The Jack D. Griffith Laboratory: Publications

2008

Elini Mumtsidu, Alexander Makhov, Peter Konarev, Dimitri Svergun, Jack Griffith and Paul Tucker. Structural Features of the Single-strand binding protein of Epstein Barr Virus. Journal of Structural Biology, 161: 172-187. 2008
Anthony J. Cesare, Cindy Groff-Vindman, Sarah A. Compton, Michael J. McEachern and Jack D. Griffith. T-loops and homologous recombination dependent t-circles in a Kluyveromyces lactis telomere mutant strain. Mol. Cell. Biol. 28: 20-29, 2008
Marcela Raices, Ramiro E. Verdun, Sarah A. Compton, Candy I. Haggblom, Jack D. Griffith, Andrew Dillin, Jan Karlseder. C. elegans telomeres contain 3' G tails and 5' C tails that are bound by two distinct OB fold containing proteins. Cell. 2008 in press.
Jack D. Griffith, Smaranda Willcox, Dennis W. Powers, Roger Nelson, and Bonnie K. Baxter. Discovery of abundant cellulose microfibers encased in 250 Ma Permian halite: a macromolecular target in the search for life on other planets. Astrobiology. 2008 in press
Etheridge, KT., Compton, SA., Barrientos, KS, Ozgus, A. Griffith, JD.,and COunter, DM. Tethering telomeric double-and single-stranded DNA binding proteins inhibits telomere elongation. J. Biol. Chem. in press. Jan 2008
Mumtsidu, E., Konarev, P., Makhov, A.M., Manolaridis, I., Griffith J.D., Svergun, D., and Tucker, P. A. Low resolution structures of the DNA-binding domain of the HSV-1 UL9 protein and of its complex with the ssDNA-binding protein ICP8. J Structural Biology, in press.
Jeonggu Sim, Sezgin Ozgur, Biing Yuan Lin, Jei-Hwa Yu, Thomas R. Broker, Louise T. Chow and Jack Griffith. Remodeling of the Human Papillomavirus Type 11 Replication Origin into Discrete Nucleoprotein Particles and Looped Structures by the E2 Protein. J. Mol. Biol. 2008, in press.

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2007

Nancy G. Nossal, Alexander M. Makhov, Paul D. Chastain, II, Charles E. Jones, and Jack D. Griffith. Architecture of the bacteriophage T4 replication complex revealed with nanoscale biopointers. J. Biol. Chem. 282: 1098-1108, 2007.
Nicole Fouche, Sezgin Ozgur, Desmandia Roy and Jack D. Griffith. Replication fork regression in repetitive DNAs. Nucl. Acids. Res. 34: 6044-6050, 2006
Nicole Fouche, Anthony J. Cesare, Smaranda Willcox, Sezgin Ozgur, Sarah A. Compton and Jack D. Griffith, The Basic Domain of TRF2 Directs Binding to DNA Junctions Irrespective of the Presence of TTAGGG Repeats. J. Biol. Chem. 281: 37486-37495, 2006
Sarah A Compton, Jun-Hyuk Choi, Anthony Cesare, Sezgin Ozgur, Jack Griffith. Xrcc3 and Nbs1 are required for Telomere Length Maintenance and Production of Telomeric Circles in Human ALT cells. in press, Cancer Res, Feb 15 2007; 67(4)
Mumtsido, E., Makhov, AM., Roessle, M., Bathke, A. and Tucker PA. Structural features of the Bluetongue virus NS2 protein. J. Structural Biology. 160: 157-167. 2007
Yuan Yuan, Sarah Compton, Krystof Sobczak, Myrna Stenberg, Charles Thornton, Jack Griffith, and Maurice Swanson. Muscleblind-Like 1 Interacts with RNA Hairpins in Splicing Target and Pathogenic RNAs. Nuc. Acids. Res. 35: 5474-5486, 2007.
Kenney Kuo, Jack D. Griffith, and Kenneth Kreuzer. 5-Azacytidine induced methyltransferase-DNA adducts block DNA replication in vivo. Cancer Res. 67(17):8248-54. 2007.

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2006

Alexander Makhov and Jack Griffith. Visualization of the Annealing of Complementary Single-stranded DNA Catalyzed by the Herpes Simplex Virus Type 1 ICP8 SSB/Recombinase. J Mol Biol. 355:911-22. 2006
Ji, Y., Gu, J., Makhov, A., Griffith, JD, and Mitchell, BS. Regulation of the interaction of inosine monophosphate dehydrogenase with mycophenolic Acid by GTP. J Biol Chem. 281:206-12. 2006
Debra Weigl, Mike Molloy, Tim Clayton, Jack Griffith, Clara Smith, Terry Steward, Barbara Merrill, Randolph DePrince, Carl Jone and Magnus Persmark. Characterization of a topologically aberrant plasmid population from pilot-scale production of clinical-grade DNA. Journal of Biotechnology 121: 1-12. 2006
Electron Microscopic Visualization of Telomerase from Euplotes aediculatus Bound to a Model Telomere DNA Nicole Fouché, Ian K. Moon, Brian R. Keppler, Jack D. Griffith and Michael B. Jarstfer. Biochemistry 45: 9624-9631. 2006
Role of p38 in Replication of Trypanosoma brucei Kinetoplast DNA. Beiyu Liu, Dario Kalame, Akhilesh Pandey, Jack D. Griffith and Paul T. Englund. Mol. Cell. Biology, 26: 5382-5393, 2006.

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2005

Makhov AM, Griffith JD. Visualization of the Annealing of Complementary Single-stranded DNA Catalyzed by the Herpes Simplex Virus Type 1 ICP8 SSB/Recombinase. J Mol Biol. 2005 Nov 28
Ji Y, Gu J, Makhov AM, Griffith JD, Mitchell BS.Regulation of the interaction of inosine monophosphate dehydrogenase with mycophenolic acid by GTP. J Biol Chem. 2005 Oct 21
Subramanian D, Griffith JD.p53 monitors replication fork regression by binding to "Chickenfoot" intermediates. J Biol Chem. 2005 Oct 4
Tomaska L, Makhov AM, Griffith JD, Nosek J. t-Loops in yeast mitochondria. Mitochondrion. 2002 May;1(5):455-9.
Groff-Vindman C, Cesare AJ, Natarajan S, Griffith JD, McEachern MJ. Recombination at long mutant telomeres produces tiny single- and double-stranded telomeric circles. Mol Cell Biol. 2005 Jun;25(11):4406-12.
Subramanian D, Griffith JD. Modulation of p53 binding to Holliday junctions and 3-cytosine bulges by phosphorylation events. Biochemistry. 2005 Feb 22;44(7):2536-44.
Nosek J, Rycovska A, Makhov AM, Griffith JD, Tomaska L. Amplification of telomeric arrays via rolling-circle mechanism. J Biol Chem. 2005 Mar 18;280(11):10840-5.
Grove DE, Willcox S, Griffith JD, Bryant FR. Differential single-stranded DNA binding properties of the paralogous SsbA and SsbB proteins from Streptococcus pneumoniae. J Biol Chem. 2005 Mar 25;280(12):11067-73
Deepa Subramanian and Jack D. Griffith. Modulation of p53 binding to Holliday junctions and 3-cytosine bulges by phosphorylation events. Biochemistry, 44: 2536-2544, 2005.
Jozef Nosek, Adriana Rycovska, Judita Slezakova, Alexander M. Makhov, Jack D. Griffith, and Lubomir Tomaska. Amplification of telomeric arrays via rolling-circle mechanism. J. Biol. Chem. 10840-10845. 2005.
Grove DE, Willcox S, Griffith JD, Bryant FR. Differential single-stranded DNA binding properties of the paralogous SsbA and SsbB proteins from streptococcus pneumoniae. J Biol Chem. 11067-11073, 2005
Cindy Groff-Vindman, Anthony J. Cesare, Shobhana Natarajan, Jack D. Griffith and Michael J. McEachern Recombination at long mutant telomeres produces tiny ss and ds telomeric circles Mol. Cell. Biol. 11: 4406-4412, 2005
Deepa Subramanian and Jack Griffith. p53 monitors replication fork regression by binding to "Chicken foot" Intermediates. J. Biol. Chem. 280: 42568-42572, 2005
Martin, M., Cho, J., Cesare, A., Griffith, JD., and Attardi, G . Termination Factor-Mediated DNA Loop between Termination and Initiation Sites Drives Mitochondrial rRNA Synthesis. Cell. 123:1227-40, 2005

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2004

Cesare AJ, Griffith JD. Telomeric DNA in ALT cells is characterized by free telomeric circles and heterogeneous t-loops. Mol Cell Biol. 2004 Nov;24(22):9948-57.
Makhov AM, Taylor DW, Griffith JD. Two-dimensional crystallization of herpes simplex virus type 1 single-stranded DNA-binding protein, ICP8, on a lipid monolayer. Biochim Biophys Acta. 2004 Sep 1;1701(1-2):101-8.
Tomaska L, Willcox S, Slezakova J, Nosek J, Griffith JD. Taz1 binding to a fission yeast model telomere: formation of telomeric loops and higher order structures. J Biol Chem. 2004 Dec 3;279(49):50764-72. Epub 2004 Sep 21.
Reuven NB, Willcox S, Griffith JD, Weller SK Catalysis of strand exchange by the HSV-1 UL12 and ICP8 proteins: potent ICP8 recombinase activity is revealed upon resection of dsDNA substrate by nuclease. J Mol Biol. 2004 Sep 3;342(1):57-71.
Makhov AM, Subramanian D, Holley-Guthrie E, Kenney SC, Griffith JD. The Epstein-Barr virus polymerase accessory factor BMRF1 adopts a ring-shaped structure as visualized by electron microscopy. J Biol Chem. 2004 Sep 24;279(39):40358-61. Epub 2004 Jul 30.
Sar F, Lindsey-Boltz LA, Subramanian D, Croteau DL, Hutsell SQ, Griffith JD, Sancar A. Human claspin is a ring-shaped DNA-binding protein with high affinity to branched DNA structures. J Biol Chem. 2004 Sep 17;279(38):39289-95. Epub 2004 Jun 28.
Chastain PD 2nd, Bowers JL, Lee DG, Bell SP, Griffith JD. Mapping subunit location on the Saccharomyces cerevisiae origin recognition complex free and bound to DNA using a novel nanoscale biopointer. J Biol Chem. 2004 Aug 27;279(35):36354-62. Epub 2004 Jun 16.
Paul D. Chastain II, Jayson L. Bowers, Daniel G. Lee, Stephen P. Bell, and Jack D. Griffith. Mapping Subunit Location on the S. cerevisiae ORC free and Bound to DNA using a Novel Nanoscale Biopointer. J Biol Chem, 279: 36,354-36, 362. 2004
Alexander M. Makhov, Dianne W. Taylor, and Jack D. Griffith. Two-dimensional crystallization of herpes simplex virus type 1 single stranded DNA-binding protein, ICP8, on a lipid monolayer. Biochim. Biophys. Act, 170: 101-108, 2004
Funda Sar, Laura A Lindsey-Boltz, Deepa Subramanian, Deborah L. Croteau, Stephanie Q. Hutsell, Jack D. Griffith, and Aziz Sancar. Human Claspin is a Ring- shaped DNA binding Protein with High Affinity to Branched DNA Structures. J Biol. Chem., 279: 39,289-39,295. 2004
Nina B. Reuven, Smaranda Willcox, Jack D. Griffith, and Sandra K. Weller. Catalysis of strand exchange by the HSV-1 UL12 and ICP8 proteins: potent ICP8 recombinase activity is revealed upon resection of dsDNA substrate by nucleases. J Mol Biol. 342: 57-71. 2004
Alexander Makhov, Deepa Subramanian, Elizabeth Holley-Guthrie, Shannon C Kenney and Jack D Griffith. The Epstein-Barr Virus Polymerase Accessory Factor BMRF1 Adopts a Ring-shaped Structure as Visualized by Electron Microscopy. J Biol Chem. 279: 40358-61. 2004
Lubomir Tomaska, Smaranda Willcox, Judita Slezakova, Jozef Nosek, and Jack D. Griffith. Taz1 binding to a fission yeast model telomere: formation of t-loops and higher order structures. J Biol Chem, 279: 50764-50772, 2004.
Anthony J. Cesare and Jack D. Griffith. Telomeric DNA in ALT cells is characterized by free telomeric circles and heterogeneous t-loops. Mol. Cell. Biol 24: 9948-9957. 2004.

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2003

He, Z.G., Rezende, L.F., Willcox, S., Griffith, J.D. and Richardson, C.C. (2003) The carboxyl-terminal domain of bacteriophage T7 single-stranded DNA- binding protein modulates DNA binding and interaction with T7 DNA polymerase. J Biol Chem, 24, 24,

Rezende, L.F., Willcox, S., Griffith, J.D. and Richardson, C.C. (2003) A single-stranded DNA-binding protein of bacteriophage T7 defective in DNA annealing. J Biol Chem, 14, 14
Chastain, P.D., 2nd, Makhov, A.M., Nossal, N.G. and Griffith, J. (2003) Architecture of the replication complex and DNA loops at the fork generated by the bacteriophage t4 proteins. J Biol Chem, 278, 21276-85
Bermudez, V.P., Lindsey-Boltz, L.A., Cesare, A.J., Maniwa, Y., Griffith, J.D., Hurwitz, J. and Sancar, A. (2003) Loading of the human 9-1-1 checkpoint complex onto DNA by the checkpoint clamp loader hRad17-replication factor C complex in vitro. Proc Natl Acad Sci U S A, 100, 1633-8.
Makhov, A.M., Lee, S.S., Lehman, I.R. and Griffith, J.D. (2003) Origin-specific unwinding of herpes simplex virus 1 DNA by the viral UL9 and ICP8 proteins: visualization of a specific preunwinding complex. Proc Natl Acad Sci U S A, 100, 898-903
Makhov, A.M., Lee, S.S., Lehman, I.R. and Griffith, J.D. (2003) Origin-specific unwinding of herpes simplex virus 1 DNA by the viral UL9 and ICP8 proteins: visualization of a specific preunwinding complex. Proc Natl Acad Sci U S A, 100, 898-903

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2002

Vetcher, A.A., Napierala, M., Iyer, R.R., Chastain, P.D., Griffith, J.D. and Wells, R.D. (2002) Sticky DNA, a long GAA.GAA.TTC triplex that is formed intramolecularly, in the sequence of intron 1 of the frataxin gene. J Biol Chem, 277, 39217-27.
Lin, B.Y., Makhov, A.M., Griffith, J.D., Broker, T.R. and Chow, L.T. (2002) Chaperone proteins abrogate inhibition of the human papillomavirus (HPV) E1 replicative helicase by the HPV E2 protein. Mol Cell Biol, 22, 6592-604.
Yang, Q., Zhang, R., Wang, X.W., Spillare, E.A., Linke, S.P., Subramanian, D., Griffith, J.D., Li, J.L., Hickson, I.D., Shen, J.C., Loeb, L.A., Mazur, S.J., Appella, E., Brosh, R.M., Jr., Karmakar, P., Bohr, V.A. and Harris, C.C. (2002) The processing of Holliday junctions by BLM and WRN helicases is regulated by p53. J Biol Chem, 277, 31980-7.
DeFazio, L.G., Stansel, R.M., Griffith, J.D. and Chu, (2002) Synapsis of DNA ends by DNA-dependent protein kinase. Embo J, 21, 3192-200.
Subramanian, D. and Griffith, J.D. (2002) Interactions between p53, hMSH2-hMSH6 and HMG I(Y) on Holliday junctions and bulged bases. Nucleic Acids Res, 30, 2427-34.
Unsal-Kacmaz, K., Makhov, A.M., Griffith, J.D. and Sancar, A. (2002) Preferential binding of ATR protein to UV-damaged DNA. Proc Natl Acad Sci U S A, 99, 6673-8.
Griffith, J.D., Lindsey-Boltz, L.A. and Sancar, A. (2002) Structures of the human Rad17-replication factor C and checkpoint Rad 9- 1-1 complexes visualized by glycerol spray/low voltage microscopy. J Biol Chem, 277, 15233-6.
Stansel, R.M., Subramanian, D. and Griffith, J.D. (2002) p53 binds telomeric single strand overhangs and t-loop junctions in vitro. J Biol Chem, 277, 11625-8.
Lee J, Chastain PD 2nd, Griffith JD, and Richardson CC. Lagging strand synthesis in coordinated DNA synthesis by bacteriophage t7 replication proteins. J Mol Biol. 2002 Feb 8;316(1):19-34. (full text)

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2001

Stansel RM, de Lange T, and Griffith JD.T-loop assembly in vitro involves binding of TRF2 near the 3' telomeric overhang. EMBO J 2001 Oct 1;

Degtyareva N, Subramanian D, Griffith JD. Analysis of the binding of p53 to DNAs containing mismatched and bulged bases.J Biol Chem. 2001 Mar 23;276(12):8778-84. (full text).

Vologodskii AV, Zhang W, Rybenkov VV, Podtelezhnikov AA, Subramanian D, Griffith JD, Cozzarelli NR. Mechanism of topology simplification by type II DNA topoisomerases.Proc Natl Acad Sci U S A 2001 Mar 13;98(6):3045-3049. (full text)

Munoz-Jordan JL, Cross GA, de Lange T, Griffith JD. t-loops at trypanosome telomeres. EMBO J. 2001 Feb 1;20(3):579-88. (full text)

Tomaska L, Makhov AM, Nosek J, Kucejova B, Griffith JD. Electron microscopic analysis supports a dual role for the mitochondrial telomere-binding protein of Candida parapsilosis. J Mol Biol. 2001 Jan 5;305(1):61-9.

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2000

Tomaska L, Nosek J, Makhov AM, Pastorakova A, Griffith JD. Extragenomic double-stranded DNA circles in yeast with linear mitochondrial genomes: potential involvement in telomere maintenance. Nucleic Acids Res. 2000 Nov 15;28(22):4479-87.(full text)
Chastain PD 2nd, Makhov AM, Nossal NG, Griffith JD. Analysis of the Okazaki fragment distributions along single long DNAs replicated by the bacteriophage T4 proteins. Mol Cell. 2000 Oct;6(4):803-14.
Lee DG, Makhov AM, Klemm RD, Griffith JD, Bell SP. Regulation of origin recognition complex conformation and ATPase activity: differential effects of single-stranded and double-stranded DNA binding. EMBO J. 2000 Sep 1;19(17):4774-82.(full text)
Bagga R, Michalowski S, Sabnis R, Griffith JD, Emerson BM. HMG I/Y regulates long-range enhancer-dependent transcription on DNA and chromatin by changes in DNA topology. NucleicAcids Res 2000 Jul 1;28(13):2541-50
Lim A, Makhov AM, Bond J, Inouye H, Connors LH, Griffith JD, Erickson BW, Kirschner DA,Costello CE. Betabellins 15D and 16D, de Novo Designed beta-Sandwich Proteins That Have Amyloidogenic Properties. J Struct Biol 2000 Jun;130(2/3):363-370.
Young SM Jr, McCarty DM, Degtyareva N, Samulski RJ. Roles of Adeno-Associated Virus Rep Protein and Human Chromosome 19 in Site-Specific Recombination.J Virol 2000 May;74(9):3953-66.

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1999

Kirkpatrick DT, Wang YH, Dominska M, Griffith JD, Petes TD. Control of meiotic recombination and gene expression in yeast by a simple repetitive DNA sequence that excludes nucleosomes. MolCell Biol 1999 Nov;19(11):7661-71. (full text)
Lim A, Makhov AM, Saderholm MJ, Griffith JD, Erickson BW. Biophysical characterization of betabellin 16D: a beta-sandwich protein that forms narrow fibrils which associate into broad ribbons.Biochem Biophys Res Commun. 1999 Oct 22;264(2):498-504.
Bianchi A, Stansel RM, Fairall L, Griffith JD, Rhodes D, de Lange T. TRF1 binds a bipartite telomeric site with extreme spatial flexibility. EMBO J 1999 Oct 15;18(20):5735-44.
Cordeiro-Stone M, Makhov AM, Zaritskaya LS, Griffith JD. Analysis of DNA replication forks encountering a pyrimidine dimer in the template to the leading strand.J Mol Biol 1999 Jun 25;289(5):1207-18.
Griffith JD, Comeau L, Rosenfield S, Stansel RM, Bianchi A, Moss H, de Lange T. Mammalian telomeres end in a large duplex loop. Cell 1999 May 14;97(4):503-14.
Sakamoto N, Chastain PD, Parniewski P, Ohshima K, Pandolfo M, Griffith JD, Wells RD.Sticky DNA: self-association properties of long GAA.TTC repeats in R.R.Y triplex structures from Friedreich's ataxia. Mol Cell 1999 Apr;3(4):465-75.
Gradia S, Subramanian D, Wilson T, Acharya S, Makhov A, Griffith J, Fishel R. hMSH2-hMSH6 forms a hydrolysis-independent sliding clamp on mismatched DNA. Mol Cell. 1999 Feb;3(2):255-61.

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1998

Liu JS, Kuo SR, Makhov AM, Cyr DM, Griffith JD, Broker TR, Chow LT. Human Hsp70 and Hsp40 chaperone proteins facilitate human papillomavirus-11 E1 protein binding to the origin and stimulate cell-free DNA replication.J Biol Chem 1998 Nov 13;273(46):30704-12. (full text)
Lim A, Saderholm MJ, Makhov AM, Kroll M, Yan Y, Perera L, Griffith JD, Erickson BW. Engineering of betabellin-15D: a 64 residue beta sheet protein that forms long narrow multimeric fibrils. Protein Sci 1998 Jul;7(7):1545-54.
Park K, Debyser Z, Tabor S, Richardson CC, Griffith JD. Formation of a DNA loop at the replication fork generated by bacteriophage T7 replication proteins. J Biol Chem 1998 Feb 27;273(9):5260-70. (full text)
Pearson CE, Wang YH, Griffith JD, Sinden RR. Structural analysis of slipped-strand DNA (S-DNA) formed in (CTG)n. (CAG)n repeats from the myotonic dystrophy locus.Nucleic Acids Res 1998 Feb 1;26(3):816-23. (full text)

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1997

Kim TK, Lagrange T, Wang YH, Griffith JD, Reinberg D, Ebright RH. Trajectory of DNA in the RNA polymerase II transcription preinitiation complex. Proc Natl Acad Sci U S A 1997 Nov 11;94(23):12268-73. (full text)
Allen DJ, Makhov A, Grilley M, Taylor J, Thresher R, Modrich P, Griffith JD. MutS mediates heteroduplex loop formation by a translocation mechanism.EMBO J 1997 Jul 16;16(14):4467-76. (full text)
Griffith JD, Lee S, Wang YH. Visualizing nucleic acids and their complexes using electron microscopy.Curr Opin Struct Biol 1997 Jun;7(3):362-6.
Kong D, Griffith JD, Richardson CC. Gene 4 helicase of bacteriophage T7 mediates strand transfer through pyrimidine dimers, mismatches, and nonhomologous regions.Proc Natl Acad Sci U S A 1997 Apr 1;94(7):2987-92. (full text)

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1996

Stevens SW, Griffith JD. Sequence analysis of the human DNA flanking sites of human immunodeficiency virus type 1 integration. J Virol 1996 Sep;70(9):6459-62. (full text)
Wang YH, Griffith JD. The [(G/C)3NN]n motif: a common DNA repeat that excludes nucleosomes.Proc Natl Acad Sci U S A 1996 Aug 20;93(17):8863-7. (full text)
Dlakic M, Park K, Griffith JD, Harvey SC, Harrington RE. The organic crystallizing agent 2-methyl-2,4-pentanediol reduces DNA curvature by means of structural changes in A-tracts.J Biol Chem 1996 Jul 26;271(30):17911-9. (full text)
Makhov AM, Boehmer PE, Lehman IR, Griffith JD.Visualization of the unwinding of long DNA chains by the herpes simplex virus type 1 UL9 protein and ICP8.J Mol Biol 1996 May 24;258(5):789-99.
Makhov AM, Boehmer PE, Lehman IR, Griffith JD. The herpes simplex virus type 1 origin-binding protein carries out origin specific DNA unwinding and forms stem-loop structures.EMBO J 1996 Apr 1;15(7):1742-50.
Stanfield-Oakley SA, Griffith JD. Nucleosomal arrangement of HIV-1 DNA: maps generated from an integrated genome and an EBV-based episomal model.J Mol Biol 1996 Mar 1;256(3):503-16.
Skaliter R, Makhov AM, Griffith JD, Lehman IR.Rolling circle DNA replication by extracts of herpes simplex virus type 1-infected human cells.J Virol 1996 Feb;70(2):1132-6. (full text)

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