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Robert Anthony Bambara, Ph.D.

Robert Anthony Bambara, Ph.D.

About Me

Faculty Appointments

Professor Emeritus - Department of Microbiology and Immunology (SMD)

Professor Emeritus - Department of Biochemistry and Biophysics (SMD) - Joint

Credentials

Education

PhD | Cornell University. Molecular Biology. 1974

BA | Northwestern University. Chemistry. 1970

Research

AIDS Research: HIV-1 Acquired a Cellular Gene to Promote Viral Replication. Examining a critical step in viral replication called minus strand transfer, we found that it involves circularization of the viral RNA. Using high speed computing and computational biology methods, we discovered that the...
AIDS Research: HIV-1 Acquired a Cellular Gene to Promote Viral Replication. Examining a critical step in viral replication called minus strand transfer, we found that it involves circularization of the viral RNA. Using high speed computing and computational biology methods, we discovered that the sequences involved in the circularization included a small gene, apparently acquired by the virus thousands of years ago from the genome of an infected host. The gene has been retained in recognizable forms, because it is a rare example of a host gene that has been hijacked by a virus to support viral replication. The gene sequence suggests that HIV evolved first in African cats, before being transferred to monkeys and humans. Moreover, the presence of the gene in only some monkey viruses, suggests that it could make the difference between viruses causing virulent rather than latent infections. Future work involves molecular paleontology of the gene and examination of its role in promoting virus growth.

Carcinogenesis: Mechanisms of DNA Repair and Replication. Human cells defend against aging and cancer by accurate replication of DNA and efficient DNA repair. We recently discovered that human cells have developed a unique mechanism to protect the information in genes that express proteins in active chromatin. The same acetyl-transferase that makes regions of chromatin more accessible for transcription alters the functions of specific replication and repair proteins. These proteins become extra-efficient at removing lesions in the DNA, and preventing replication errors, but only in active genes. These results indicate that the cells can regulate the effectiveness with which they protect DNA from aging. This finding offers a unique opportunity to influence that regulation to delay the onset of cancers by up-regulating the efficiency with which we protect our DNA. Future work will involve investigating the mechanisms of the regulation in cells, biochemical assays, and in reconstituted chromatin.

Publications

Journal Articles

DNA Polymerase Delta Exhibits Altered Catalytic Properties on Lysine Acetylation.

Njeri C, Pepenella S, Battapadi T, Bambara RA, Balakrishnan L

Genes.. 2023 March 2314 (4)Epub 03/23/2023.

G-quadruplex ligands targeting telomeres do not inhibit HIV promoter activity and cooperate with latency reversing agents in killing latently infected cells.

Piekna-Przybylska D, Bambara RA, Maggirwar SB, Dewhurst S

Cell cycle.. 2020 September 19 (18):2298-2313. Epub 08/17/2020.

Cidofovir Diphosphate Inhibits Adenovirus 5 DNA Polymerase via both Nonobligate Chain Termination and Direct Inhibition, and Polymerase Mutations Confer Cidofovir Resistance on Intact Virus.

Chamberlain J, Sortino K, Sethna P, Bae A, Lanier R, Bambara RA, Dewhurst S

Antimicrobial agents and chemotherapy.. 2019 January 63 (1)Epub 12/21/2018.

Deficiency in DNA damage response, a new characteristic of cells infected with latent HIV-1.

Piekna-Przybylska D, Sharma G, Maggirwar SB, Bambara RA

Cell cycle.. 2017 May 1916 (10):968-978. Epub 04/07/2017.

Acetylation regulates DNA repair mechanisms in human cells.

Piekna-Przybylska D, Bambara RA, Balakrishnan L

Cell cycle.. 2016 June 215 (11):1506-17. Epub 04/22/2016.

Anti-HIV host factor SAMHD1 regulates viral sensitivity to nucleoside reverse transcriptase inhibitors via modulation of cellular deoxyribonucleoside triphosphate (dNTP) levels.

Amie SM, Daly MB, Noble E, Schinazi RF, Bambara RA, Kim B

The Journal of biological chemistry.. 2014 June 13289 (24):16640. Epub 1900 01 01.

GTP is the primary activator of the anti-HIV restriction factor SAMHD1.

Amie SM, Bambara RA, Kim B

The Journal of biological chemistry.. 2014 June 13289 (24):16641. Epub 1900 01 01.

U3 region in the HIV-1 genome adopts a G-quadruplex structure in its RNA and DNA sequence.

Piekna-Przybylska D, Sullivan MA, Sharma G, Bambara RA

Biochemistry.. 2014 April 2953 (16):2581-93. Epub 04/15/2014.

Reverse transcriptase backbone can alter the polymerization and RNase activities of non-nucleoside reverse transcriptase mutants K101E+G190S.

Wang J, Li D, Bambara RA, Dykes C

The Journal of general virology.. 2013 October 94 (Pt 10):2297-2308. Epub 06/26/2013.

GTP is the primary activator of the anti-HIV restriction factor SAMHD1.

Amie SM, Bambara RA, Kim B

The Journal of biological chemistry.. 2013 August 30288 (35):25001-25006. Epub 07/23/2013.

Mechanism of HIV-1 RNA dimerization in the central region of the genome and significance for viral evolution.

Piekna-Przybylska D, Sharma G, Bambara RA

The Journal of biological chemistry.. 2013 August 16288 (33):24140-50. Epub 07/09/2013.

Efavirenz stimulates HIV-1 reverse transcriptase RNase H activity by a mechanism involving increased substrate binding and secondary cleavage activity.

Muchiri JM, Li D, Dykes C, Bambara RA

Biochemistry.. 2013 July 2352 (29):4981-90. Epub 07/09/2013.

Anti-HIV host factor SAMHD1 regulates viral sensitivity to nucleoside reverse transcriptase inhibitors via modulation of cellular deoxyribonucleoside triphosphate (dNTP) levels.

Amie SM, Daly MB, Noble E, Schinazi RF, Bambara RA, Kim B

The Journal of biological chemistry.. 2013 July 12288 (28):20683-91. Epub 06/05/2013.

L74V increases the reverse transcriptase content of HIV-1 virions with non-nucleoside reverse transcriptase drug-resistant mutations L100I+K103N and K101E+G190S, which results in increased fitness.

Wang J, Li D, Bambara RA, Yang H, Dykes C

The Journal of general virology.. 2013 July 94 (Pt 7):1597-1607. Epub 03/27/2013.

Okazaki fragment metabolism.

Balakrishnan L, Bambara RA

Cold Spring Harbor perspectives in biology.. 2013 February 15 (2)Epub 02/01/2013.

Flap endonuclease 1.

Balakrishnan L, Bambara RA

Annual review of biochemistry.. 2013 82 :119-38. Epub 02/28/2013.

Msh2-Msh3 interferes with Okazaki fragment processing to promote trinucleotide repeat expansions.

Kantartzis A, Williams GM, Balakrishnan L, Roberts RL, Surtees JA, Bambara RA

Cell reports.. 2012 August 302 (2):216-22. Epub 08/02/2012.

Biochemical analyses indicate that binding and cleavage specificities define the ordered processing of human Okazaki fragments by Dna2 and FEN1.

Gloor JW, Balakrishnan L, Campbell JL, Bambara RA

Nucleic acids research.. 2012 August 40 (14):6774-86. Epub 05/07/2012.

Frequent incorporation of ribonucleotides during HIV-1 reverse transcription and their attenuated repair in macrophages.

Kennedy EM, Amie SM, Bambara RA, Kim B

The Journal of biological chemistry.. 2012 April 20287 (17):14280-8. Epub 03/01/2012.

Telomere proteins POT1, TRF1 and TRF2 augment long-patch base excision repair in vitro.

Miller A, Balakrishnan L, Buncher NA, Opresko PL, Bambara RA

Cell cycle.. 2012 March 111 (5):998-1007. Epub 03/01/2012.

Altered strand transfer activity of a multiple-drug-resistant human immunodeficiency virus type 1 reverse transcriptase mutant with a dipeptide fingers domain insertion.

Nguyen LA, Daddacha W, Rigby S, Bambara RA, Kim B

Journal of molecular biology.. 2012 January 13415 (2):248-62. Epub 11/12/2011.

Nonnucleoside reverse transcriptase inhibitor-resistant HIV is stimulated by efavirenz during early stages of infection.

Wang J, Zhang G, Bambara RA, Li D, Liang H, Wu H, Smith HM, Lowe NR, Demeter LM, Dykes C

Journal of virology.. 2011 October 85 (20):10861-73. Epub 08/10/2011.

HIV-1 reverse transcriptase dissociates during strand transfer.

Muchiri JM, Rigby ST, Nguyen LA, Kim B, Bambara RA

Journal of molecular biology.. 2011 September 23412 (3):354-64. Epub 07/29/2011.

HIV-1 nucleocapsid protein increases strand transfer recombination by promoting dimeric G-quartet formation.

Shen W, Gorelick RJ, Bambara RA

The Journal of biological chemistry.. 2011 August 26286 (34):29838-47. Epub 07/07/2011.

The changing view of Dna2.

Balakrishnan L, Bambara RA

Cell cycle.. 2011 August 1510 (16):2620-1. Epub 08/15/2011.

The RNA surveillance protein SMG1 activates p53 in response to DNA double-strand breaks but not exogenously oxidized mRNA.

Gewandter JS, Bambara RA, O'Reilly MA

Cell cycle.. 2011 August 110 (15):2561-7. Epub 08/01/2011.

Characterization of the endonuclease and ATP-dependent flap endo/exonuclease of Dna2.

Fortini BK, Pokharel S, Polaczek P, Balakrishnan L, Bambara RA, Campbell JL

The Journal of biological chemistry.. 2011 July 8286 (27):23763-70. Epub 05/13/2011.

Eukaryotic lagging strand DNA replication employs a multi-pathway mechanism that protects genome integrity.

Balakrishnan L, Bambara RA

The Journal of biological chemistry.. 2011 March 4286 (9):6865-70. Epub 12/21/2010.

Sequences in the U3 region of human immunodeficiency virus 1 improve efficiency of minus strand transfer in infected cells.

Piekna-Przybylska D, Dykes C, Demeter LM, Bambara RA

Virology.. 2011 February 20410 (2):368-74. Epub 12/30/2010.

Requirements for efficient minus strand strong-stop DNA transfer in human immunodeficiency virus 1.

Piekna-Przybylska D, Bambara RA

RNA biology.. 2011 8 (2):230-6. Epub 03/01/2011.

An alternative pathway for Okazaki fragment processing: resolution of fold-back flaps by Pif1 helicase.

Pike JE, Henry RA, Burgers PM, Campbell JL, Bambara RA

The Journal of biological chemistry.. 2010 December 31285 (53):41712-23. Epub 10/19/2010.

Dna2 exhibits a unique strand end-dependent helicase function.

Balakrishnan L, Polaczek P, Pokharel S, Campbell JL, Bambara RA

The Journal of biological chemistry.. 2010 December 10285 (50):38861-8. Epub 10/06/2010.

Flap endonuclease 1 mechanism analysis indicates flap base binding prior to threading.

Gloor JW, Balakrishnan L, Bambara RA

The Journal of biological chemistry.. 2010 November 5285 (45):34922-31. Epub 08/25/2010.

Components of the secondary pathway stimulate the primary pathway of eukaryotic Okazaki fragment processing.

Henry RA, Balakrishnan L, Tan Ying-Lin S, Campbell JL, Bambara RA

The Journal of biological chemistry.. 2010 September 10285 (37):28496-505. Epub 07/13/2010.

Reduced fitness in cell culture of HIV-1 with nonnucleoside reverse transcriptase inhibitor-resistant mutations correlates with relative levels of reverse transcriptase content and RNase H activity in virions.

Wang J, Bambara RA, Dykes C

Journal of virology.. 2010 September 84 (18):9377-89. Epub 06/30/2010.

Reconstitution of eukaryotic lagging strand DNA replication.

Balakrishnan L, Gloor JW, Bambara RA

Methods : a companion to Methods in enzymology.. 2010 July 51 (3):347-57. Epub 02/21/2010.

Acetylation of Dna2 endonuclease/helicase and flap endonuclease 1 by p300 promotes DNA stability by creating long flap intermediates.

Balakrishnan L, Stewart J, Polaczek P, Campbell JL, Bambara RA

The Journal of biological chemistry.. 2010 February 12285 (7):4398-404. Epub 12/17/2009.

Dna2 is a structure-specific nuclease, with affinity for 5'-flap intermediates.

Stewart JA, Campbell JL, Bambara RA

Nucleic acids research.. 2010 January 38 (3):920-30. Epub 11/24/2009.

A sequence similar to tRNA 3 Lys gene is embedded in HIV-1 U3-R and promotes minus-strand transfer.

Piekna-Przybylska D, Dichiacchio L, Mathews DH, Bambara RA

Nature structural & molecular biology.. 2010 January 17 (1):83-9. Epub 12/06/2009.

Factors that determine the efficiency of HIV-1 strand transfer initiated at a specific site.

Rigby ST, Van Nostrand KP, Rose AE, Gorelick RJ, Mathews DH, Bambara RA

Journal of molecular biology.. 2009 December 11394 (4):694-707. Epub 10/21/2009.

A recombination hot spot in HIV-1 contains guanosine runs that can form a G-quartet structure and promote strand transfer in vitro.

Shen W, Gao L, Balakrishnan M, Bambara RA

The Journal of biological chemistry.. 2009 December 4284 (49):33883-93. Epub 10/12/2009.

Pif1 helicase lengthens some Okazaki fragment flaps necessitating Dna2 nuclease/helicase action in the two-nuclease processing pathway.

Pike JE, Burgers PM, Campbell JL, Bambara RA

The Journal of biological chemistry.. 2009 September 11284 (37):25170-80. Epub 07/15/2009.

Long patch base excision repair proceeds via coordinated stimulation of the multienzyme DNA repair complex.

Balakrishnan L, Brandt PD, Lindsey-Boltz LA, Sancar A, Bambara RA

The Journal of biological chemistry.. 2009 May 29284 (22):15158-72. Epub 03/27/2009.

Mechanism analysis indicates that recombination events in HIV-1 initiate and complete over short distances, explaining why recombination frequencies are similar in different sections of the genome.

Rigby ST, Rose AE, Hanson MN, Bambara RA

Journal of molecular biology.. 2009 April 24388 (1):30-47. Epub 02/20/2009.

Significance of the dissociation of Dna2 by flap endonuclease 1 to Okazaki fragment processing in Saccharomyces cerevisiae.

Stewart JA, Campbell JL, Bambara RA

The Journal of biological chemistry.. 2009 March 27284 (13):8283-91. Epub 01/29/2009.

A succession of mechanisms stimulate efficient reconstituted HIV-1 minus strand strong stop DNA transfer.

Song M, Balakrishnan M, Gorelick RJ, Bambara RA

Biochemistry.. 2009 March 348 (8):1810-9. Epub 1900 01 01.

Dynamic removal of replication protein A by Dna2 facilitates primer cleavage during Okazaki fragment processing in Saccharomyces cerevisiae.

Stewart JA, Miller AS, Campbell JL, Bambara RA

The Journal of biological chemistry.. 2008 November 14283 (46):31356-65. Epub 09/17/2008.

Pif1 helicase directs eukaryotic Okazaki fragments toward the two-nuclease cleavage pathway for primer removal.

Rossi ML, Pike JE, Wang W, Burgers PM, Campbell JL, Bambara RA

The Journal of biological chemistry.. 2008 October 10283 (41):27483-27493. Epub 08/09/2008.

Catalysis of strand annealing by replication protein A derives from its strand melting properties.

Bartos JD, Willmott LJ, Binz SK, Wold MS, Bambara RA

The Journal of biological chemistry.. 2008 August 1283 (31):21758-68. Epub 06/03/2008.

hSMG-1 and ATM sequentially and independently regulate the G1 checkpoint during oxidative stress.

Gehen SC, Staversky RJ, Bambara RA, Keng PC, O'Reilly MA

Oncogene.. 2008 July 327 (29):4065-74. Epub 03/10/2008.

Strand transfer events during HIV-1 reverse transcription.

Basu VP, Song M, Gao L, Rigby ST, Hanson MN, Bambara RA

Virus research.. 2008 June 134 (1-2):19-38. Epub 02/14/2008.

Gene expression profiling reveals that the regulation of estrogen-responsive element-independent genes by 17 beta-estradiol-estrogen receptor beta is uncoupled from the induction of phenotypic changes in cell models.

Li X, Nott SL, Huang Y, Hilf R, Bambara RA, Qiu X, Yakovlev A, Welle S, Muyan M

Journal of molecular endocrinology.. 2008 May 40 (5):211-29. Epub 1900 01 01.

Reduced dNTP binding affinity of 3TC-resistant M184I HIV-1 reverse transcriptase variants responsible for viral infection failure in macrophage.

Jamburuthugoda VK, Santos-Velazquez JM, Skasko M, Operario DJ, Purohit V, Chugh P, Szymanski EA, Wedekind JE, Bambara RA, Kim B

The Journal of biological chemistry.. 2008 April 4283 (14):9206-16. Epub 01/24/2008.

Apparent defects in processive DNA synthesis, strand transfer, and primer elongation of Met-184 mutants of HIV-1 reverse transcriptase derive solely from a dNTP utilization defect.

Gao L, Hanson MN, Balakrishnan M, Boyer PL, Roques BP, Hughes SH, Kim B, Bambara RA

The Journal of biological chemistry.. 2008 April 4283 (14):9196-205. Epub 01/24/2008.

Proximity and branch migration mechanisms in HIV-1 minus strand strong stop DNA transfer.

Song M, Basu VP, Hanson MN, Roques BP, Bambara RA

The Journal of biological chemistry.. 2008 February 8283 (6):3141-3150. Epub 12/11/2007.

Mechanisms that prevent template inactivation by HIV-1 reverse transcriptase RNase H cleavages.

Purohit V, Roques BP, Kim B, Bambara RA

The Journal of biological chemistry.. 2007 April 27282 (17):12598-609. Epub 03/02/2007.

Insights into the multiple roles of pausing in HIV-1 reverse transcriptase-promoted strand transfers.

Gao L, Balakrishnan M, Roques BP, Bambara RA

The Journal of biological chemistry.. 2007 March 2282 (9):6222-31. Epub 01/03/2007.

Downregulation of PCNA potentiates p21-mediated growth inhibition in response to hyperoxia.

Gehen SC, Vitiello PF, Bambara RA, Keng PC, O'Reilly MA

American journal of physiology. Lung cellular and molecular physiology.. 2007 March 292 (3):L716-24. Epub 11/03/2006.

Flap endonuclease disengages Dna2 helicase/nuclease from Okazaki fragment flaps.

Stewart JA, Campbell JL, Bambara RA

The Journal of biological chemistry.. 2006 December 15281 (50):38565-72. Epub 10/11/2006.

Evidence that creation of invasion sites determines the rate of strand transfer mediated by HIV-1 reverse transcriptase.

Hanson MN, Balakrishnan M, Roques BP, Bambara RA

Journal of molecular biology.. 2006 November 10363 (5):878-90. Epub 08/30/2006.

Reduced dNTP interaction of human immunodeficiency virus type 1 reverse transcriptase promotes strand transfer.

Operario DJ, Balakrishnan M, Bambara RA, Kim B

The Journal of biological chemistry.. 2006 October 27281 (43):32113-21. Epub 08/21/2006.

Mechanisms by which Bloom protein can disrupt recombination intermediates of Okazaki fragment maturation.

Bartos JD, Wang W, Pike JE, Bambara RA

The Journal of biological chemistry.. 2006 October 27281 (43):32227-39. Epub 08/31/2006.

Reconstituted Okazaki fragment processing indicates two pathways of primer removal.

Rossi ML, Bambara RA

The Journal of biological chemistry.. 2006 September 8281 (36):26051-61. Epub 07/11/2006.

Stimulation of HIV-1 minus strand strong stop DNA transfer by genomic sequences 3' of the primer binding site.

Song M, Balakrishnan M, Chen Y, Roques BP, Bambara RA

The Journal of biological chemistry.. 2006 August 25281 (34):24227-35. Epub 06/15/2006.

The Rad9 protein enhances survival and promotes DNA repair following exposure to ionizing radiation.

Brandt PD, Helt CE, Keng PC, Bambara RA

Biochemical and biophysical research communications.. 2006 August 18347 (1):232-7. Epub 06/21/2006.

HIV-1 reverse transcriptase mutants resistant to nonnucleoside reverse transcriptase inhibitors do not adversely affect DNA synthesis: pre-steady-state and steady-state kinetic studies.

Domaoal RA, Bambara RA, Demeter LM

Journal of acquired immune deficiency syndromes : JAIDS.. 2006 August 142 (4):405-11. Epub 1900 01 01.

Mechanism of stimulation of human DNA ligase I by the Rad9-rad1-Hus1 checkpoint complex.

Wang W, Lindsey-Boltz LA, Sancar A, Bambara RA

The Journal of biological chemistry.. 2006 July 28281 (30):20865-20872. Epub 05/25/2006.

The HIV-1 reverse transcriptase mutants G190S and G190A, which confer resistance to non-nucleoside reverse transcriptase inhibitors, demonstrate reductions in RNase H activity and DNA synthesis from tRNA(Lys, 3) that correlate with reductions in replication efficiency.

Wang J, Dykes C, Domaoal RA, Koval CE, Bambara RA, Demeter LM

Virology.. 2006 May 10348 (2):462-74. Epub 02/28/2006.

Lagging strand replication proteins in genome stability and DNA repair.

Rossi ML, Purohit V, Brandt PD, Bambara RA

Chemical reviews.. 2006 February 106 (2):453-73. Epub 1900 01 01.

A tale of two estrogen receptors (ERs): how differential ER-estrogen responsive element interactions contribute to subtype-specific transcriptional responses.

Huang J, Li X, Qiao T, Bambara RA, Hilf R, Muyan M

Nuclear receptor signaling. 2006 4 :e015. Epub 07/07/2006.

Evidence that HIV-1 reverse transcriptase employs the DNA 3' end-directed primary/secondary RNase H cleavage mechanism during synthesis and strand transfer.

Purohit V, Balakrishnan M, Kim B, Bambara RA

The Journal of biological chemistry.. 2005 December 9280 (49):40534-43. Epub 10/11/2005.

Molecular basis of therapeutic strategies for breast cancer.

Huang J, Li X, Hilf R, Bambara RA, Muyan M

Current drug targets. Immune, endocrine and metabolic disorders. 2005 December 5 (4):379-96. Epub 1900 01 01.

Effects of donor and acceptor RNA structures on the mechanism of strand transfer by HIV-1 reverse transcriptase.

Hanson MN, Balakrishnan M, Roques BP, Bambara RA

Journal of molecular biology.. 2005 November 4353 (4):772-87. Epub 09/26/2005.

Binding of estrogen receptor beta to estrogen response element in situ is independent of estradiol and impaired by its amino terminus.

Huang J, Li X, Maguire CA, Hilf R, Bambara RA, Muyan M

Molecular endocrinology.. 2005 November 19 (11):2696-712. Epub 06/23/2005.

Acceptor RNA cleavage profile supports an invasion mechanism for HIV-1 minus strand transfer.

Chen Y, Balakrishnan M, Roques BP, Bambara RA

The Journal of biological chemistry.. 2005 April 15280 (15):14443-52. Epub 01/18/2005.

Evidence that DNA damage detection machinery participates in DNA repair.

Helt CE, Wang W, Keng PC, Bambara RA

Cell cycle.. 2005 April 4 (4):529-32. Epub 04/10/2005.

Human Bloom protein stimulates flap endonuclease 1 activity by resolving DNA secondary structure.

Wang W, Bambara RA

The Journal of biological chemistry.. 2005 February 18280 (7):5391-9. Epub 12/04/2004.

Ataxia telangiectasia mutated (ATM) and ATM and Rad3-related protein exhibit selective target specificities in response to different forms of DNA damage.

Helt CE, Cliby WA, Keng PC, Bambara RA, O'Reilly MA

The Journal of biological chemistry.. 2005 January 14280 (2):1186-92. Epub 11/08/2004.

Dna2p helicase/nuclease is a tracking protein, like FEN1, for flap cleavage during Okazaki fragment maturation.

Kao HI, Campbell JL, Bambara RA

The Journal of biological chemistry.. 2004 December 3279 (49):50840-9. Epub 09/22/2004.

Macrophage tropism of HIV-1 depends on efficient cellular dNTP utilization by reverse transcriptase.

Diamond TL, Roshal M, Jamburuthugoda VK, Reynolds HM, Merriam AR, Lee KY, Balakrishnan M, Bambara RA, Planelles V, Dewhurst S, Kim B

The Journal of biological chemistry.. 2004 December 3279 (49):51545-53. Epub 09/26/2004.

Inhibition of HIV type 1 replication using lentiviral-mediated delivery of mutant tRNA(Lys3)A58U.

Renda MJ, Bradel-Tretheway B, Planelles V, Bambara RA, Dewhurst S

AIDS research and human retroviruses.. 2004 December 20 (12):1324-34. Epub 1900 01 01.

The human Rad9-Rad1-Hus1 checkpoint complex stimulates flap endonuclease 1.

Wang W, Brandt P, Rossi ML, Lindsey-Boltz L, Podust V, Fanning E, Sancar A, Bambara RA

Proceedings of the National Academy of Sciences of the United States of America.. 2004 November 30101 (48):16762-7. Epub 11/19/2004.

Identification of a preferred region for recombination and mutation in HIV-1 gag.

Dykes C, Balakrishnan M, Planelles V, Zhu Y, Bambara RA, Demeter LM

Virology.. 2004 September 1326 (2):262-79. Epub 1900 01 01.

Single-chain estrogen receptors (ERs) reveal that the ERalpha/beta heterodimer emulates functions of the ERalpha dimer in genomic estrogen signaling pathways.

Li X, Huang J, Yi P, Bambara RA, Hilf R, Muyan M

Molecular and cellular biology.. 2004 September 24 (17):7681-94. Epub 1900 01 01.

Saccharomyces cerevisiae flap endonuclease 1 uses flap equilibration to maintain triplet repeat stability.

Liu Y, Zhang H, Veeraraghavan J, Bambara RA, Freudenreich CH

Molecular and cellular biology.. 2004 May 24 (9):4049-64. Epub 1900 01 01.

A role for dNTP binding of human immunodeficiency virus type 1 reverse transcriptase in viral mutagenesis.

Weiss KK, Chen R, Skasko M, Reynolds HM, Lee K, Bambara RA, Mansky LM, Kim B

Biochemistry.. 2004 April 2043 (15):4490-500. Epub 1900 01 01.

Targeting estrogen responsive elements (EREs): design of potent transactivators for ERE-containing genes.

Huang J, Li X, Yi P, Hilf R, Bambara RA, Muyan M

Molecular and cellular endocrinology.. 2004 April 15218 (1-2):65-78. Epub 1900 01 01.

On the roles of Saccharomyces cerevisiae Dna2p and Flap endonuclease 1 in Okazaki fragment processing.

Kao HI, Veeraraghavan J, Polaczek P, Campbell JL, Bambara RA

The Journal of biological chemistry.. 2004 April 9279 (15):15014-24. Epub 01/26/2004.

The Cdk and PCNA domains on p21Cip1 both function to inhibit G1/S progression during hyperoxia.

Helt CE, Staversky RJ, Lee YJ, Bambara RA, Keng PC, O'Reilly MA

American journal of physiology. Lung cellular and molecular physiology.. 2004 March 286 (3):L506-13. Epub 08/22/2003.

WRN helicase and FEN-1 form a complex upon replication arrest and together process branchmigrating DNA structures associated with the replication fork.

Sharma S, Otterlei M, Sommers JA, Driscoll HC, Dianov GL, Kao HI, Bambara RA, Brosh RM

Molecular biology of the cell.. 2004 February 15 (2):734-50. Epub 12/02/2003.

Inhibition of HIV Type1 Replication Using Lentiviral-Mediated Delivery of Mutant tRNA(Lys3)A58U

Renda, M. J.; Bradel-Tretheway, B.; Planelles, V.; Bambara, R. A.; Dewhurst, S.;.

AIDS Res. & Human Retroviruses. 2004; 20(3): 1324-1334.

Flap endonuclease 1: a central component of DNA metabolism.

Liu Y, Kao HI, Bambara RA

Annual review of biochemistry.. 2004 73 :589-615. Epub 1900 01 01.

Analysis of DNA replication intermediates suggests mechanisms of repeat sequence expansion.

Veeraraghavan J, Rossi ML, Bambara RA

The Journal of biological chemistry.. 2003 October 31278 (44):42854-66. Epub 08/05/2003.

Steps of the acceptor invasion mechanism for HIV-1 minus strand strong stop transfer.

Chen Y, Balakrishnan M, Roques BP, Bambara RA

The Journal of biological chemistry.. 2003 October 3278 (40):38368-75. Epub 07/22/2003.

Role of the Reverse Transcriptase, Nucleocapsid Protein, and Template Structure in the Two-step Transfer Mechanism in Retroviral Recombination.

Roda RH, Balakrishnan M, Hanson MN, Wohrl BM, Le Grice SF, Roques BP, Gorelick RJ, Bambara RA

The Journal of biological chemistry.. 2003 August 22278 (34):31536-46. Epub 06/11/2003.

Mechanistic understanding of an altered fidelity simian immunodeficiency virus reverse transcriptase mutation, V148I, identified in a pig-tailed macaque.

Diamond TL, Souroullas G, Weiss KK, Lee KY, Bambara RA, Dewhurst S, Kim B

The Journal of biological chemistry.. 2003 August 8278 (32):29913-24. Epub 05/08/2003.

Analysis of human flap endonuclease 1 mutants reveals a mechanism to prevent triplet repeat expansion.

Liu Y, Bambara RA

The Journal of biological chemistry.. 2003 April 18278 (16):13728-39. Epub 01/28/2003.

Template dimerization promotes an acceptor invasion-induced transfer mechanism during human immunodeficiency virus type 1 minus-strand synthesis.

Balakrishnan M, Roques BP, Fay PJ, Bambara RA

Journal of virology.. 2003 April 77 (8):4710-21. Epub 1900 01 01.

Mechanism of minus strand strong stop transfer in HIV-1 reverse transcription.

Chen Y, Balakrishnan M, Roques BP, Fay PJ, Bambara RA

The Journal of biological chemistry.. 2003 March 7278 (10):8006-17. Epub 12/23/2002.

The protein components and mechanism of eukaryotic Okazaki fragment maturation.

Kao HI, Bambara RA

Critical reviews in biochemistry and molecular biology. 2003 38 (5):433-52. Epub 1900 01 01.

Strand transfer occurs in retroviruses by a pause-initiated two-step mechanism.

Roda RH, Balakrishnan M, Kim JK, Roques BP, Fay PJ, Bambara RA

The Journal of biological chemistry.. 2002 December 6277 (49):46900-11. Epub 10/04/2002.

AP endonuclease 1 coordinates flap endonuclease 1 and DNA ligase I activity in long patch base excision repair.

Ranalli TA, Tom S, Bambara RA

The Journal of biological chemistry.. 2002 November 1277 (44):41715-24. Epub 08/27/2002.

Flap endonuclease 1 efficiently cleaves base excision repair and DNA replication intermediates assembled into nucleosomes.

Huggins CF, Chafin DR, Aoyagi S, Henricksen LA, Bambara RA, Hayes JJ

Molecular cell.. 2002 November 10 (5):1201-11. Epub 1900 01 01.

Substrate requirements for secondary cleavage by HIV-1 reverse transcriptase RNase H.

Wisniewski M, Chen Y, Balakrishnan M, Palaniappan C, Roques BP, Fay PJ, Bambara RA

The Journal of biological chemistry.. 2002 August 9277 (32):28400-10. Epub 05/21/2002.

Differences in the abilities of estrogen receptors to integrate activation functions are critical for subtype-specific transcriptional responses.

Yi P, Bhagat S, Hilf R, Bambara RA, Muyan M

Molecular endocrinology.. 2002 August 16 (8):1810-27. Epub 1900 01 01.

Structural regions of ERalpha critical for synergistic transcriptional responses contain co-factor interacting surfaces.

Sathya G, Yi P, Bhagat S, Bambara RA, Hilf R, Muyan M

Molecular and cellular endocrinology.. 2002 June 28192 (1-2):171-85. Epub 1900 01 01.

Mechanistic role of residue Gln151 in error prone DNA synthesis by human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT). Pre-steady state kinetic study of the Q151N HIV-1 RT mutant with increased fidelity.

Weiss KK, Bambara RA, Kim B

The Journal of biological chemistry.. 2002 June 21277 (25):22662-9. Epub 04/01/2002.

DNA ligase I competes with FEN1 to expand repetitive DNA sequences in vitro.

Henricksen LA, Veeraraghavan J, Chafin DR, Bambara RA

The Journal of biological chemistry.. 2002 June 21277 (25):22361-9. Epub 04/10/2002.

Cleavage specificity of Saccharomyces cerevisiae flap endonuclease 1 suggests a double-flap structure as the cellular substrate.

Kao HI, Henricksen LA, Liu Y, Bambara RA

The Journal of biological chemistry.. 2002 April 26277 (17):14379-89. Epub 02/01/2002.

The effects of estrogen-responsive element- and ligand-induced structural changes on the recruitment of cofactors and transcriptional responses by ER alpha and ER beta.

Yi P, Driscoll MD, Huang J, Bhagat S, Hilf R, Bambara RA, Muyan M

Molecular endocrinology.. 2002 April 16 (4):674-93. Epub 1900 01 01.

Mechanism underlying replication protein a stimulation of DNA ligase I.

Ranalli TA, DeMott MS, Bambara RA

The Journal of biological chemistry.. 2002 January 18277 (3):1719-27. Epub 11/06/2001.

RPA Governs Endonuclease Switching During Processing of Okazaki Fragments in Eukaryotes

Kao, H.I.; Bambara, R.A.;.

Chemtracts - Biochemistry & Molecular Biology, Eukaryotic DNA Replication. 2002; : 326-333.

Regulatory roles of p21 and apurinic/apyrimidinic endonuclease 1 in base excision repair.

Tom S, Ranalli TA, Podust VN, Bambara RA

The Journal of biological chemistry.. 2001 December 28276 (52):48781-9. Epub 10/18/2001.

Mutation of the methylated tRNA(Lys)(3) residue A58 disrupts reverse transcription and inhibits replication of human immunodeficiency virus type 1.

Renda MJ, Rosenblatt JD, Klimatcheva E, Demeter LM, Bambara RA, Planelles V

Journal of virology.. 2001 October 75 (20):9671-8. Epub 1900 01 01.

The kissing hairpin sequence promotes recombination within the HIV-I 5' leader region.

Balakrishnan M, Fay PJ, Bambara RA

The Journal of biological chemistry.. 2001 September 28276 (39):36482-92. Epub 06/29/2001.

Fusion estrogen receptor proteins: toward the development of receptor-based agonists and antagonists.

Muyan M, Yi P, Sathya G, Willmert LJ, Driscoll MD, Hilf R, Bambara RA

Molecular and cellular endocrinology.. 2001 September 182 (2):249-63. Epub 1900 01 01.

Identification of rad27 mutations that confer differential defects in mutation avoidance, repeat tract instability, and flap cleavage.

Xie Y, Liu Y, Argueso JL, Henricksen LA, Kao HI, Bambara RA, Alani E

Molecular and cellular biology.. 2001 August 21 (15):4889-99. Epub 1900 01 01.

DNA ligase I and proliferating cell nuclear antigen form a functional complex.

Tom S, Henricksen LA, Park MS, Bambara RA

The Journal of biological chemistry.. 2001 July 6276 (27):24817-25. Epub 04/30/2001.

The Y181C mutant of HIV-1 reverse transcriptase resistant to nonnucleoside reverse transcriptase inhibitors alters the size distribution of RNase H cleavages.

Archer RH, Wisniewski M, Bambara RA, Demeter LM

Biochemistry.. 2001 April 340 (13):4087-95. Epub 1900 01 01.

The sequential mechanism of HIV reverse transcriptase RNase H.

Wisniewski M, Balakrishnan M, Palaniappan C, Fay PJ, Bambara RA

The Journal of biological chemistry.. 2000 December 1275 (48):37664-71. Epub 1900 01 01.

Unique progressive cleavage mechanism of HIV reverse transcriptase RNase H.

Wisniewski M, Balakrishnan M, Palaniappan C, Fay PJ, Bambara RA

Proceedings of the National Academy of Sciences of the United States of America.. 2000 October 2497 (22):11978-83. Epub 1900 01 01.

Human DNA ligase I efficiently seals nicks in nucleosomes.

Chafin DR, Vitolo JM, Henricksen LA, Bambara RA, Hayes JJ

The EMBO journal.. 2000 October 1619 (20):5492-501. Epub 1900 01 01.

Mutants of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase resistant to nonnucleoside reverse transcriptase inhibitors demonstrate altered rates of RNase H cleavage that correlate with HIV-1 replication fitness in cell culture.

Archer RH, Dykes C, Gerondelis P, Lloyd A, Fay P, Reichman RC, Bambara RA, Demeter LM

Journal of virology.. 2000 September 74 (18):8390-401. Epub 1900 01 01.

Inhibition of flap endonuclease 1 by flap secondary structure and relevance to repeat sequence expansion.

Henricksen LA, Tom S, Liu Y, Bambara RA

The Journal of biological chemistry.. 2000 June 2275 (22):16420-7. Epub 1900 01 01.

Mechanism whereby proliferating cell nuclear antigen stimulates flap endonuclease 1.

Tom S, Henricksen LA, Bambara RA

The Journal of biological chemistry.. 2000 April 7275 (14):10498-505. Epub 1900 01 01.

Effect of flap modifications on human FEN1 cleavage.

Bornarth CJ, Ranalli TA, Henricksen LA, Wahl AF, Bambara RA

Biochemistry.. 1999 October 538 (40):13347-54. Epub 1900 01 01.

Mutations in the primer grip region of HIV reverse transcriptase can increase replication fidelity.

Wisniewski M, Palaniappan C, Fu Z, Le Grice SF, Fay P, Bambara RA

The Journal of biological chemistry.. 1999 October 1274 (40):28175-84. Epub 1900 01 01.

The P236L delavirdine-resistant human immunodeficiency virus type 1 mutant is replication defective and demonstrates alterations in both RNA 5'-end- and DNA 3'-end-directed RNase H activities.

Gerondelis P, Archer RH, Palaniappan C, Reichman RC, Fay PJ, Bambara RA, Demeter LM

Journal of virology.. 1999 July 73 (7):5803-13. Epub 1900 01 01.

An explanation for observed estrogen receptor binding to single-stranded estrogen-responsive element DNA.

Driscoll MD, Sathya G, Saidi LF, DeMott MS, Hilf R, Bambara RA

Molecular endocrinology.. 1999 June 13 (6):958-68. Epub 1900 01 01.

Cleavage of substrates with mismatched nucleotides by Flap endonuclease-1. Implications for mammalian Okazaki fragment processing.

Rumbaugh JA, Henricksen LA, DeMott MS, Bambara RA

The Journal of biological chemistry.. 1999 May 21274 (21):14602-8. Epub 1900 01 01.

Sequence requirements for estrogen receptor binding to estrogen response elements.

Driscoll MD, Sathya G, Muyan M, Klinge CM, Hilf R, Bambara RA

The Journal of biological chemistry.. 1998 November 6273 (45):29321-30. Epub 1900 01 01.

Processing of an HIV replication intermediate by the human DNA replication enzyme FEN1.

Rumbaugh JA, Fuentes GM, Bambara RA

The Journal of biological chemistry.. 1998 October 30273 (44):28740-5. Epub 1900 01 01.

Replication protein A stimulates long patch DNA base excision repair.

DeMott MS, Zigman S, Bambara RA

The Journal of biological chemistry.. 1998 October 16273 (42):27492-8. Epub 1900 01 01.

Comparison of tamoxifen ligands on estrogen receptor interaction with estrogen response elements.

Klinge CM, Studinski-Jones AL, Kulakosky PC, Bambara RA, Hilf R

Molecular and cellular endocrinology.. 1998 August 25143 (1-2):79-90. Epub 1900 01 01.

Junction ribonuclease: an activity in Okazaki fragment processing.

Murante RS, Henricksen LA, Bambara RA

Proceedings of the National Academy of Sciences of the United States of America.. 1998 March 395 (5):2244-9. Epub 1900 01 01.

Control of initiation of viral plus strand DNA synthesis by HIV reverse transcriptase.

Palaniappan C, Kim JK, Wisniewski M, Fay PJ, Bambara RA

The Journal of biological chemistry.. 1998 February 13273 (7):3808-16. Epub 1900 01 01.

Multiprotein reactions in mammalian DNA replication.

Henricksen LA, Bambara RA

Leukemia research.. 1998 January 22 (1):1-5. Epub 1900 01 01.

Chicken ovalbumin upstream promoter-transcription factor interacts with estrogen receptor, binds to estrogen response elements and half-sites, and inhibits estrogen-induced gene expression.

Klinge CM, Silver BF, Driscoll MD, Sathya G, Bambara RA, Hilf R

The Journal of biological chemistry.. 1997 December 12272 (50):31465-74. Epub 1900 01 01.

Effects of multiple estrogen responsive elements, their spacing, and location on estrogen response of reporter genes.

Sathya G, Li W, Klinge CM, Anolik JH, Hilf R, Bambara RA

Molecular endocrinology.. 1997 December 11 (13):1994-2003. Epub 1900 01 01.

Creation and removal of embedded ribonucleotides in chromosomal DNA during mammalian Okazaki fragment processing.

Rumbaugh JA, Murante RS, Shi S, Bambara RA

The Journal of biological chemistry.. 1997 September 5272 (36):22591-9. Epub 1900 01 01.

Evidence for a unique mechanism of strand transfer from the transactivation response region of HIV-1.

Kim JK, Palaniappan C, Wu W, Fay PJ, Bambara RA

The Journal of biological chemistry.. 1997 July 4272 (27):16769-77. Epub 1900 01 01.

Inhibition of HIV-1 replication using a mutated tRNALys-3 primer.

Lu Y, Planelles V, Li X, Palaniappan C, Day B, Challita-Eid P, Amado R, Stephens D, Kohn DB, Bakker A, Fay P, Bambara RA, Rosenblatt JD

The Journal of biological chemistry.. 1997 June 6272 (23):14523-31. Epub 1900 01 01.

Mutations within the primer grip region of HIV-1 reverse transcriptase result in loss of RNase H function.

Palaniappan C, Wisniewski M, Jacques PS, Le Grice SF, Fay PJ, Bambara RA

The Journal of biological chemistry.. 1997 April 25272 (17):11157-64. Epub 1900 01 01.

Enzymes and reactions at the eukaryotic DNA replication fork.

Bambara RA, Murante RS, Henricksen LA

The Journal of biological chemistry.. 1997 February 21272 (8):4647-50. Epub 1900 01 01.

hsp70 is not required for high affinity binding of purified calf uterine estrogen receptor to estrogen response element DNA in vitro.

Klinge CM, Brolly CL, Bambara RA, Hilf R

The Journal of steroid biochemistry and molecular biology.. 1997 63 (4-6):283-301. Epub 1900 01 01.

Stability of the ligand-estrogen receptor interaction depends on estrogen response element flanking sequences and cellular factors.

Anolik JH, Klinge CM, Brolly CL, Bambara RA, Hilf R

The Journal of steroid biochemistry and molecular biology.. 1996 December 59 (5-6):413-29. Epub 1900 01 01.

Strand displacement synthesis in the central polypurine tract region of HIV-1 promotes DNA to DNA strand transfer recombination.

Fuentes GM, Palaniappan C, Fay PJ, Bambara RA

The Journal of biological chemistry.. 1996 November 22271 (47):29605-11. Epub 1900 01 01.

Mechanism of tracking and cleavage of adduct-damaged DNA substrates by the mammalian 5'- to 3'-exonuclease/endonuclease RAD2 homologue 1 or flap endonuclease 1.

Barnes CJ, Wahl AF, Shen B, Park MS, Bambara RA

The Journal of biological chemistry.. 1996 November 22271 (47):29624-31. Epub 1900 01 01.

Human RAD2 homolog 1 5'- to 3'-exo/endonuclease can efficiently excise a displaced DNA fragment containing a 5'-terminal abasic lesion by endonuclease activity.

DeMott MS, Shen B, Park MS, Bambara RA, Zigman S

The Journal of biological chemistry.. 1996 November 22271 (47):30068-76. Epub 1900 01 01.

Calf RTH-1 nuclease can remove the initiator RNAs of Okazaki fragments by endonuclease activity.

Murante RS, Rumbaugh JA, Barnes CJ, Norton JR, Bambara RA

The Journal of biological chemistry.. 1996 October 18271 (42):25888-97. Epub 1900 01 01.

Misincorporation by HIV-1 reverse transcriptase promotes recombination via strand transfer synthesis.

Palaniappan C, Wisniewski M, Wu W, Fay PJ, Bambara RA

The Journal of biological chemistry.. 1996 September 13271 (37):22331-8. Epub 1900 01 01.

Role of calf RTH-1 nuclease in removal of 5'-ribonucleotides during Okazaki fragment processing.

Huang L, Rumbaugh JA, Murante RS, Lin RJ, Rust L, Bambara RA

Biochemistry.. 1996 July 1635 (28):9266-77. Epub 1900 01 01.

Differences in mutagenesis during minus strand, plus strand and strand transfer (recombination) synthesis of the HIV-1 gene in vitro.

Wu W, Palaniappan C, Bambara RA, Fay PJ

Nucleic acids research.. 1996 May 124 (9):1710-8. Epub 1900 01 01.

Relationship between plus strand DNA synthesis removal of downstream segments of RNA by human immunodeficiency virus, murine leukemia virus and avian myeloblastoma virus reverse transcriptases.

Fuentes GM, Fay PJ, Bambara RA

Nucleic acids research.. 1996 May 124 (9):1719-26. Epub 1900 01 01.

Site-directed estrogen receptor antibodies stabilize 4-hydroxytamoxifen ligand, but not estradiol, and indicate ligand-specific differences in the recognition of estrogen response element DNA in vitro.

Klinge CM, Traish AM, Driscoll MD, Hilf R, Bambara RA

Steroids.. 1996 May 61 (5):278-89. Epub 1900 01 01.

Footprint analysis of estrogen receptor binding to adjacent estrogen response elements.

Driscoll MD, Klinge CM, Hilf R, Bambara RA

The Journal of steroid biochemistry and molecular biology.. 1996 April 58 (1):45-61. Epub 1900 01 01.

Strand displacement synthesis of the long terminal repeats by HIV reverse transcriptase.

Fuentes GM, Rodríguez-Rodríguez L, Palaniappan C, Fay PJ, Bambara RA

The Journal of biological chemistry.. 1996 January 26271 (4):1966-71. Epub 1900 01 01.

Helix structure and ends of RNA/DNA hybrids direct the cleavage specificity of HIV-1 reverse transcriptase RNase H.

Palaniappan C, Fuentes GM, Rodríguez-Rodríguez L, Fay PJ, Bambara RA

The Journal of biological chemistry.. 1996 January 26271 (4):2063-70. Epub 1900 01 01.

Dissociation of 4-hydroxytamoxifen, but not estradiol or tamoxifen aziridine, from the estrogen receptor as the receptor binds estrogen response element DNA.

Klinge CM, Traish AM, Bambara RA, Hilf R

The Journal of steroid biochemistry and molecular biology.. 1996 January 57 (1-2):51-66. Epub 1900 01 01.

Calf 5' to 3' exo/endonuclease must slide from a 5' end of the substrate to perform structure-specific cleavage.

Murante RS, Rust L, Bambara RA

The Journal of biological chemistry.. 1995 December 22270 (51):30377-83. Epub 1900 01 01.

Use of an oligoribonucleotide containing the polypurine tract sequence as a primer by HIV reverse transcriptase.

Fuentes GM, Rodríguez-Rodríguez L, Fay PJ, Bambara RA

The Journal of biological chemistry.. 1995 November 24270 (47):28169-76. Epub 1900 01 01.

Influence of human immunodeficiency virus nucleocapsid protein on synthesis and strand transfer by the reverse transcriptase in vitro.

Rodríguez-Rodríguez L, Tsuchihashi Z, Fuentes GM, Bambara RA, Fay PJ

The Journal of biological chemistry.. 1995 June 23270 (25):15005-11. Epub 1900 01 01.

Nevirapine alters the cleavage specificity of ribonuclease H of human immunodeficiency virus 1 reverse transcriptase.

Palaniappan C, Fay PJ, Bambara RA

The Journal of biological chemistry.. 1995 March 3270 (9):4861-9. Epub 1900 01 01.

Cooperative binding of estrogen receptor to DNA depends on spacing of binding sites, flanking sequence, and ligand.

Anolik JH, Klinge CM, Hilf R, Bambara RA

Biochemistry.. 1995 February 2834 (8):2511-20. Epub 1900 01 01.

Strand transfer mediated by human immunodeficiency virus reverse transcriptase in vitro is promoted by pausing and results in misincorporation.

Wu W, Blumberg BM, Fay PJ, Bambara RA

The Journal of biological chemistry.. 1995 January 6270 (1):325-32. Epub 1900 01 01.

Reconstitution of mammalian DNA replication.

Bambara RA, Huang L

Progress in nucleic acid research and molecular biology. 1995 51 :93-122. Epub 1900 01 01.

Methods of analyzing processivity.

Bambara RA, Fay PJ, Mallaber LM

Methods in enzymology.. 1995 262 :270-80. Epub 1900 01 01.

Characterization of an RNase H deficient mutant of human immunodeficiency virus-1 reverse transcriptase having an aspartate to asparagine change at position 498.

DeStefano JJ, Wu W, Seehra J, McCoy J, Laston D, Albone E, Fay PJ, Bambara RA

Biochimica et biophysica acta.. 1994 October 181219 (2):380-8. Epub 1900 01 01.

Structure-specific cleavage of the RNA primer from Okazaki fragments by calf thymus RNase HI.

Huang L, Kim Y, Turchi JJ, Bambara RA

The Journal of biological chemistry.. 1994 October 14269 (41):25922-7. Epub 1900 01 01.

Enzymatic completion of mammalian lagging-strand DNA replication.

Turchi JJ, Huang L, Murante RS, Kim Y, Bambara RA

Proceedings of the National Academy of Sciences of the United States of America.. 1994 October 1191 (21):9803-7. Epub 1900 01 01.

Quantitative analysis of RNA cleavage during RNA-directed DNA synthesis by human immunodeficiency and avian myeloblastosis virus reverse transcriptases.

DeStefano JJ, Mallaber LM, Fay PJ, Bambara RA

Nucleic acids research.. 1994 September 1122 (18):3793-800. Epub 1900 01 01.

The calf 5'- to 3'-exonuclease is also an endonuclease with both activities dependent on primers annealed upstream of the point of cleavage.

Murante RS, Huang L, Turchi JJ, Bambara RA

The Journal of biological chemistry.. 1994 January 14269 (2):1191-6. Epub 1900 01 01.

The mechanism of human immunodeficiency virus reverse transcriptase-catalyzed strand transfer from internal regions of heteropolymeric RNA templates.

DeStefano JJ, Bambara RA, Fay PJ

The Journal of biological chemistry.. 1994 January 7269 (1):161-8. Epub 1900 01 01.

Activity of calf thymus DNA helicase E on cis-diamminedichloroplatinum (II)-damaged DNA.

Huang L, Turchi JJ, Wahl AF, Bambara RA

The Journal of biological chemistry.. 1993 December 15268 (35):26731-7. Epub 1900 01 01.

Differential impact of flanking sequences on estradiol- vs 4-hydroxytamoxifen-liganded estrogen receptor binding to estrogen responsive element DNA.

Anolik JH, Klinge CM, Bambara RA, Hilf R

The Journal of steroid biochemistry and molecular biology.. 1993 December 46 (6):713-30. Epub 1900 01 01.

Pausing by retroviral DNA polymerases promotes strand transfer from internal regions of RNA donor templates to homopolymeric acceptor templates.

Buiser RG, Bambara RA, Fay PJ

Biochimica et biophysica acta.. 1993 October 191216 (1):20-30. Epub 1900 01 01.

Determinants of the RNase H cleavage specificity of human immunodeficiency virus reverse transcriptase.

DeStefano JJ, Mallaber LM, Fay PJ, Bambara RA

Nucleic acids research.. 1993 September 1121 (18):4330-8. Epub 1900 01 01.

Completion of mammalian lagging strand DNA replication using purified proteins.

Turchi JJ, Bambara RA

The Journal of biological chemistry.. 1993 July 15268 (20):15136-41. Epub 1900 01 01.

Parameters that influence the binding of human immunodeficiency virus reverse transcriptase to nucleic acid structures.

DeStefano JJ, Bambara RA, Fay PJ

Biochemistry.. 1993 July 1332 (27):6908-15. Epub 1900 01 01.

Effects of the anticancer drug cis-diamminedichloroplatinum(II) on the activities of calf thymus DNA polymerase epsilon.

Huang L, Turchi JJ, Wahl AF, Bambara RA

Biochemistry.. 1993 January 2632 (3):841-8. Epub 1900 01 01.

DNA substrate specificity of DNA helicase E from calf thymus.

Turchi JJ, Murante RS, Bambara RA

Nucleic acids research.. 1992 November 2520 (22):6075-80. Epub 1900 01 01.

Requirements for strand transfer between internal regions of heteropolymer templates by human immunodeficiency virus reverse transcriptase.

DeStefano JJ, Mallaber LM, Rodriguez-Rodriguez L, Fay PJ, Bambara RA

Journal of virology.. 1992 November 66 (11):6370-8. Epub 1900 01 01.

A 5' to 3' exonuclease functionally interacts with calf DNA polymerase epsilon.

Siegal G, Turchi JJ, Myers TW, Bambara RA

Proceedings of the National Academy of Sciences of the United States of America.. 1992 October 1589 (20):9377-81. Epub 1900 01 01.

Antiestrogen-liganded estrogen receptor interaction with estrogen responsive element DNA in vitro.

Klinge CM, Bambara RA, Hilf R

The Journal of steroid biochemistry and molecular biology.. 1992 October 43 (4):249-62. Epub 1900 01 01.

DNA helicase E and DNA polymerase epsilon functionally interact for displacement synthesis.

Turchi JJ, Siegal G, Bambara RA

Biochemistry.. 1992 September 2231 (37):9008-15. Epub 1900 01 01.

Parameters that influence processive synthesis and site-specific termination by human immunodeficiency virus reverse transcriptase on RNA and DNA templates.

DeStefano JJ, Buiser RG, Mallaber LM, Fay PJ, Bambara RA

Biochimica et biophysica acta.. 1992 July 151131 (3):270-80. Epub 1900 01 01.

A novel DNA helicase from calf thymus.

Siegal G, Turchi JJ, Jessee CB, Myers TW, Bambara RA

The Journal of biological chemistry.. 1992 July 5267 (19):13629-35. Epub 1900 01 01.

Cooperative estrogen receptor interaction with consensus or variant estrogen responsive elements in vitro.

Klinge CM, Peale FV, Hilf R, Bambara RA, Zain S

Cancer research.. 1992 March 152 (5):1073-81. Epub 1900 01 01.

Structural relationships between two forms of DNA polymerase epsilon from calf thymus.

Siegal G, Turchi JJ, Jessee CB, Mallaber LM, Bambara RA, Myers TW

The Journal of biological chemistry.. 1992 February 25267 (6):3991-9. Epub 1900 01 01.

Characteristics of ATPgS-Induced Complexes Formed between Escherichia coli DNA Polymerase III Holoenzyme and Primed DNA

Kwon, O.; Bambara, R. A.;.

Mol. Cells (Korea). 1992; 2(3): 53-60.

What differentiates antiestrogen-liganded vs estradiol-liganded estrogen receptor action?

Klinge CM, Bambara RA, Hilf R

Oncology research.. 1992 4 (4-5):137-44. Epub 1900 01 01.

Human immunodeficiency virus reverse transcriptase displays a partially processive 3' to 5' endonuclease activity.

DeStefano JJ, Buiser RG, Mallaber LM, Bambara RA, Fay PJ

The Journal of biological chemistry.. 1991 December 25266 (36):24295-301. Epub 1900 01 01.

Fidelity of mammalian DNA replication and replicative DNA polymerases.

Thomas DC, Roberts JD, Sabatino RD, Myers TW, Tan CK, Downey KM, So AG, Bambara RA, Kunkel TA

Biochemistry.. 1991 December 2430 (51):11751-9. Epub 1900 01 01.

Requirements for the catalysis of strand transfer synthesis by retroviral DNA polymerases.

Buiser RG, DeStefano JJ, Mallaber LM, Fay PJ, Bambara RA

The Journal of biological chemistry.. 1991 July 15266 (20):13103-9. Epub 1900 01 01.

Polymerization and RNase H activities of the reverse transcriptases from avian myeloblastosis, human immunodeficiency, and Moloney murine leukemia viruses are functionally uncoupled.

DeStefano JJ, Buiser RG, Mallaber LM, Myers TW, Bambara RA, Fay PJ

The Journal of biological chemistry.. 1991 April 25266 (12):7423-31. Epub 1900 01 01.

Estrogen receptor alters the topology of plasmid DNA containing estrogen responsive elements.

Ishibe Y, Klinge CM, Hilf R, Bambara RA

Biochemical and biophysical research communications.. 1991 April 15176 (1):486-91. Epub 1900 01 01.

Properties of DNA polymerases delta and epsilon, and their roles in eukaryotic DNA replication.

Bambara RA, Jessee CB

Biochimica et biophysica acta.. 1991 January 171088 (1):11-24. Epub 1900 01 01.

Substrate specificity of the exonuclease associated with calf DNA polymerase.

Sabatino RD, Myers TW, Bambara RA

Cancer research.. 1990 September 150 (17):5340-4. Epub 1900 01 01.

Revised nomenclature for eukaryotic DNA polymerases.

Burgers PM, Bambara RA, Campbell JL, Chang LM, Downey KM, Hübscher U, Lee MY, Linn SM, So AG, Spadari S

European journal of biochemistry. 1990 August 17191 (3):617-8. Epub 1900 01 01.

A microtiter well assay for quantitative measurement of estrogen receptor binding to estrogen-responsive elements.

Ludwig LB, Klinge CM, Peale FV, Bambara RA, Zain S, Hilf R

Molecular endocrinology.. 1990 July 4 (7):1027-33. Epub 1900 01 01.

Nuclease sensitivity of estradiol-charged estrogen receptor binding sites in nuclei isolated from normal and neoplastic rat mammary tissues.

Klinge CM, Bambara RA, Zain S, Hilf R

Journal of steroid biochemistry.. 1990 June 36 (1-2):7-14. Epub 1900 01 01.

Selective inhibition of DNA primase activity associated with DNA polymerase alpha from calf thymus.

Bodner JB, Bambara RA

Cancer biochemistry biophysics. 1990 January 11 (1):7-12. Epub 1900 01 01.

DNA Polymerase Delta, in The Eukaryotic Nucleus

Bambara, R. A.; yers, T. W.; Sabatino, R. D.;.

Molecular Biochemistry and Macromolecular Assemblies. Eds., Strauss, P. and S. Wilson. Telford Press, Caldwell, NJ. 1990; 1(3): 69-94.

Proliferating Cell Nuclear Antigen Dependent and Independent Forms of Calf Thymus DNA Polymerase Delta

Myers, T. W.; Bambara, R. A. ;.

UCLA Symposia on Molecular and Cellular Biology, New Series. Eds., Srere, P., M. Jones and C. Mathews. Alan R. Liss, Inc., NY. 1990; 134(3): 165-180.

Alterations in the phosphorylation and activity of DNA polymerase alpha correlate with the change in replicative DNA synthesis as quiescent cells re-enter the cell cycle.

Cripps-Wolfman J, Henshaw EC, Bambara RA

The Journal of biological chemistry.. 1989 November 25264 (33):19478-86. Epub 1900 01 01.

Rapid purification of the estrogen receptor by sequence-specific DNA affinity chromatography.

Peale FV, Ishibe Y, Klinge CM, Zain S, Hilf R, Bambara RA

Biochemistry.. 1989 October 3128 (22):8671-5. Epub 1900 01 01.

Antiestrogen(4-hydroxytamoxifen)-charged estrogen receptor binding to nuclei from normal and neoplastic rat mammary tissues is not affected by host hormonal status.

Klinge CM, Knox DT, Bambara RA, Zain S, Hilf R

Journal of steroid biochemistry.. 1989 September 33 (3):335-40. Epub 1900 01 01.

Gene expression of PCNA/cyclin in adult tissues and the R3230AC mammary tumor of rat.

Liu YC, Bambara RA

Biochemical and biophysical research communications.. 1989 June 15161 (2):873-82. Epub 1900 01 01.

Requirement for proliferating cell nuclear antigen expression during stages of the Chinese hamster ovary cell cycle.

Liu YC, Marraccino RL, Keng PC, Bambara RA, Lord EM, Chou WG, Zain SB

Biochemistry.. 1989 April 428 (7):2967-74. Epub 1900 01 01.

Effects of host hormonal status on binding of activated estrogen receptor to nuclei from R3230AC and 7,12-dimethylbenz[a]anthracene-induced mammary tumors.

Klinge CM, Bambara RA, Zain S, Hilf R

Cancer research.. 1989 March 149 (5):1165-70. Epub 1900 01 01.

Analysis of Mutational Mechanisms with Eukaryotic DNA Polymerases

Kunkel, T. A.; Bambara, R. A.; Bebenek, K.; Roberts, J. D.; Sabatino, R. D.; Smith, M. P.; Soni, A. ;.

UCLA Symposia on Molecular and Cellular Biology, New Series, Vol. 82, Eds., E. Friedberg and Hanawalt, P.. Alan R. Liss, Inc., NY. 1989; 1(3): 521-528.

Calf thymus DNA polymerases alpha and delta are capable of highly processive DNA synthesis.

Sabatino RD, Myers TW, Bambara RA, Kwon-Shin O, Marraccino RL, Frickey PH

Biochemistry.. 1988 April 1927 (8):2998-3004. Epub 1900 01 01.

Properties of the 3' to 5' exonuclease associated with calf DNA polymerase delta.

Sabatino RD, Bambara RA

Biochemistry.. 1988 April 527 (7):2266-71. Epub 1900 01 01.

Properties of a high-affinity DNA binding site for estrogen receptor.

Peale FV, Ludwig LB, Zain S, Hilf R, Bambara RA

Proceedings of the National Academy of Sciences of the United States of America.. 1988 February 85 (4):1038-42. Epub 1900 01 01.

Cell cycle dependent activities of DNA polymerases alpha and delta in Chinese hamster ovary cells.

Marraccino RL, Wahl AF, Keng PC, Lord EM, Bambara RA

Biochemistry.. 1987 December 126 (24):7864-70. Epub 1900 01 01.

Characterization of a cytosolic inhibitor of calf estrogen receptor binding to nuclei.

Lerea CC, Klinge CM, Bambara RA, Zain S, Hilf R

Endocrinology.. 1987 September 121 (3):1146-54. Epub 1900 01 01.

Exonucleolytic proofreading by calf thymus DNA polymerase delta.

Kunkel TA, Sabatino RD, Bambara RA

Proceedings of the National Academy of Sciences of the United States of America.. 1987 July 84 (14):4865-9. Epub 1900 01 01.

Estrogen receptor binding to nuclei from normal and neoplastic rat mammary tissues in vitro.

Klinge CM, Bambara RA, Zain S, Hilf R

Cancer research.. 1987 June 147 (11):2852-9. Epub 1900 01 01.

Properties of initiation complexes formed between Escherichia coli DNA polymerase III holoenzyme and primed DNA in the absence of ATP.

Kwon-Shin O, Bodner JB, McHenry CS, Bambara RA

The Journal of biological chemistry.. 1987 February 15262 (5):2121-30. Epub 1900 01 01.

Purification of a calf thymus DNA-dependent adenosinetriphosphatase that prefers a primer-template junction effector.

Hockensmith JW, Wahl AF, Kowalski S, Bambara RA

Biochemistry.. 1986 December 225 (24):7812-21. Epub 1900 01 01.

Properties of two forms of DNA polymerase delta from calf thymus.

Wahl AF, Crute JJ, Sabatino RD, Bodner JB, Marraccino RL, Harwell LW, Lord EM, Bambara RA

Biochemistry.. 1986 December 225 (24):7821-7. Epub 1900 01 01.

The beta subunit of the Escherichia coli DNA polymerase III holoenzyme interacts functionally with the catalytic core in the absence of other subunits.

LaDuca RJ, Crute JJ, McHenry CS, Bambara RA

The Journal of biological chemistry.. 1986 June 5261 (16):7550-7. Epub 1900 01 01.

Purification and characterization of two new high molecular weight forms of DNA polymerase delta.

Crute JJ, Wahl AF, Bambara RA

Biochemistry.. 1986 January 1425 (1):26-36. Epub 1900 01 01.

Inhibition of mammalian DNA polymerases by hematoporphyrin derivative and photoradiation.

Crute JJ, Wahl AF, Bambara RA, Murant RS, Gibson SL, Hilf R

Cancer research.. 1986 January 46 (1):153-9. Epub 1900 01 01.

Interactions of estrogen-receptor and antiestrogen-receptor complexes with nuclei in vitro.

Cushing CL, Bambara RA, Hilf R

Endocrinology.. 1985 June 116 (6):2419-29. Epub 1900 01 01.

An analysis of the decrease in the assayed level of charged bovine estrogen receptor observed at physiological ionic strength.

Peale FV, Bond J, Hilf R, Bambara R

Journal of steroid biochemistry.. 1985 February 22 (2):161-7. Epub 1900 01 01.

Is Ap4A an activator of eukaryotic DNA replication?

Bambara RA, Crute JJ, Wahl AF

Cancer investigation.. 1985 3 (5):473-9. Epub 1900 01 01.

Analysis of the mechanism of ATP stimulation of calf thymus DNA alpha-polymerase.

Lawton KG, Wierowski JV, Schechter S, Hilf R, Bambara RA

Biochemistry.. 1984 September 1123 (19):4294-300. Epub 1900 01 01.

Bovine estrogen receptor binds chromatin at pre-existing nuclease hypersensitive sites.

Pratt K, Wierowski JV, Hilf R, Bambara RA

Molecular and cellular endocrinology.. 1984 May 35 (2-3):205-14. Epub 1900 01 01.

Immunoaffinity purification and properties of a high molecular weight calf thymus DNA alpha-polymerase.

Wahl AF, Kowalski SP, Harwell LW, Lord EM, Bambara RA

Biochemistry.. 1984 April 2423 (9):1895-9. Epub 1900 01 01.

Site-specific pausing of deoxyribonucleic acid synthesis catalyzed by four forms of Escherichia coli DNA polymerase III.

LaDuca RJ, Fay PJ, Chuang C, McHenry CS, Bambara RA

Biochemistry.. 1983 October 2522 (22):5177-88. Epub 1900 01 01.

Excess beta subunit can bypass the ATP requirement for highly processive synthesis by the Escherichia coli DNA polymerase III holoenzyme.

Crute JJ, LaDuca RJ, Johanson KO, McHenry CS, Bambara RA

The Journal of biological chemistry.. 1983 September 25258 (18):11344-9. Epub 1900 01 01.

Alternative explanation for excision repair deficiency caused by the polAex1 mutation.

Wahl AF, Hockensmith JW, Kowalski S, Bambara RA

Journal of bacteriology.. 1983 August 155 (2):922-5. Epub 1900 01 01.

Stimulation of calf thymus DNA alpha-polymerase by ATP.

Wierowski JV, Lawton KG, Hockensmith JW, Bambara RA

The Journal of biological chemistry.. 1983 May 25258 (10):6250-4. Epub 1900 01 01.

Size classes of products synthesized processively by two subassemblies of Escherichia coli DNA polymerase III holoenzyme.

Fay PJ, Johanson KO, McHenry CS, Bambara RA

The Journal of biological chemistry.. 1982 May 25257 (10):5692-9. Epub 1900 01 01.

Elongation of RNA-primed DNA templates by DNA polymerase alpha from Drosophila melanogaster embryos.

Villani G, Fay PJ, Bambara RA, Lehman IR

The Journal of biological chemistry.. 1981 August 10256 (15):8202-7. Epub 1900 01 01.

Short deoxyribonucleic acid repair patch length in Escherichia coli is determined by the processive mechanism of deoxyribonucleic acid polymerase I.

Matson SW, Bambara RA

Journal of bacteriology.. 1981 April 146 (1):275-84. Epub 1900 01 01.

Duplex DNA binding activity of the avian myeloblastosis virus DNA polymerase.

Matson SW, Bambara RA

Biochimica et biophysica acta.. 1981 January 29652 (1):29-38. Epub 1900 01 01.

Size classes of products synthesized processively by DNA polymerase III and DNA polymerase III holoenzyme of Escherichia coli.

Fay PJ, Johanson KO, McHenry CS, Bambara RA

The Journal of biological chemistry.. 1981 January 25256 (2):976-83. Epub 1900 01 01.

Kinetic characteristics which distinguish two forms of calf thymus DNA polymerase alpha.

Hockensmith JW, Bambara RA

Biochemistry.. 1981 January 620 (1):227-32. Epub 1900 01 01.

Mechanism of inhibition of the avian myeloblastosis virus deoxyribonucleic acid polymerase by adriamycin.

Matson SW, Fay PJ, Bambara RA

Biochemistry.. 1980 May 1319 (10):2089-96. Epub 1900 01 01.

Assessment of Processivity in DNA Polymerase Mechanisms

Bambara, R.; Uyemura, D.;.

Comments on Mol. and Cell. Biophys. 1980; 1(3): 69-80.

On the processive mechanism of Escherichia coli DNA Polymerase I. The polA5 mutation.

Matson SW, Capaldo-Kimball FN, Bambara RA

The Journal of biological chemistry.. 1978 November 10253 (21):7851-6. Epub 1900 01 01.

On the processive mechanism of Escherichia coli DNA polymerase I. Quantitative assessment of processivity.

Bambara RA, Uyemura D, Choi T

The Journal of biological chemistry.. 1978 January 25253 (2):413-23. Epub 1900 01 01.

On the processive mechanism of Escherichia coli DNA polymerase I. Delayed initiation of polymerization.

Bambara RA, Uyemura D, Lehman IR

The Journal of biological chemistry.. 1976 July 10251 (13):4090-4. Epub 1900 01 01.

On the processive mechanism of Escherichia coli DNA polymerase I.

Uyemura D, Bambara R, Lehman IR

The Journal of biological chemistry.. 1975 November 25250 (22):8577-84. Epub 1900 01 01.

DNA sequence analysis. Terminal sequences of bacteriophage phi80.

Bambara R, Wu R

The Journal of biological chemistry.. 1975 June 25250 (12):4607-18. Epub 1900 01 01.

Recent advances in DNA sequence analysis.

Wu R, Bambara R, Jay E

CRC critical reviews in biochemistry. 1975 February 2 (4):455-512. Epub 1900 01 01.

On the statistical significance of primary structural features found in DNA-protein interaction sites

Dykes, G.; Bambara, R.; Marians, K.; Wu, R.;.

Nucleic Acids Res. 1975; 02(33): 327-45.

DNA sequence analysis: a formula to predict electrophoretic mobilities of oligonucleotides on cellulose acetate.

Bambara R, Jay E, Wu R

Nucleic acids research.. 1974 November 1 (11):1503-20. Epub 1900 01 01.

DNA sequence analysis: a general, simple and rapid method for sequencing large oligodeoxyribonucleotide fragments by mapping.

Jay E, Bambara R, Padmanabhan R, Wu R

Nucleic acids research.. 1974 March 1 (3):331-53. Epub 1900 01 01.

Nucleotide sequence analysis of bacteriophage DNA.

Wu R, Padmanabhan R, Bambara R

Methods in enzymology.. 1974 29 :231-53. Epub 1900 01 01.

Nucleotide sequence analysis of DNA. XI. The 3' terminal sequences of bacteriophage lambda and phi 80 DNA.

Ghangas GS, Jay E, Bambara R, Wu R

Biochemical and biophysical research communications.. 1973 October 154 (3):998-1007. Epub 1900 01 01.

Nucleotide sequence analysis of DNA. X. Complete nucleotide sequence of the cohesive ends of bacteriophage phi80 DNA.

Bambara R, Padmanabhan R, Wu R

Journal of molecular biology.. 1973 April 2575 (4):741-4. Epub 1900 01 01.

Structure of Porphyrins in Relation to Reversible Oxidation and Reduction Reactions

Ryan, F. J.; Bambara, R. A.; Loach, P. A.;.

Bioorganic Chem. 1972; 2(3): 44-58.

Identification of the Major Ultraviolet Absorbance Photochanges in Photosynthetic Systems

Loach, P. A.; Bambara, R. A.; Ryan, F. J. ;.

Photochem. Photobiol. 1971; 13(3): 247-257.