Robert A. Bambara

Pif1 Helicase Lengthens Some Okazaki Fragment Flaps Necessitating Dna2 Nuclease/Helicase Action in the Two-nuclease Processing Pathway (2009)

Pike, Jason E., Burgers, Peter M. J., Campbell, Judith L., Bambara, Robert A.

We have developed a system to reconstitute all of the proposed steps of Okazaki fragment processing using purified yeast proteins and model substrates. DNA polymerase δ was shown to extend an...

Significance of the dissociation of Dna2 by flap endonuclease 1 to Okazaki fragment processing in Saccharomyces cerevisiae (2009)

Stewart, Jason A., Campbell, Judith L., Bambara, Robert A.

Okazaki fragments are initiated by short RNA/DNA primers, which are displaced into flap intermediates for processing. Flap endonuclease 1 (FEN1) and Dna2 are responsible for flap cleavage....

Dynamic removal of replication protein A by Dna2 facilitates primer cleavage during Okazaki fragment processing in Saccharomyces cerevisiae (2008)

Stewart, Jason A., Miller, Adam S., Campbell, Judith L., Bambara, Robert A.

Eukaryotic Okazaki fragments are initiated by an RNA/DNA primer, which is removed before the fragments are joined. Polymerase d displaces the primer into a flap for processing. Dna2 nuclease/helicase...

Pif1 helicase directs eukaryotic Okazaki fragments toward the two-nuclease cleavage pathway for primer removal (2008)

Rossi, Marie L., Pike, Jason E., Wang, Wensheng, Burgers, Peter M. J., Campbell, Judith L., Bambara, Robert A.

Eukaryotic Okazaki fragment maturation requires complete removal of the initiating RNA primer before ligation occurs. Polymerase delta (Pol delta) extends the upstream Okazaki fragment and displaces...

Pif1 helicase directs eukaryotic Okazaki fragments toward the two-nuclease cleavage pathway for primer removal (2008)

Rossi, Marie L., Pike, Jason E., Wang, Wensheng, Burgers, Peter M. J., Campbell, Judith L., Bambara, Robert A.

Eukaryotic Okazaki fragment maturation requires complete removal of the initiating RNA primer before ligation occurs. Polymerase delta (Pol delta) extends the upstream Okazaki fragment and displaces...

Flap Endonuclease Disengages Dna2 Helicase/Nuclease from Okazaki Fragment Flaps (2006)

Stewart, Jason A., Campbell, Judith L., Bambara, Robert A.

Okazaki fragments contain an initiator RNA/DNA primer that must be removed before the fragments are joined. In eukaryotes, the primer region is raised into a flap by the strand displacement activity...

Dna2p Helicase/Nuclease Is a Tracking Protein, Like FEN1, for Flap Cleavage during Okazaki Fragment Maturation (2004)

Kao, Hui-I, Campbell, Judith L., Bambara, Robert A.

During cellular DNA replication the lagging strand is generated as discontinuous segments called Okazaki fragments. Each contains an initiator RNA primer that is removed prior to joining of the...

Role of the reverse transcriptase, nucleocapsid protein, and template structure in the two-step transfer mechanism in retroviral recombination (2003)

Roda,Ricardo H., Balakrishnan,Mini, Hanson,Mark N., Wöhrl,Birgitta M., Roques,Bernard P., ...

Role of the reverse transcriptase, nucleocapsid protein, and template structure in the two-step transfer mechanism in retroviral recombination (2003)

Roda, Ricardo H., Balakrishnan, Mini, Hanson, Mark N., Wöhrl, Birgitta M., Roques, Bernard P., ...

Quantitative analysis of RNA cleavage during RNAdirected DNA synthesis by human immunodeficiency and avian myeloblastosis virus reverse transcriptases (1994)

DeStefano, Jeffrey J., Mallaber, Lisa M., Fay, Philip J., Bambara, Robert A.

We have determined the extent of RNA cleavage carried out during DNA synthesis by either human immunodeficiency virus (HIV) or avian myeloblastosis virus (AMV) reverse transcriptases (RTs)....

Determinants of the RNase H cleavage specificity of human immunodeficiency virus reverse transcriptase (1993)

Destefano, Jeffrey J., Mallaber, Lisa M., Fay, Philip J., Bambara, Robert A.

We examined the ribonuclease H (RNase H) specificity of human Immunodeficiency virus reverse transcriptase (HIV-RT) using heteropolymeric RNAs hybridized to complementary DNAs. Experiments were...

DNA substrate specificity of DNA helicase E from calf thymus (1992)

Turchi, John J., Murante, Richard S., Bambara, Robert A.

DNA helicase E from calf thymus has been characterized with respect to DNA substrate specificity. The helicase was capable of displacing DNA fragments up to 140 nucleotides in length, but was unable...

Unique progressive cleavage mechanism of HIV reverse transcriptase RNase H

Wisniewski, Michele, Balakrishnan, Mini, Palaniappan, C., Fay, Philip J., Bambara, Robert A.

HIV-1 reverse transcriptase (RT) degrades the plus strand viral RNA genome while synthesizing the minus strand of DNA. Many RNA fragments, including the polypurine tracts, remain annealed to the new...

Junction ribonuclease: An activity in Okazaki fragment processing

Murante, Richard S., Henricksen, Leigh A., Bambara, Robert A.

The initiator RNAs of mammalian Okazaki fragments are thought to be removed by RNase HI and the 5′-3′ flap endonuclease (FEN1). Earlier evidence indicated that the cleavage site of RNase HI is...

Identification of rad27 Mutations That Confer Differential Defects in Mutation Avoidance, Repeat Tract Instability, and Flap Cleavage

Xie, Yali, Liu, Yuan, Argueso, Juan Lucas, Henricksen, Leigh A., Kao, Hui-I, Bambara, Robert A., ...

In eukaryotes, the nuclease activity of Rad27p (Fen1p) is thought to play a critical role in lagging-strand DNA replication by removing ribonucleotides present at the 5′ ends of Okazaki fragments....

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, Peter, Archer, Richard H., Palaniappan, Chockalingam, Reichman, Richard C., Fay, Philip J., Bambara, Robert A., ...

The nonnucleoside reverse transcriptase (RT) inhibitor (NNRTI) delavirdine (DLV) selects in vitro for the human immunodeficiency virus type 1 (HIV-1) RT mutation P236L, which confers high-level...

Mutation of the Methylated tRNA\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{Lys}}}\end{equation*}\end{document} Residue A58 Disrupts Reverse Transcription and Inhibits Replication of Human Immunodeficiency Virus Type 1

Renda, Matthew J., Rosenblatt, Joseph D., Klimatcheva, Ekaterina, Demeter, Lisa M., Bambara, Robert A., Planelles, Vicente

Cellular tRNA\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs}...

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, Richard H., Dykes, Carrie, Gerondelis, Peter, Lloyd, Amanda, Fay, Philip, Reichman, Richard C., ...

Three mutants of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (V106A, V179D, and Y181C), which occur in clinical isolates and confer resistance to nonnucleoside reverse...

Template Dimerization Promotes an Acceptor Invasion-Induced Transfer Mechanism during Human Immunodeficiency Virus Type 1 Minus-Strand Synthesis

Balakrishnan, Mini, Roques, Bernard P., Fay, Philip J., Bambara, Robert A.

The biochemical mechanism of template switching by human immunodeficiency virus type 1 (HIV-1) reverse transcriptase and the role of template dimerization were examined. Homologous donor-acceptor...

Human DNA ligase I efficiently seals nicks in nucleosomes

Chafin, David R., Vitolo, Joseph M., Henricksen, Leigh A., Bambara, Robert A., Hayes, Jeffrey J.

The access to DNA within nucleosomes is greatly restricted for most enzymes and trans-acting factors that bind DNA. We report here that human DNA ligase I, which carries out the final step of...

WRN Helicase and FEN-1 Form a Complex upon Replication Arrest and Together Process Branchmigrating DNA Structures Associated with the Replication Fork

Sharma, Sudha, Otterlei, Marit, Sommers, Joshua A., Driscoll, Henry C., Dianov, Grigory L., Kao, Hui-I, ...

Werner Syndrome is a premature aging disorder characterized by genomic instability, elevated recombination, and replication defects. It has been hypothesized that defective processing of certain...

Saccharomyces cerevisiae Flap Endonuclease 1 Uses Flap Equilibration To Maintain Triplet Repeat Stability

Liu, Yuan, Zhang, Haihua, Veeraraghavan, Janaki, Bambara, Robert A., Freudenreich, Catherine H.

Flap endonuclease 1 (FEN1) is a central component of Okazaki fragment maturation in eukaryotes. Genetic analysis of Saccharomyces cerevisiae FEN1 (RAD27) also reveals its important role in preventing...

Single-Chain Estrogen Receptors (ERs) Reveal that the ERα/β Heterodimer Emulates Functions of the ERα Dimer in Genomic Estrogen Signaling Pathways

Li, Xiaodong, Huang, Jing, Yi, Ping, Bambara, Robert A., Hilf, Russell, Muyan, Mesut

The effects of estrogens, particularly 17β-estradiol (E2), are mediated by estrogen receptor α (ERα) and ERβ. Upon binding to E2, ERs homo- and heterodimerize when coexpressed. The ER dimer then...

The human Rad9–Rad1–Hus1 checkpoint complex stimulates flap endonuclease 1

Wang, Wensheng, Brandt, Patrick, Rossi, Marie L., Lindsey-Boltz, Laura, Podust, Vladimir, Fanning, Ellen, ...

The toroidal damage checkpoint complex Rad9–Rad1–Hus1 (9-1-1) has been characterized as a sensor of DNA damage. Flap endonuclease 1 (FEN1) is a structure-specific nuclease involved both in...

Macrophage tropism of HIV-1 depends upon efficient cellular dNTP utilization by reverse transcriptase+

Diamond, Tracy L., Roshal, Mikhail, Jamburuthugoda, Varuni K., Reynolds, Holly M., Merriam, Aaron R., Lee, Kwi Y., ...

Retroviruses utilize cellular dNTPs to perform proviral DNA synthesis in infected host cells. Unlike oncoretroviruses, which replicate only in dividing cells, lentiviruses, such as HIV-1 and SIV, are...

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

Huang, Jing, Li, Xiaodong, Qiao, Tao, Bambara, Robert A., Hilf, Russell, Muyan, Mesut

The interaction of ERα and ERβ with ERE constitutes the initial step in the canonical nuclear E2 signaling in which E2-ERβ is a weaker transactivator than E2-ERα. This perspective summarizes...

Unique progressive cleavage mechanism of HIV reverse transcriptase RNase H

Wisniewski, Michele, Balakrishnan, Mini, Palaniappan, C., Fay, Philip J., Bambara, Robert A.

HIV-1 reverse transcriptase (RT) degrades the plus strand viral RNA genome while synthesizing the minus strand of DNA. Many RNA fragments, including the polypurine tracts, remain annealed to the new...

Junction ribonuclease: An activity in Okazaki fragment processing

Murante, Richard S., Henricksen, Leigh A., Bambara, Robert A.

The initiator RNAs of mammalian Okazaki fragments are thought to be removed by RNase HI and the 5′-3′ flap endonuclease (FEN1). Earlier evidence indicated that the cleavage site of RNase HI is...

Identification of rad27 Mutations That Confer Differential Defects in Mutation Avoidance, Repeat Tract Instability, and Flap Cleavage

Xie, Yali, Liu, Yuan, Argueso, Juan Lucas, Henricksen, Leigh A., Kao, Hui-I, Bambara, Robert A., ...

In eukaryotes, the nuclease activity of Rad27p (Fen1p) is thought to play a critical role in lagging-strand DNA replication by removing ribonucleotides present at the 5′ ends of Okazaki fragments....

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, Peter, Archer, Richard H., Palaniappan, Chockalingam, Reichman, Richard C., Fay, Philip J., Bambara, Robert A., ...

The nonnucleoside reverse transcriptase (RT) inhibitor (NNRTI) delavirdine (DLV) selects in vitro for the human immunodeficiency virus type 1 (HIV-1) RT mutation P236L, which confers high-level...

Mutation of the Methylated tRNA\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{Lys}}}\end{equation*}\end{document} Residue A58 Disrupts Reverse Transcription and Inhibits Replication of Human Immunodeficiency Virus Type 1

Renda, Matthew J., Rosenblatt, Joseph D., Klimatcheva, Ekaterina, Demeter, Lisa M., Bambara, Robert A., Planelles, Vicente

Cellular tRNA\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs}...

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, Richard H., Dykes, Carrie, Gerondelis, Peter, Lloyd, Amanda, Fay, Philip, Reichman, Richard C., ...

Three mutants of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (V106A, V179D, and Y181C), which occur in clinical isolates and confer resistance to nonnucleoside reverse...

Template Dimerization Promotes an Acceptor Invasion-Induced Transfer Mechanism during Human Immunodeficiency Virus Type 1 Minus-Strand Synthesis

Balakrishnan, Mini, Roques, Bernard P., Fay, Philip J., Bambara, Robert A.

The biochemical mechanism of template switching by human immunodeficiency virus type 1 (HIV-1) reverse transcriptase and the role of template dimerization were examined. Homologous donor-acceptor...

Human DNA ligase I efficiently seals nicks in nucleosomes

Chafin, David R., Vitolo, Joseph M., Henricksen, Leigh A., Bambara, Robert A., Hayes, Jeffrey J.

The access to DNA within nucleosomes is greatly restricted for most enzymes and trans-acting factors that bind DNA. We report here that human DNA ligase I, which carries out the final step of...

WRN Helicase and FEN-1 Form a Complex upon Replication Arrest and Together Process Branchmigrating DNA Structures Associated with the Replication Fork

Sharma, Sudha, Otterlei, Marit, Sommers, Joshua A., Driscoll, Henry C., Dianov, Grigory L., Kao, Hui-I, ...

Werner Syndrome is a premature aging disorder characterized by genomic instability, elevated recombination, and replication defects. It has been hypothesized that defective processing of certain...

Saccharomyces cerevisiae Flap Endonuclease 1 Uses Flap Equilibration To Maintain Triplet Repeat Stability

Liu, Yuan, Zhang, Haihua, Veeraraghavan, Janaki, Bambara, Robert A., Freudenreich, Catherine H.

Flap endonuclease 1 (FEN1) is a central component of Okazaki fragment maturation in eukaryotes. Genetic analysis of Saccharomyces cerevisiae FEN1 (RAD27) also reveals its important role in preventing...

Single-Chain Estrogen Receptors (ERs) Reveal that the ERα/β Heterodimer Emulates Functions of the ERα Dimer in Genomic Estrogen Signaling Pathways

Li, Xiaodong, Huang, Jing, Yi, Ping, Bambara, Robert A., Hilf, Russell, Muyan, Mesut

The effects of estrogens, particularly 17β-estradiol (E2), are mediated by estrogen receptor α (ERα) and ERβ. Upon binding to E2, ERs homo- and heterodimerize when coexpressed. The ER dimer then...

The human Rad9–Rad1–Hus1 checkpoint complex stimulates flap endonuclease 1

Wang, Wensheng, Brandt, Patrick, Rossi, Marie L., Lindsey-Boltz, Laura, Podust, Vladimir, Fanning, Ellen, ...

The toroidal damage checkpoint complex Rad9–Rad1–Hus1 (9-1-1) has been characterized as a sensor of DNA damage. Flap endonuclease 1 (FEN1) is a structure-specific nuclease involved both in...

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

Huang, Jing, Li, Xiaodong, Qiao, Tao, Bambara, Robert A., Hilf, Russell, Muyan, Mesut

The interaction of ERα and ERβ with ERE constitutes the initial step in the canonical nuclear E2 signaling in which E2-ERβ is a weaker transactivator than E2-ERα. This perspective summarizes...

Reduced dNTP Binding Affinity of 3TC-resistant M184I HIV-1 Reverse Transcriptase Variants Responsible for Viral Infection Failure in Macrophage*

Jamburuthugoda, Varuni K, Santos-Velazquez, Jose M., Skasko, Mark, Operario, Darwin J., Purohit, Vandana, Chugh, Pauline, ...

We characterized HIV-1 reverse transcriptase (RT) variants either with or without the (-)-2′,3′-deoxy-3′-thiacytidine-resistant M184I mutation isolated from a single HIV-1 infected patient....

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, Lu, Hanson, Mark Nils, Balakrishnan, Mini, Boyer, Paul L., Roques, Bernard P., Hughes, Stephen H., ...

The 2′,3′-dideoxy-3′-thiacytidine drug-resistant M184I HIV-1 reverse transcriptase (RT) has been shown to synthesize DNA with decreased processivity compared with the wild-type RT. M184A...

Catalysis of Strand Annealing by Replication Protein A Derives from Its Strand Melting Properties*

Bartos, Jeremy D., Willmott, Lyndsay J., Binz, Sara K., Wold, Marc S., Bambara, Robert A.

Eukaryotic DNA-binding protein replication protein A (RPA) has a strand melting property that assists polymerases and helicases in resolving DNA secondary structures. Curiously, previous results...

Pif1 Helicase Directs Eukaryotic Okazaki Fragments toward the Two-nuclease Cleavage Pathway for Primer Removal*

Rossi, Marie L., Pike, Jason E., Wang, Wensheng, Burgers, Peter M. J., Campbell, Judith L., Bambara, Robert A.

Eukaryotic Okazaki fragment maturation requires complete removal of the initiating RNA primer before ligation occurs. Polymerase δ (Pol δ) extends the upstream Okazaki fragment and displaces the...

Dynamic Removal of Replication Protein A by Dna2 Facilitates Primer Cleavage during Okazaki Fragment Processing in Saccharomyces cerevisiae*

Stewart, Jason A., Miller, Adam S., Campbell, Judith L., Bambara, Robert A.

Eukaryotic Okazaki fragments are initiated by a RNA/DNA primer, which is removed before the fragments are joined. Polymerase δ displaces the primer into a flap for processing. Dna2 nuclease/helicase...