SYLVIE DOUBLIE

Summary

Affiliation: University of Vermont
Country: USA

Publications

  1. pmc Crystal structure of the 25 kDa subunit of human cleavage factor Im
    Molly Coseno
    Department of Microbiology and Department of Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
    Nucleic Acids Res 36:3474-83. 2008
  2. pmc The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity
    SYLVIE DOUBLIE
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, USA
    Proc Natl Acad Sci U S A 101:10284-9. 2004
  3. pmc The C-terminal lysine of Ogg2 DNA glycosylases is a major molecular determinant for guanine/8-oxoguanine distinction
    Frédérick Faucher
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, USA
    J Mol Biol 397:46-56. 2010
  4. pmc Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase
    Frédérick Faucher
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, USA
    DNA Repair (Amst) 8:1283-9. 2009
  5. ncbi request reprint Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family
    Matthew Hogg
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
    J Biol Chem 282:1432-44. 2007
  6. pmc Structural studies of a bacterial tRNA(HIS) guanylyltransferase (Thg1)-like protein, with nucleotide in the activation and nucleotidyl transfer sites
    Samantha J Hyde
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
    PLoS ONE 8:e67465. 2013
  7. ncbi request reprint Bumps in the road: how replicative DNA polymerases see DNA damage
    Matthew Hogg
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
    Curr Opin Struct Biol 15:86-93. 2005
  8. pmc Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin
    Pierre Aller
    Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, Vermont 05405, USA
    Biochemistry 49:2502-9. 2010
  9. pmc The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site
    Karl E Zahn
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, United States
    Biochemistry 50:10350-8. 2011
  10. pmc Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing
    Qin Yang
    Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
    Proc Natl Acad Sci U S A 107:10062-7. 2010

Collaborators

Detail Information

Publications42

  1. pmc Crystal structure of the 25 kDa subunit of human cleavage factor Im
    Molly Coseno
    Department of Microbiology and Department of Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
    Nucleic Acids Res 36:3474-83. 2008
    ....
  2. pmc The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity
    SYLVIE DOUBLIE
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, USA
    Proc Natl Acad Sci U S A 101:10284-9. 2004
    ..This "zincless finger" appears to be required for NEIL1 activity, because mutating a very highly conserved arginine within this motif greatly reduces the glycosylase activity of the enzyme...
  3. pmc The C-terminal lysine of Ogg2 DNA glycosylases is a major molecular determinant for guanine/8-oxoguanine distinction
    Frédérick Faucher
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, USA
    J Mol Biol 397:46-56. 2010
    ..Furthermore, this work provides a structural rationale for the lack of opposite base specificity in this family of enzymes...
  4. pmc Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase
    Frédérick Faucher
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, USA
    DNA Repair (Amst) 8:1283-9. 2009
    ..A structural comparison with human OGG1 provides a rationale for the lack of opposite base specificity displayed by the bacterial Ogg...
  5. ncbi request reprint Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family
    Matthew Hogg
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
    J Biol Chem 282:1432-44. 2007
    ....
  6. pmc Structural studies of a bacterial tRNA(HIS) guanylyltransferase (Thg1)-like protein, with nucleotide in the activation and nucleotidyl transfer sites
    Samantha J Hyde
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
    PLoS ONE 8:e67465. 2013
    ..The BtTLP structural data, combined with kinetic analysis of selected variants, provide new insight into the role of key residues in the activation step. ..
  7. ncbi request reprint Bumps in the road: how replicative DNA polymerases see DNA damage
    Matthew Hogg
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
    Curr Opin Struct Biol 15:86-93. 2005
    ..These structures illustrate why some lesions can be bypassed readily, whereas others are strong blocks to DNA replication...
  8. pmc Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin
    Pierre Aller
    Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, Vermont 05405, USA
    Biochemistry 49:2502-9. 2010
    ....
  9. pmc The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site
    Karl E Zahn
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, United States
    Biochemistry 50:10350-8. 2011
    ..Taken together, these data imply that the nonuniform templating by 5-OHC is due to weakened stacking capabilities, which allows dAMP incorporation to proceed in a manner similar to that observed opposite abasic sites...
  10. pmc Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing
    Qin Yang
    Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
    Proc Natl Acad Sci U S A 107:10062-7. 2010
    ..Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap(4)A (diadenosine tetraphosphate) by CFI(m)25 suggests a potential role for small molecules in the regulation of mRNA 3' processing...
  11. pmc Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping
    Qin Yang
    Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, Burlington, VT 05405, USA
    Structure 19:368-77. 2011
    ..The intrinsic ability of CFI(m) to direct RNA looping may provide a mechanism for its function in the regulation of alternative poly(A) site selection...
  12. pmc A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol
    Pierre Aller
    Department of Microbiology and Molecular Genetics, Markey Center for Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, VT 05405, USA
    Proc Natl Acad Sci U S A 104:814-8. 2007
    ....
  13. pmc The E295K cancer variant of human polymerase β favors the mismatch conformational pathway during nucleotide selection
    Brian E Eckenroth
    From the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405 and
    J Biol Chem 288:34850-60. 2013
    ..Comparison with published structures provides insight into the structural rearrangements within pol β that occur during the process of nucleotide discrimination. ..
  14. pmc Structural characterization of a mouse ortholog of human NEIL3 with a marked preference for single-stranded DNA
    Minmin Liu
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, USA
    Structure 21:247-56. 2013
    ..These structural features provide insight into the substrate specificity and marked preference of Neil3 for ssDNA...
  15. pmc Structural and biochemical studies of a plant formamidopyrimidine-DNA glycosylase reveal why eukaryotic Fpg glycosylases do not excise 8-oxoguanine
    Stéphanie Duclos
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, Burlington, VT 05405 0068, USA
    DNA Repair (Amst) 11:714-25. 2012
    ..Although the exact role of the loop remains to be further explored, it is now clear that this protein segment is specific to the processing of 8-oxoG...
  16. pmc Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA
    Kayo Imamura
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
    J Biol Chem 287:4288-98. 2012
    ..This finding suggests that lesion recognition by Nei occurs before the damaged base flips into the glycosylase active site...
  17. ncbi request reprint Caught bending the A-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide
    Karl E Zahn
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
    Biochemistry 46:10551-61. 2007
    ....
  18. ncbi request reprint Overproduction, crystallization and preliminary crystallographic analysis of a novel human DNA-repair enzyme that recognizes oxidative DNA damage
    Viswanath Bandaru
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, USA
    Acta Crystallogr D Biol Crystallogr 60:1142-4. 2004
    ..The unliganded NEIL1 crystallizes in space group R3, with unit-cell parameters a = b = 132.2, c = 51.1 A. Complete data sets were collected from native, selenomethionyl and iodinated NEIL1 to 2.1, 2.3 and 2.4 angstroms, respectively...
  19. pmc Crystal structure of human poly(a) polymerase gamma reveals a conserved catalytic core for canonical poly(a) polymerases
    Qin Yang
    Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, USA Electronic address
    J Mol Biol 426:43-50. 2014
    ..The structure revealed that PAPγ closely resembles its PAPα ortholog. An analysis of residue conservation reveals a conserved catalytic binding pocket, whereas residues at the surface of the polymerase are more divergent. ..
  20. pmc Structural characterization of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase in its apo form and in complex with 8-oxodeoxyguanosine
    Frédérick Faucher
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, USA
    J Mol Biol 387:669-79. 2009
    ..A structural comparison of CacOgg with human OGG1, in complex with 8-oxoG containing DNA, provides a structural rationale for the lack of opposite base specificity displayed by CacOgg...
  21. pmc Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69
    Matthew Hogg
    Department of Microbiology and Molecular Genetics, 95 Carrigan Drive, University of Vermont, Burlington, Vermont 05405, USA
    Biochemistry 49:2317-25. 2010
    ..We have also solved the crystal structure of the L561A variant forming an 8-oxoG.dATP mispair and show that the propensity for forming this mispair depends on an enlarged polymerase active site...
  22. pmc A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex
    Pierre Aller
    Department of Microbiology andMolecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
    J Mol Biol 412:22-34. 2011
    ....
  23. pmc Crystal structure of DNA polymerase β with DNA containing the base lesion spiroiminodihydantoin in a templating position
    Brian E Eckenroth
    Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont 05405, United States
    Biochemistry 53:2075-7. 2014
    ..The resulting conformation positions the dSp1 A-ring as the base-pairing face whereas the B-ring of dSp1 protrudes into the major groove. ..
  24. pmc Neil3, the final frontier for the DNA glycosylases that recognize oxidative damage
    Minmin Liu
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405 0086, USA
    Mutat Res 743:4-11. 2013
    ..Although the biological functions of Neil3 still remain an enigma, this review highlights recent biochemical and structural data that may ultimately shed light on its biological role...
  25. ncbi request reprint Infidelity out in the open
    SYLVIE DOUBLIE
    Department of Microbiology and Molecular Genetics, The University of Vermont, Burlington, VT 05405, USA
    Structure 12:1749-50. 2004
    ..this issue of Structure). The N-domain of the polymerase, which is closed when the correct nucleotide pairs with the template base, adopts a partially open conformation suboptimal for catalysis...
  26. pmc DNA polymerases provide a canon of strategies for translesion synthesis past oxidatively generated lesions
    Karl E Zahn
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
    Curr Opin Struct Biol 21:358-69. 2011
    ....
  27. pmc Purification, crystallization and preliminary X-ray diffraction of a disulfide cross-linked complex between bovine poly(A) polymerase and a chemically modified 15-mer oligo(A) RNA
    Qin Yang
    Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, Vermont 05405, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 67:241-4. 2011
    ..The crystals, which belonged to space group P2 and harbored two protein-RNA complexes per asymmetric unit, diffracted X-rays to 2.25 Å resolution...
  28. pmc Lesion bypass activity of DNA polymerase θ (POLQ) is an intrinsic property of the pol domain and depends on unique sequence inserts
    Matthew Hogg
    Department of Microbiology and Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, VT 05405, USA
    J Mol Biol 405:642-52. 2011
    ..However, removal of insertions 2 and 3 reduces activity on undamaged DNA and completely abrogates the ability of the enzyme to bypass abasic sites or thymine glycol lesions...
  29. pmc Structural investigation of a viral ortholog of human NEIL2/3 DNA glycosylases
    Aishwarya Prakash
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, United States
    DNA Repair (Amst) 12:1062-71. 2013
    ..Mutation of the adjacent His73 causes the enzyme to be more productive thereby suggesting a plausible role for this residue in the DNA lesion search process. ..
  30. pmc The structure of human cleavage factor I(m) hints at functions beyond UGUA-specific RNA binding: a role in alternative polyadenylation and a potential link to 5' capping and splicing
    Qin Yang
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT, USA
    RNA Biol 8:748-53. 2011
    ....
  31. pmc Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA
    Kayo Imamura
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405 0068, USA
    J Biol Chem 284:26174-83. 2009
    ..In the MvNei1.tetrahydrofuran complex a tyrosine located at the tip of the putative lesion recognition loop stacks against the furan ring; the tyrosine is predicted to adopt a different conformation to accommodate a modified base...
  32. pmc The Fpg/Nei family of DNA glycosylases: substrates, structures, and search for damage
    Aishwarya Prakash
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, Vermont, USA
    Prog Mol Biol Transl Sci 110:71-91. 2012
    ..This review summarizes the current structural knowledge of the Fpg/Nei family members, emphasizes their substrate specificities, and describes how these enzymes search for lesions...
  33. pmc Genome and cancer single nucleotide polymorphisms of the human NEIL1 DNA glycosylase: Activity, structure, and the effect of editing
    Aishwarya Prakash
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405 0068, United States
    DNA Repair (Amst) 14:17-26. 2014
    ....
  34. pmc Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site
    Matthew Hogg
    Department of Microbiology and Molecular Genetics, Markey Center for Molecular Genetics, University of Vermont, Burlington, VT, USA
    EMBO J 23:1483-93. 2004
    ..The polymerase incorporates dAMP across the lesion under crystallization conditions, indicating that the different conformations observed in the crystal may be part of the active site switching reaction pathway...
  35. doi request reprint The soul of a new structure-function machine
    SYLVIE DOUBLIE
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
    Structure 16:3-4. 2008
  36. pmc Structural biology of poly(A) site definition
    Qin Yang
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, USA
    Wiley Interdiscip Rev RNA 2:732-47. 2011
    ..WIREs RNA 2011 2 732-747 DOI: 10.1002/wrna.88 For further resources related to this article, please visit the WIREs website...
  37. pmc Phosphonoformic acid inhibits viral replication by trapping the closed form of the DNA polymerase
    Karl E Zahn
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
    J Biol Chem 286:25246-55. 2011
    ..The closed state of the fingers domain traps the variant polymerase in the untranslocated state and increases affinity for PFA. This finding provides a model for the mechanism of UL54 stalling by PFA...
  38. pmc Crystal structures of two archaeal 8-oxoguanine DNA glycosylases provide structural insight into guanine/8-oxoguanine distinction
    Frédérick Faucher
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, Burlington, VT 05405 0068, USA
    Structure 17:703-12. 2009
    ..This prediction was substantiated by measuring the glycosylase/lyase activity of a C-terminal deletion mutant of MjaOgg...
  39. pmc Structural and functional analysis of the CspB protease required for Clostridium spore germination
    Chloe M Adams
    Graduate Program in Cell, Molecular and Biomedical Sciences, University of Vermont, Burlington, Vermont, United States of America
    PLoS Pathog 9:e1003165. 2013
    ..difficile. Collectively, our study provides the first molecular insight into CspB activity and function. These studies may inform the development of inhibitors that can prevent clostridial spore germination and thus disease transmission...
  40. pmc tRNA(His) guanylyltransferase (THG1), a unique 3'-5' nucleotidyl transferase, shares unexpected structural homology with canonical 5'-3' DNA polymerases
    Samantha J Hyde
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
    Proc Natl Acad Sci U S A 107:20305-10. 2010
    ..The ability of the same structural architecture to catalyze both 5'-3' and 3'-5' reactions raises important questions concerning selection of the 5'-3' mechanism during the evolution of nucleotide polymerases...
  41. ncbi request reprint Crystallographic software: a sustainable resource for the community
    Stephen J Everse
    Department of Biochemistry, University of Vermont, Burlington, VT, USA
    Methods Mol Biol 364:273-8. 2007
    ..Links to download the programs, available tutorials, and references to cite when using the program/site are also provided...
  42. ncbi request reprint Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog
    Karen S Champagne
    Department of Microbiology and Molecular Genetics and Biochemistry, University of Vermont, Burlington, Vermont 05405, USA
    J Biol Chem 280:34096-104. 2005
    ....

Research Grants8

  1. CRYSTALLOGRAPHIC STUDIES OF EUKARYOTIC POLY(A)POLYMERASE
    SYLVIE DOUBLIE; Fiscal Year: 2001
    ..It is expected that these results will not only provide a sound structural basis for understanding the mechanism of polyadenylation at the molecular level but will also shed light on the mechanisms of processivity and repression. ..
  2. CRYSTALLOGRAPHIC STUDIES OF EUKARYOTIC POLY(A)POLYMERASE
    SYLVIE DOUBLIE; Fiscal Year: 2006
    ..It is expected that these results will not only provide a sound structural basis for understanding the mechanism of polyadenylation at the molecular level but will also shed light on the mechanisms of processivity and repression. ..
  3. Processing of Radiation Damage by Translesion DNA Synthesis
    SYLVIE DOUBLIE; Fiscal Year: 2009
    ..This research bears directly on public health since it addresses the fundamental mechanisms underpinning cell killing and mutagenesis by therapeutic levels of ionizing radiation. ..
  4. Processing of Radiation Damage by Translesion DNA Synthesis
    SYLVIE DOUBLIE; Fiscal Year: 2010
    ..This research bears directly on public health since it addresses the fundamental mechanisms underpinning cell killing and mutagenesis by therapeutic levels of ionizing radiation. ..
  5. CRYSTALLOGRAPHIC STUDIES OF EUKARYOTIC POLY(A)POLYMERASE
    SYLVIE DOUBLIE; Fiscal Year: 2002
    ..It is expected that these results will not only provide a sound structural basis for understanding the mechanism of polyadenylation at the molecular level but will also shed light on the mechanisms of processivity and repression. ..
  6. CRYSTALLOGRAPHIC STUDIES OF EUKARYOTIC POLY(A)POLYMERASE
    SYLVIE DOUBLIE; Fiscal Year: 2003
    ..It is expected that these results will not only provide a sound structural basis for understanding the mechanism of polyadenylation at the molecular level but will also shed light on the mechanisms of processivity and repression. ..
  7. CRYSTALLOGRAPHIC STUDIES OF EUKARYOTIC POLY(A)POLYMERASE
    SYLVIE DOUBLIE; Fiscal Year: 2004
    ..It is expected that these results will not only provide a sound structural basis for understanding the mechanism of polyadenylation at the molecular level but will also shed light on the mechanisms of processivity and repression. ..