Susan S Wallace

Summary

Affiliation: University of Vermont
Country: USA

Publications

  1. ncbi request reprint Solution-state NMR investigation of DNA binding interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): a dynamic description of the DNA/protein interface
    Garry W Buchko
    Biological Sciences Division, Battelle, Pacific Northwest National Laboratory, P O Box 999, Richland, WA 99352, USA
    DNA Repair (Amst) 4:327-39. 2005
  2. ncbi request reprint Biological consequences of free radical-damaged DNA bases
    Susan S Wallace
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, VT 05405 0068, USA
    Free Radic Biol Med 33:1-14. 2002
  3. ncbi request reprint The enigma of endonuclease VIII
    Susan S Wallace
    Department of Microbiology and Molecular Genetics, Markey Center for Molecular Genetics, University of Vermont, 95 Carrigan Drive, Stafford Hall, Burlington, VT 05405 0068, USA
    DNA Repair (Amst) 2:441-53. 2003
  4. pmc The mouse ortholog of NEIL3 is a functional DNA glycosylase in vitro and in vivo
    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 0086, USA
    Proc Natl Acad Sci U S A 107:4925-30. 2010
  5. pmc The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts
    Yin Guo
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Dr, Burlington, VT 05405 0068, United States
    DNA Repair (Amst) 9:177-90. 2010
  6. 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
  7. 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
  8. 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
  9. pmc Plant and fungal Fpg homologs are formamidopyrimidine DNA glycosylases but not 8-oxoguanine DNA glycosylases
    Scott D Kathe
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT 05405 0068, United States
    DNA Repair (Amst) 8:643-53. 2009
  10. 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

Collaborators

Detail Information

Publications60

  1. ncbi request reprint Solution-state NMR investigation of DNA binding interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): a dynamic description of the DNA/protein interface
    Garry W Buchko
    Biological Sciences Division, Battelle, Pacific Northwest National Laboratory, P O Box 999, Richland, WA 99352, USA
    DNA Repair (Amst) 4:327-39. 2005
    ..Such motion, especially at the DNA binding surface, may be key to its processive search for DNA damage and its catalytic functions once it recognizes damaged DNA...
  2. ncbi request reprint Biological consequences of free radical-damaged DNA bases
    Susan S Wallace
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, VT 05405 0068, USA
    Free Radic Biol Med 33:1-14. 2002
    ..Taken together, the data suggest that the principal biological consequences of endogenously produced and unrepaired free radical-damaged DNA bases are mutations...
  3. ncbi request reprint The enigma of endonuclease VIII
    Susan S Wallace
    Department of Microbiology and Molecular Genetics, Markey Center for Molecular Genetics, University of Vermont, 95 Carrigan Drive, Stafford Hall, Burlington, VT 05405 0068, USA
    DNA Repair (Amst) 2:441-53. 2003
  4. pmc The mouse ortholog of NEIL3 is a functional DNA glycosylase in vitro and in vivo
    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 0086, USA
    Proc Natl Acad Sci U S A 107:4925-30. 2010
    ....
  5. pmc The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts
    Yin Guo
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Dr, Burlington, VT 05405 0068, United States
    DNA Repair (Amst) 9:177-90. 2010
    ..The kinetic parameters of the MtuFpg1, MtuNei1 and MtuNth proteins on selected substrates were also determined and compared to those of their E. coli homologs...
  6. 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...
  7. 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
    ....
  8. 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...
  9. pmc Plant and fungal Fpg homologs are formamidopyrimidine DNA glycosylases but not 8-oxoguanine DNA glycosylases
    Scott D Kathe
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT 05405 0068, United States
    DNA Repair (Amst) 8:643-53. 2009
    ..Surprisingly, the activity of AthFpg1 on an AP site opposite a G was extremely robust with a k(obs) of over 2500min(-1)...
  10. 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...
  11. pmc Rules of engagement for base excision repair in chromatin
    Ian D Odell
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
    J Cell Physiol 228:258-66. 2013
    ..This review highlights studies of how oxidatively damaged DNA in nucleosomes is discovered and repaired, and offers a working model of events associated with BER in chromatin that we hope will have heuristic value...
  12. 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...
  13. 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
    ....
  14. 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
    ....
  15. 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...
  16. 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...
  17. pmc Clostridium acetobutylicum 8-oxoguanine DNA glycosylase (Ogg) differs from eukaryotic Oggs with respect to opposite base discrimination
    Susan M Robey-Bond
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont 05405 0068, USA
    Biochemistry 47:7626-36. 2008
    ....
  18. 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...
  19. pmc Non-specific DNA binding interferes with the efficient excision of oxidative lesions from chromatin by the human DNA glycosylase, NEIL1
    Ian D Odell
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, United States
    DNA Repair (Amst) 9:134-43. 2010
    ..These results suggest that, in vivo, NEIL1 functions either at nucleosome-free regions (such as those near replication forks) or with cofactors that limit its non-specific binding to DNA...
  20. 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...
  21. 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...
  22. pmc Contribution of DNA unwrapping from histone octamers to the repair of oxidatively damaged DNA in nucleosomes
    Robyn L Maher
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
    DNA Repair (Amst) 12:964-71. 2013
    ..Thus, chromatin remodeling, either BER-specific or that associated with transcription, replication, or other DNA repair processes, probably contributes to efficient BER in vivo...
  23. pmc Neil3 and NEIL1 DNA glycosylases remove oxidative damages from quadruplex DNA and exhibit preferences for lesions in the telomeric sequence context
    Jia Zhou
    From the Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, Vermont 05405 0068 and
    J Biol Chem 288:27263-72. 2013
    ....
  24. 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...
  25. 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
    ....
  26. 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...
  27. pmc Human endonuclease VIII-like (NEIL) proteins in the giant DNA Mimivirus
    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, United States
    DNA Repair (Amst) 6:1629-41. 2007
    ....
  28. pmc Base excision repair and cancer
    Susan S Wallace
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, 05405 0068, United States
    Cancer Lett 327:73-89. 2012
    ..The biallelic germ line mutations that result in MUTYH-associated colon cancer are also discussed...
  29. pmc Expression and purification of active mouse and human NEIL3 proteins
    Minmin Liu
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Dr Burlington, VT 05405 0086, USA
    Protein Expr Purif 84:130-9. 2012
    ..The purified Neil3 proteins are suitable for biochemical, structural and functional studies...
  30. pmc Using shifts in amino acid frequency and substitution rate to identify latent structural characters in base-excision repair enzymes
    Ramiro Barrantes-Reynolds
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
    PLoS ONE 6:e25246. 2011
    ..Structural motifs may serve as important phylogenetic characters and modeling transitions involving structural motifs may provide a much deeper understanding of protein evolution...
  31. pmc Nucleosome disruption by DNA ligase III-XRCC1 promotes efficient base excision repair
    Ian D Odell
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
    Mol Cell Biol 31:4623-32. 2011
    ..Collectively, these findings provide insights into rate-limiting steps that govern BER in chromatin and reveal a unique role for ligase IIIα-XRCC1 in enhancing the efficiency of the final two steps in the BER of lesions in nucleosomes...
  32. 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
    ....
  33. ncbi request reprint Engineering functional changes in Escherichia coli endonuclease III based on phylogenetic and structural analyses
    Takashi Watanabe
    Department of Microbiology and Molecular Genetics, The University of Vermont, Burlington, Vermont 05405, USA
    J Biol Chem 280:34378-84. 2005
    ..Thus phylogeny-based scanning mutagenesis has allowed us to identify novel roles for amino acids in the substrate binding pocket of EcoNth in base recognition and/or catalysis...
  34. ncbi request reprint Base excision repair by hNTH1 and hOGG1: a two edged sword in the processing of DNA damage in gamma-irradiated human cells
    Ning Yang
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, 95 Carrigan Drive, Stafford Hall, Burlington, VT 05405 0068, USA
    DNA Repair (Amst) 5:43-51. 2006
    ..Here, overexpression of hNTH1 and hOGG1 resulted in reduced cell killing while suppression of glycosylase expression resulted in elevated cell death...
  35. pmc Kinetics of error generation in homologous B-family DNA polymerases
    Matthew Hogg
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
    Nucleic Acids Res 34:2528-35. 2006
    ..These results show that there are kinetic differences between the two enzymes but they are not large enough to preclude structural assumptions for T4 DNA polymerase based on the known structure of the RB69 DNA polymerase...
  36. 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
    ....
  37. 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...
  38. ncbi request reprint Oxidative DNA glycosylases: recipes from cloning to characterization
    Viswanath Bandaru
    Department of Microbiology and Molecular Genetics, Markey Center for Molecular Genetics, University of Vermont, Burlington, USA
    Methods Enzymol 408:15-33. 2006
    ..These methodologies can be translated readily to novel DNA glycosylases or to DNA glycosylases that recognize other types of DNA damages...
  39. 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...
  40. 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...
  41. pmc Rapid determination of the active fraction of DNA repair glycosylases: a novel fluorescence assay for trapped intermediates
    Jeffrey O Blaisdell
    Department of Microbiology and Molecular Genetics, Markey Center for Molecular Genetics, University of Vermont, Burlington, VT, USA
    Nucleic Acids Res 35:1601-11. 2007
    ..The validity of the approach was demonstrated by direct comparison with current gel-based methods. Additionally, the results are supported by in silico modeling based on available crystal structures...
  42. ncbi request reprint Single-stranded breaks in DNA but not oxidative DNA base damages block transcriptional elongation by RNA polymerase II in HeLa cell nuclear extracts
    Scott D Kathe
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, Vermont 05405 0068, USA
    J Biol Chem 279:18511-20. 2004
    ..Thus, DNA strand breaks but not oxidative DNA base damages blocked transcription by RNA polymerase II...
  43. ncbi request reprint A novel human DNA glycosylase that removes oxidative DNA damage and is homologous to Escherichia coli endonuclease VIII
    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
    DNA Repair (Amst) 1:517-29. 2002
    ..Furthermore, inactivation of active site residues shown to be important in Escherichia coli Nei inactivate the human enzyme. The hNEI1 gene is located on the long arm of chromosome 15 that is frequently deleted in human cancers...
  44. pmc Initiation of base excision repair of oxidative lesions in nucleosomes by the human, bifunctional DNA glycosylase NTH1
    Amalthiya Prasad
    Department of Microbiology and Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, VT 05405, USA
    Mol Cell Biol 27:8442-53. 2007
    ..These observations suggest that access to sterically occluded lesions entails the partial, reversible unwrapping of DNA from the histone octamer, allowing hNTH1 to capture its DNA substrate when it is in an unwound state...
  45. pmc A novel bicistronic vector for overexpressing Mycobacterium tuberculosis proteins in Escherichia coli
    Yin Guo
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Dr Burlington, VT 05405 0068, USA
    Protein Expr Purif 65:230-7. 2009
    ..Thus the bicistronic expression system can be used to improve translation efficiency of mRNAs and achieve high-level expression of mycobacterial genes in E. coli...
  46. ncbi request reprint Attempted base excision repair of ionizing radiation damage in human lymphoblastoid cells produces lethal and mutagenic double strand breaks
    Ning Yang
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, 95 Carrigan Drive, Stafford Hall, Burlington, VT 05405 0068, USA
    DNA Repair (Amst) 3:1323-34. 2004
    ..These data show that attempted repair of radiation damage, presumably at clustered damage sites, by the oxidative DNA glycosylases can lead to the formation of potentially lethal and mutagenic double strand breaks in human cells...
  47. pmc Two glycosylase families diffusively scan DNA using a wedge residue to probe for and identify oxidatively damaged bases
    Shane R Nelson
    Department of Molecular Physiology and Biophysics, The University of Vermont, Burlington, VT 05405 0075 and
    Proc Natl Acad Sci U S A 111:E2091-9. 2014
    ....
  48. 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. ..
  49. ncbi request reprint 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...
  50. 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...
  51. 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...
  52. 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
    ....
  53. pmc Single Qdot-labeled glycosylase molecules use a wedge amino acid to probe for lesions while scanning along DNA
    Andrew R Dunn
    The Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
    Nucleic Acids Res 39:7487-98. 2011
    ..The search mechanism for an Fpg variant, F111A, lacking a phenylalanine wedge residue no longer displayed slow, sub-diffusive motion compared to wild type, suggesting that Fpg base interrogation may be accomplished by Phe(111) insertion...
  54. ncbi request reprint Decline of nuclear and mitochondrial oxidative base excision repair activity in late passage human diploid fibroblasts
    Guang Ping Shen
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, 95 Carrigan Drive, Stafford Hall, Burlington, VT 05405 0068, USA
    DNA Repair (Amst) 2:673-93. 2003
    ..Taken together the data support the concept that the increase in oxidative damage in the mitochondrial DNA of senescing cells and tissues from aging animals is due to reduced base excision repair activity...
  55. pmc DNA glycosylases search for and remove oxidized DNA bases
    Susan S Wallace
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, Vermont
    Environ Mol Mutagen 54:691-704. 2013
    ..Also single-molecule approaches show that DNA glycosylases search for their substrates in a sea of undamaged DNA by using a wedge residue that is inserted into the DNA helix to probe for the presence of damage...
  56. pmc Germ-line variant of human NTH1 DNA glycosylase induces genomic instability and cellular transformation
    Heather A Galick
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT 05405 0068, USA
    Proc Natl Acad Sci U S A 110:14314-9. 2013
    ..The DNA damage response is also activated in D239Y-expressing cells. In combination, our data suggest that individuals possessing the D239Y variant are at risk for genomic instability and cancer. ..
  57. ncbi request reprint Human DNA polymerase kappa bypasses and extends beyond thymine glycols during translesion synthesis in vitro, preferentially incorporating correct nucleotides
    Paula L Fischhaber
    Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9072, USA
    J Biol Chem 277:37604-11. 2002
    ..Our findings suggest a role for polkappa in both nonmutagenic and mutagenic bypass of oxidative damage...
  58. ncbi request reprint Base excision repair: NMR backbone assignments of Escherichia coli formamidopyrimidine-DNA glycosylase
    Garry W Buchko
    J Biomol NMR 22:301-2. 2002
  59. ncbi request reprint Characterization of a novel metabolic strategy used by drug-resistant tumor cells
    Mary Ellen Harper
    Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
    FASEB J 16:1550-7. 2002
    ..In addition, drug-resistant cells express high levels of mitochondrial uncoupling protein 2 (UCP2). The discovery of this metabolic strategy potentially facilitates the design of novel therapeutic approaches to drug resistance...
  60. ncbi request reprint A new technique for the quantitative assessment of 8-oxoguanine in nuclear DNA as a marker of oxidative stress. Application to dystrophin-deficient DMD skeletal muscles
    Yoshiko Nakae
    Department of Oral and Maxillofacial Anatomy, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima 770 8504, Japan
    Histochem Cell Biol 124:335-45. 2005
    ....