro are runs of guanines, which readily assemble into structures stabilized by G quartets. G quartets can stabilize a variety of distinct structures, which we refer to collectively as G4 DNA. Our laboratory has identified and characterized activities that recognize G4 DNA with high affinity and specificity and dynamically alter its structure. The affinity and specificity of these factors for G4 DNA substrates argue that G4 DNA forms in vivo, and that it is the target for specific factors involved in DNA metabolism. We now propose (1) to ask directly if G4 DNA forms in vivo; (2) to learn how G4 DNA is recognized by RecQ family helicases; (3) to study how G4 DNA causes or contributes to genomic instability associated with cancer predisposition; (4) to study cleavage of G4 DNA in mammalian cells; (5) and to ask whether repair pathways eliminate G4 DNA. The proposed experiments will provide detailed mechanistic understanding of how DNA sequence impacts chromosome replication and genomic structure. They will elucidate mechanisms of maintenance of critical regions of the human genome, the rDNA and telomeres. They will also have immediate impact on our understanding of human health and disease, because the failure to remove G4 DNA may be associated with genetic instability that leads to malignancy.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM065988-01
Application #
6514000
Study Section
Mammalian Genetics Study Section (MGN)
Program Officer
Wolfe, Paul B
Project Start
2002-08-01
Project End
2004-07-31
Budget Start
2002-08-01
Budget End
2003-07-31
Support Year
1
Fiscal Year
2002
Total Cost
$113,700
Indirect Cost
Name
University of Washington
Department
Microbiology/Immun/Virology
Type
Schools of Medicine
DUNS #
135646524
City
Seattle
State
WA
Country
United States
Zip Code
98195
Gray, Lucas T; Vallur, Aarthy C; Eddy, Johanna et al. (2014) G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD. Nat Chem Biol 10:313-8
Eddy, Johanna; Vallur, Aarthy C; Varma, Sudir et al. (2011) G4 motifs correlate with promoter-proximal transcriptional pausing in human genes. Nucleic Acids Res 39:4975-83
Vallur, Aarthy C; Maizels, Nancy (2010) Distinct activities of exonuclease 1 and flap endonuclease 1 at telomeric g4 DNA. PLoS One 5:e8908
Eddy, Johanna; Maizels, Nancy (2009) Selection for the G4 DNA motif at the 5' end of human genes. Mol Carcinog 48:319-25
Eddy, Johanna; Maizels, Nancy (2008) Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes. Nucleic Acids Res 36:1321-33
Vallur, Aarthy C; Maizels, Nancy (2008) Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions. Proc Natl Acad Sci U S A 105:16508-12
Duquette, Michelle L; Huber, Michael D; Maizels, Nancy (2007) G-rich proto-oncogenes are targeted for genomic instability in B-cell lymphomas. Cancer Res 67:2586-94
Eddy, Johanna; Maizels, Nancy (2006) Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res 34:3887-96
Maizels, Nancy (2006) Dynamic roles for G4 DNA in the biology of eukaryotic cells. Nat Struct Mol Biol 13:1055-9
Huber, Michael D; Duquette, Michelle L; Shiels, Jerome C et al. (2006) A conserved G4 DNA binding domain in RecQ family helicases. J Mol Biol 358:1071-80

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