Research Topics
Genomes and Genes | Susan S WallaceSummaryAffiliation: University of Vermont Country: USA Publications
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Publications
Solution-state NMR investigation of DNA binding interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): a dynamic description of the DNA/protein interfaceGarry 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...- Biological consequences of free radical-damaged DNA basesSusan 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... - The enigma of endonuclease VIIISusan 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 
The mouse ortholog of NEIL3 is a functional DNA glycosylase in vitro and in vivoMinmin 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....- The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterpartsYin 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... - The C-terminal lysine of Ogg2 DNA glycosylases is a major molecular determinant for guanine/8-oxoguanine distinctionFrédérick 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... - Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoinPierre Aller
Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, Vermont 05405, USA
Biochemistry 49:2502-9. 2010.... - Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylaseFrédérick 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... - Plant and fungal Fpg homologs are formamidopyrimidine DNA glycosylases but not 8-oxoguanine DNA glycosylasesScott 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)... - Rules of engagement for base excision repair in chromatinIan 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... - Structural and biochemical studies of a plant formamidopyrimidine-DNA glycosylase reveal why eukaryotic Fpg glycosylases do not excise 8-oxoguanineStéphanie 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... - Overproduction, crystallization and preliminary crystallographic analysis of a novel human DNA-repair enzyme that recognizes oxidative DNA damageViswanath 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... - Structural characterization of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase in its apo form and in complex with 8-oxodeoxyguanosineFrédérick 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... - Clostridium acetobutylicum 8-oxoguanine DNA glycosylase (Ogg) differs from eukaryotic Oggs with respect to opposite base discriminationSusan 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.... - A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycolPierre 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.... - 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 familyMatthew Hogg
Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
J Biol Chem 282:1432-44. 2007.... - Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNAKayo 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... - Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69Matthew 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... - Non-specific DNA binding interferes with the efficient excision of oxidative lesions from chromatin by the human DNA glycosylase, NEIL1Ian 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... - The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active siteKarl 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... - Caught bending the A-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotideKarl E Zahn
Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
Biochemistry 46:10551-61. 2007.... - Bumps in the road: how replicative DNA polymerases see DNA damageMatthew 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... - Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNAKayo 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... - Human endonuclease VIII-like (NEIL) proteins in the giant DNA MimivirusViswanath 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.... - Expression and purification of active mouse and human NEIL3 proteinsMinmin 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... - Base excision repair and cancerSusan 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... - Using shifts in amino acid frequency and substitution rate to identify latent structural characters in base-excision repair enzymesRamiro 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... - A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complexPierre Aller
Department of Microbiology andMolecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
J Mol Biol 412:22-34. 2011.... - Nucleosome disruption by DNA ligase III-XRCC1 promotes efficient base excision repairIan 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... - DNA polymerases provide a canon of strategies for translesion synthesis past oxidatively generated lesionsKarl 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.... - Engineering functional changes in Escherichia coli endonuclease III based on phylogenetic and structural analysesTakashi 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... - Base excision repair by hNTH1 and hOGG1: a two edged sword in the processing of DNA damage in gamma-irradiated human cellsNing 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... - Kinetics of error generation in homologous B-family DNA polymerasesMatthew 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... - Oxidative DNA glycosylases: recipes from cloning to characterizationViswanath 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... - Rapid determination of the active fraction of DNA repair glycosylases: a novel fluorescence assay for trapped intermediatesJeffrey 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... - Single-stranded breaks in DNA but not oxidative DNA base damages block transcriptional elongation by RNA polymerase II in HeLa cell nuclear extractsScott 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... - Lesion bypass activity of DNA polymerase θ (POLQ) is an intrinsic property of the pol domain and depends on unique sequence insertsMatthew 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... - The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activitySYLVIE 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... - A novel bicistronic vector for overexpressing Mycobacterium tuberculosis proteins in Escherichia coliYin 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... - Initiation of base excision repair of oxidative lesions in nucleosomes by the human, bifunctional DNA glycosylase NTH1Amalthiya 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... - A novel human DNA glycosylase that removes oxidative DNA damage and is homologous to Escherichia coli endonuclease VIIIViswanath 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... - Attempted base excision repair of ionizing radiation damage in human lymphoblastoid cells produces lethal and mutagenic double strand breaksNing 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... 
Structural characterization of a mouse ortholog of human NEIL3 with a marked preference for single-stranded DNAMinmin 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...- Crystal structures of two archaeal 8-oxoguanine DNA glycosylases provide structural insight into guanine/8-oxoguanine distinctionFrédérick 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... - Crystallographic snapshots of a replicative DNA polymerase encountering an abasic siteMatthew 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... - Decline of nuclear and mitochondrial oxidative base excision repair activity in late passage human diploid fibroblastsGuang-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... - Single Qdot-labeled glycosylase molecules use a wedge amino acid to probe for lesions while scanning along DNAAndrew 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... - The Fpg/Nei family of DNA glycosylases: substrates, structures, and search for damageAishwarya 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... - Human DNA polymerase kappa bypasses and extends beyond thymine glycols during translesion synthesis in vitro, preferentially incorporating correct nucleotidesPaula 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... - 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 musclesYoshiko 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.... - Base excision repair: NMR backbone assignments of Escherichia coli formamidopyrimidine-DNA glycosylaseGarry W Buchko
J Biomol NMR 22:301-2. 2002 - Characterization of a novel metabolic strategy used by drug-resistant tumor cellsMary-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...