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DNA Repair & Mutagenesis
Publications Archive
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2004 Publications
Affatato AA, Wolfe KJ, Lopez MS, Hallberg C, Ammenheuser MM,
Abdel-Rahman SZ. 2004. Effect of XPD/ERCC2 polymorphisms on chromosome
aberration frequencies in smokers and on sensitivity to the mutagenic
tobacco-specific nitrosamine NNK. Environ Mol Mutagen44 (1):65-73.
Albrecht T, Deng CZ, Abdel-Rahman SZ, Fons M, Cinciripini P, El-Zein RA.
2004. Differential mutagen sensitivity of peripheral blood lymphocytes
from smokers and nonsmokers: effect of human cytomegalovirus infection.
Environ Mol Mutagen43 (3):169-78.
Bassett SE, Fennewald SM, King DJ, Li X, Herzog NK, Shope R, Aronson JF,
Luxon BA, Gorenstein DG. 2004 Jul 20. Combinatorial selection and edited
combinatorial selection of phosphorothioate aptamers targeting human
nuclear factor-kappaB RelA/p50 and RelA/RelA. Biochemistry43
(28):9105-15.
Bhakat KK, Hazra TK, Mitra S. 2004. Acetylation of the human DNA
glycosylase NEIL2 and inhibition of its activity. Nucleic Acids Res32
(10):3033-9.
Connor LM, Ballinger CA, Albrecht TB, Postlethwait EM. 2004 Jun.
Interfacial phospholipids inhibit ozone-reactive absorption-mediated
cytotoxicity in vitro. Am J Physiol Lung Cell Mol Physiol286
(6):L1169-78.
Das A, Rajagopalan L, Mathura VS, Rigby SJ, Mitra S, Hazra TK. 2004 Nov
5. Identification of a zinc finger domain in the human NEIL2
(Nei-like-2) protein. J Biol Chem279 (45):47132-8.
Ding SZ, O'Hara AM, Denning TL, Dirden-Kramer B, Mifflin RC, Reyes VE,
Ryan KA, Elliott SN, Izumi T, Boldogh I, Mitra S, Ernst PB, Crowe SE.
2004 Sep. Helicobacter pylori and H2O2 increase AP endonuclease-1/redox
factor-1 expression in human gastric epithelial cells.
Gastroenterology127 (3):845-58.
Galletto R, Jezewska MJ, Bujalowski W. 2004 Oct 8. Unzipping mechanism
of the double-stranded DNA unwinding by a hexameric helicase: the effect
of the 3' arm and the stability of the dsDNA on the unwinding activity
of the Escherichia coli DnaB helicase. J Mol Biol343 (1):101-14.
Galletto R, Jezewska MJ, Bujalowski W. 2004 Oct 8. Unzipping mechanism
of the double-stranded DNA unwinding by a hexameric helicase:
quantitative analysis of the rate of the dsDNA unwinding, processivity
and kinetic step-size of the Escherichia coli DnaB helicase using rapid
quench-flow method. J Mol Biol343 (1):83-99.
Galletto R, Jezewska MJ, Bujalowski W. 2004 Aug 31. Multistep sequential
mechanism of Escherichia coli helicase PriA protein-ssDNA interactions.
Kinetics and energetics of the active ssDNA-searching site of the
enzyme. Biochemistry43 (34):11002-16.
Galletto R, Maillard R, Jezewska MJ, Bujalowski W. 2004 Aug 31. Global
conformation of the Escherichia coli replication factor DnaC protein in
absence and presence of nucleotide cofactors. Biochemistry43
(34):10988-1001.
Guzder SN, Torres-Ramos C, Johnson RE, Haracska L, Prakash L, Prakash S.
2004 Sep 15. Requirement of yeast Rad1-Rad10 nuclease for the removal of
3'-blocked termini from DNA strand breaks induced by reactive oxygen
species. Genes Dev18 (18):2283-91.
Haracska L, Torres-Ramos CA, Johnson RE, Prakash S, Prakash L. 2004 May.
Opposing effects of ubiquitin conjugation and SUMO modification of PCNA
on replicational bypass of DNA lesions in Saccharomyces cerevisiae. Mol
Cell Biol24 (10):4267-74.
Ivanciuc O, Oezguen N, Mathura VS, Schein CH, Xu Y, Braun W. 2004 Mar.
Using property based sequence motifs and 3D modeling to determine
structure and functional regions of proteins. Curr Med Chem11
(5):583-93.
Izumi T, Schein CH, Oezguen N, Feng Y, Braun W. 2004 Jan 27. Effects of
backbone contacts 3' to the abasic site on the cleavage and the product
binding by human apurinic/apyrimidinic endonuclease (APE1).
Biochemistry43 (3):684-9.
Jezewska MJ, Galletto R, Bujalowski W. 2004 Oct 8. Interactions of the
RepA helicase hexamer of plasmid RSF1010 with the ssDNA. Quantitative
analysis of stoichiometries, intrinsic affinities, cooperativities, and
heterogeneity of the total ssDNA-binding site. J Mol Biol343 (1):115-36.
Kumar R, Volk DE, Li J, Lee JC, Gorenstein DG, Thompson EB. 2004 Nov 23.
TATA box binding protein induces structure in the recombinant
glucocorticoid receptor AF1 domain. Proc Natl Acad Sci U S A101
(47):16425-30.
Lee YC, Volk DE, Thiviyanathan V, Kleerekoper Q, Gribenko AV, Zhang S,
Gorenstein DG, Makhatadze GI, Luxon BA. 2004 Jul. NMR structure of the
Apo-S100P protein. J Biomol NMR29 (3):399-402.
Mokkapati SK, Wiederhold L, Hazra TK, Mitra S. 2004 Sep 14. Stimulation
of DNA glycosylase activity of OGG1 by NEIL1: functional collaboration
between two human DNA glycosylases. Biochemistry43 (36):11596-604.
Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. 2004 Jul 15.
Replication by human DNA polymerase-iota occurs by Hoogsteen
base-pairing. Nature430 (6997):377-80.
Painter SD, Cummins SF, Nichols AE, Akalal DB, Schein CH, Braun W, Smith
JS, Susswein AJ, Levy M, de Boer PA, ter Maat A, Miller MW, Scanlan C,
Milberg RM, Sweedler JV, Nagle GT. 2004 May 4. Structural and functional
analysis of Aplysia attractins, a family of water-borne protein
pheromones with interspecific attractiveness. Proc Natl Acad Sci U S
A101 (18):6929-33.
Paolini M, Perocco P, Canistro D, Valgimigli L, Pedulli GF, Iori R,
Croce CD, Cantelli-Forti G, Legator MS, Abdel-Rahman SZ. 2004 Jan.
Induction of cytochrome P450, generation of oxidative stress and in
vitro cell-transforming and DNA-damaging activities by glucoraphanin,
the bioprecursor of the chemopreventive agent sulforaphane found in
broccoli. Carcinogenesis25 (1):61-7.
Ribar B, Izumi T, Mitra S. 2004. The major role of human AP-endonuclease
homolog Apn2 in repair of abasic sites in Schizosaccharomyces pombe.
Nucleic Acids Res32 (1):115-26.
Rijnbrand R, Thiviyanathan V, Kaluarachchi K, Lemon SM, Gorenstein DG.
2004 Oct 29. Mutational and structural analysis of stem-loop IIIC of the
hepatitis C virus and GB virus B internal ribosome entry sites. J Mol
Biol343 (4):805-17.
Szczesny B, Bhakat KK, Mitra S, Boldogh I. 2004 Oct-Nov. Age-dependent
modulation of DNA repair enzymes by covalent modification and
subcellular distribution. Mech Ageing Dev125 (10-11):755-65.
Thiviyanathan V, Yang Y, Kaluarachchi K, Rijnbrand R, Gorenstein DG,
Lemon SM. 2004 Aug 24. High-resolution structure of a picornaviral
internal cis-acting RNA replication element (cre). Proc Natl Acad Sci U
S A101 (34):12688-93.
Trincao J, Johnson RE, Wolfle WT, Escalante CR, Prakash S, Prakash L,
Aggarwal AK. 2004 May. Dpo4 is hindered in extending a G.T mismatch by a
reverse wobble. Nat Struct Mol Biol11 (5):457-62.
Uljon SN, Johnson RE, Edwards TA, Prakash S, Prakash L, Aggarwal AK.
2004 Aug. Crystal structure of the catalytic core of human DNA
polymerase kappa. Structure (Camb)12 (8):1395-404.
Volk DE, Beasley DW, Kallick DA, Holbrook MR, Barrett AD, Gorenstein DG.
2004 Sep 10. Solution structure and antibody binding studies of the
envelope protein domain III from the New York strain of West Nile virus.
J Biol Chem279 (37):38755-61.
Volk DE, Kallick DA, Holbrook MR, Beasley DW, Barrett AD, Gorenstein DG.
2004 Jul. 1H, 13C and 15N resonance assignments for domain III of the
West Nile virus envelope protein. J Biomol NMR29 (3):445-6.
Vongpunsawad S, Oezgun N, Braun W, Cattaneo R. 2004 Jan. Selectively
receptor-blind measles viruses: Identification of residues necessary for
J Virol78 (1):302-13.
Washington MT, Johnson RE, Prakash L, Prakash S. 2004 Jan. Human DNA
polymerase iota utilizes different nucleotide incorporation mechanisms
dependent upon the template base. Mol Cell Biol24 (2):936-43.
Washington MT, Minko IG, Johnson RE, Haracska L, Harris TM, Lloyd RS,
Prakash S, Prakash L. 2004 Aug. Efficient and error-free replication
past a minor-groove N2-guanine adduct by the sequential action of yeast
Rev1 and DNA polymerase zeta. Mol Cell Biol24 (16):6900-6.
Washington MT, Minko IG, Johnson RE, Wolfle WT, Harris TM, Lloyd RS,
Prakash S, Prakash L. 2004 Jul. Efficient and error-free replication
past a minor-groove DNA adduct by the sequential action of human DNA
polymerases iota and kappa. Mol Cell Biol24 (13):5687-93.
Wiederhold L, Leppard JB, Kedar P, Karimi-Busheri F, Rasouli-Nia A,
Weinfeld M, Tomkinson AE, Izumi T, Prasad R, Wilson SH, Mitra S, Hazra
TK. 2004 Jul 23. AP endonuclease-independent DNA base excision repair in
human cells. Mol Cell15 (2):209-20.
Yang X, Gorenstein DG. 2004 Nov. Progress in thioaptamer development.
Curr Drug Targets5 (8):705-15.
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