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Principal Investigator

Robert A. Bambara, Ph.D. University of Rochester work 601 Elmwood Ave Rochester NY 14642 office: KMRB 2-9649 p 585-275-3269 robert_bambara@urmc.rochester.edu

Recent Publications

The following list was auto-generated 1 week ago.

• 1. Wang J
  2. Li D
  3. Bambara RA
  4. Yang H
  5. Dykes C
  (2013 Mar 27). 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. J Gen Virol. In press.
• 1. Balakrishnan L
  2. Bambara RA
  (2013 Feb 28). Flap Endonuclease 1. Annu Rev Biochem. In press.
• 1. Balakrishnan L
  2. Bambara RA
  (2013 Feb 01). Okazaki fragment metabolism. Cold Spring Harb Perspect Biol. 5, .
• 1. Kantartzis A
  2. Williams GM
  3. Balakrishnan L
  4. Roberts RL
  5. Surtees JA
  6. Bambara RA
  (2012 Aug 30). Msh2-Msh3 interferes with Okazaki fragment processing to promote trinucleotide repeat expansions. Cell Rep. 2, 216-22.
• 1. Gloor JW
  2. Balakrishnan L
  3. Campbell JL
  4. Bambara RA
  (2012 Aug 01). Biochemical analyses indicate that binding and cleavage specificities define the ordered processing of human Okazaki fragments by Dna2 and FEN1. Nucleic Acids Res. 40, 6774-86.
• 1. Kennedy EM
  2. Amie SM
  3. Bambara RA
  4. Kim B
  (2012 Apr 20). Frequent incorporation of ribonucleotides during HIV-1 reverse transcription and their attenuated repair in macrophages. J Biol Chem. 287, 14280-8.
• 1. Miller AS
  2. Balakrishnan L
  3. Buncher NA
  4. Opresko PL
  5. Bambara RA
  (2012 Mar 01). Telomere proteins POT1, TRF1 and TRF2 augment long-patch base excision repair in vitro. Cell Cycle. 11, 998-1007.
• 1. Nguyen LA
  2. Daddacha W
  3. Rigby S
  4. Bambara RA
  5. Kim B
  (2012 Jan 13). Altered strand transfer activity of a multiple-drug-resistant human immunodeficiency virus type 1 reverse transcriptase mutant with a dipeptide fingers domain insertion. J Mol Biol. 415, 248-62.
• 1. Wang J
  2. Zhang G
  3. Bambara RA
  4. Li D
  5. Liang H
  6. Wu H
  7. Smith HM
  8. Lowe NR
  9. Demeter LM
  10. Dykes C
  (2011 Oct 01). Nonnucleoside reverse transcriptase inhibitor-resistant HIV is stimulated by efavirenz during early stages of infection. J Virol. 85, 10861-73.
• 1. Muchiri JM
  2. Rigby ST
  3. Nguyen LA
  4. Kim B
  5. Bambara RA
  (2011 Sep 23). HIV-1 reverse transcriptase dissociates during strand transfer. J Mol Biol. 412, 354-64.
• 1. Shen W
  2. Gorelick RJ
  3. Bambara RA
  (2011 Aug 26). HIV-1 nucleocapsid protein increases strand transfer recombination by promoting dimeric G-quartet formation. J Biol Chem. 286, 29838-47.
• 1. Balakrishnan L
  2. Bambara RA
  (2011 Aug 15). The changing view of Dna2. Cell Cycle. 10, 2620-1.
• 1. Gewandter JS
  2. Bambara RA
  3. O'Reilly MA
  (2011 Aug 01). The RNA surveillance protein SMG1 activates p53 in response to DNA double-strand breaks but not exogenously oxidized mRNA. Cell Cycle. 10, 2561-7.
• 1. Fortini BK
  2. Pokharel S
  3. Polaczek P
  4. Balakrishnan L
  5. Bambara RA
  6. Campbell JL
  (2011 Jul 08). Characterization of the endonuclease and ATP-dependent flap endo/exonuclease of Dna2. J Biol Chem. 286, 23763-70.
• 1. Piekna-Przybylska D
  2. Bambara RA
  (2011 May 20). Requirements for efficient minus strand strong-stop DNA transfer in human immunodeficiency virus 1. RNA Biol. 8, 230-6.
• 1. Balakrishnan L
  2. Bambara RA
  (2011 Mar 04). Eukaryotic lagging strand DNA replication employs a multi-pathway mechanism that protects genome integrity. J Biol Chem. 286, 6865-70.
• 1. Piekna-Przybylska D
  2. Dykes C
  3. Demeter LM
  4. Bambara RA
  (2011 Feb 20). Sequences in the U3 region of human immunodeficiency virus 1 improve efficiency of minus strand transfer in infected cells. Virology. 410, 368-74.
• 1. Pike JE
  2. Henry RA
  3. Burgers PM
  4. Campbell JL
  5. Bambara RA
  (2010 Dec 31). An alternative pathway for Okazaki fragment processing: resolution of fold-back flaps by Pif1 helicase. J Biol Chem. 285, 41712-23.
• 1. Balakrishnan L
  2. Polaczek P
  3. Pokharel S
  4. Campbell JL
  5. Bambara RA
  (2010 Dec 10). Dna2 exhibits a unique strand end-dependent helicase function. J Biol Chem. 285, 38861-8.
• 1. Gloor JW
  2. Balakrishnan L
  3. Bambara RA
  (2010 Nov 05). Flap endonuclease 1 mechanism analysis indicates flap base binding prior to threading. J Biol Chem. 285, 34922-31.
• 1. Henry RA
  2. Balakrishnan L
  3. Ying-Lin ST
  4. Campbell JL
  5. Bambara RA
  (2010 Sep 10). Components of the secondary pathway stimulate the primary pathway of eukaryotic Okazaki fragment processing. J Biol Chem. 285, 28496-505.
• 1. Wang J
  2. Bambara RA
  3. Demeter LM
  4. Dykes C
  (2010 Sep 01). 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. J Virol. 84, 9377-89.
• 1. Balakrishnan L
  2. Gloor JW
  3. Bambara RA
  (2010 Jul 01). Reconstitution of eukaryotic lagging strand DNA replication. Methods. 51, 347-57.
• 1. Balakrishnan L
  2. Stewart J
  3. Polaczek P
  4. Campbell JL
  5. Bambara RA
  (2010 Feb 12). Acetylation of Dna2 endonuclease/helicase and flap endonuclease 1 by p300 promotes DNA stability by creating long flap intermediates. J Biol Chem. 285, 4398-404.
• 1. Piekna-Przybylska D
  2. DiChiacchio L
  3. Mathews DH
  4. Bambara RA
  (2010 Jan 01). A sequence similar to tRNA 3 Lys gene is embedded in HIV-1 U3-R and promotes minus-strand transfer. Nat Struct Mol Biol. 17, 83-9.
• 1. Stewart JA
  2. Campbell JL
  3. Bambara RA
  (2010 Jan 01). Dna2 is a structure-specific nuclease, with affinity for 5'-flap intermediates. Nucleic Acids Res. 38, 920-30.
• 1. Rigby ST
  2. Van Nostrand KP
  3. Rose AE
  4. Gorelick RJ
  5. Mathews DH
  6. Bambara RA
  (2009 Dec 11). Factors that determine the efficiency of HIV-1 strand transfer initiated at a specific site. J Mol Biol. 394, 694-707.
• 1. Shen W
  2. Gao L
  3. Balakrishnan M
  4. Bambara RA
  (2009 Dec 04). A recombination hot spot in HIV-1 contains guanosine runs that can form a G-quartet structure and promote strand transfer in vitro. J Biol Chem. 284, 33883-93.
• 1. Pike JE
  2. Burgers PM
  3. Campbell JL
  4. Bambara RA
  (2009 Sep 11). Pif1 helicase lengthens some Okazaki fragment flaps necessitating Dna2 nuclease/helicase action in the two-nuclease processing pathway. J Biol Chem. 284, 25170-80.
• 1. Balakrishnan L
  2. Brandt PD
  3. Lindsey-Boltz LA
  4. Sancar A
  5. Bambara RA
  (2009 May 29). Long patch base excision repair proceeds via coordinated stimulation of the multienzyme DNA repair complex. J Biol Chem. 284, 15158-72.
• 1. Rigby ST
  2. Rose AE
  3. Hanson MN
  4. Bambara RA
  (2009 Apr 24). 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. J Mol Biol. 388, 30-47.
• 1. Stewart JA
  2. Campbell JL
  3. Bambara RA
  (2009 Mar 27). Significance of the dissociation of Dna2 by flap endonuclease 1 to Okazaki fragment processing in Saccharomyces cerevisiae. J Biol Chem. 284, 8283-91.
• 1. Song M
  2. Balakrishnan M
  3. Gorelick RJ
  4. Bambara RA
  (2009 Mar 03). A succession of mechanisms stimulate efficient reconstituted HIV-1 minus strand strong stop DNA transfer. Biochemistry. 48, 1810-9.
• 1. Stewart JA
  2. Miller AS
  3. Campbell JL
  4. Bambara RA
  (2008 Nov 14). Dynamic removal of replication protein A by Dna2 facilitates primer cleavage during Okazaki fragment processing in Saccharomyces cerevisiae. J Biol Chem. 283, 31356-65.
• 1. Rossi ML
  2. Pike JE
  3. Wang W
  4. Burgers PM
  5. Campbell JL
  6. Bambara RA
  (2008 Oct 10). Pif1 helicase directs eukaryotic Okazaki fragments toward the two-nuclease cleavage pathway for primer removal. J Biol Chem. 283, 27483-93.
• 1. Bartos JD
  2. Willmott LJ
  3. Binz SK
  4. Wold MS
  5. Bambara RA
  (2008 Aug 01). Catalysis of strand annealing by replication protein A derives from its strand melting properties. J Biol Chem. 283, 21758-68.
• 1. Gehen SC
  2. Staversky RJ
  3. Bambara RA
  4. Keng PC
  5. O'Reilly MA
  (2008 Jul 03). hSMG-1 and ATM sequentially and independently regulate the G1 checkpoint during oxidative stress. Oncogene. 27, 4065-74.
• 1. Basu VP
  2. Song M
  3. Gao L
  4. Rigby ST
  5. Hanson MN
  6. Bambara RA
  (2008 Jun 01). Strand transfer events during HIV-1 reverse transcription. Virus Res. 134, 19-38.
• 1. Li X
  2. Nott SL
  3. Huang Y
  4. Hilf R
  5. Bambara RA
  6. Qiu X
  7. Yakovlev A
  8. Welle S
  9. Muyan M
  (2008 May 01). 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. J Mol Endocrinol. 40, 211-29.
• 1. Gao L
  2. Hanson MN
  3. Balakrishnan M
  4. Boyer PL
  5. Roques BP
  6. Hughes SH
  7. Kim B
  8. Bambara RA
  (2008 Apr 04). 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. J Biol Chem. 283, 9196-205.
• 1. Jamburuthugoda VK
  2. Santos-Velazquez JM
  3. Skasko M
  4. Operario DJ
  5. Purohit V
  6. Chugh P
  7. Szymanski EA
  8. Wedekind JE
  9. Bambara RA
  10. Kim B
  (2008 Apr 04). Reduced dNTP binding affinity of 3TC-resistant M184I HIV-1 reverse transcriptase variants responsible for viral infection failure in macrophage. J Biol Chem. 283, 9206-16.
• 1. Song M
  2. Basu VP
  3. Hanson MN
  4. Roques BP
  5. Bambara RA
  (2008 Feb 08). Proximity and branch migration mechanisms in HIV-1 minus strand strong stop DNA transfer. J Biol Chem. 283, 3141-50.
• 1. Purohit V
  2. Roques BP
  3. Kim B
  4. Bambara RA
  (2007 Apr 27). Mechanisms that prevent template inactivation by HIV-1 reverse transcriptase RNase H cleavages. J Biol Chem. 282, 12598-609.
• 1. Gao L
  2. Balakrishnan M
  3. Roques BP
  4. Bambara RA
  (2007 Mar 02). Insights into the multiple roles of pausing in HIV-1 reverse transcriptase-promoted strand transfers. J Biol Chem. 282, 6222-31.
• 1. Gehen SC
  2. Vitiello PF
  3. Bambara RA
  4. Keng PC
  5. O'Reilly MA
  (2007 Mar 01). Downregulation of PCNA potentiates p21-mediated growth inhibition in response to hyperoxia. Am J Physiol Lung Cell Mol Physiol. 292, L716-24.
• 1. Stewart JA
  2. Campbell JL
  3. Bambara RA
  (2006 Dec 15). Flap endonuclease disengages Dna2 helicase/nuclease from Okazaki fragment flaps. J Biol Chem. 281, 38565-72.
• 1. Hanson MN
  2. Balakrishnan M
  3. Roques BP
  4. Bambara RA
  (2006 Nov 10). Evidence that creation of invasion sites determines the rate of strand transfer mediated by HIV-1 reverse transcriptase. J Mol Biol. 363, 878-90.
• 1. Bartos JD
  2. Wang W
  3. Pike JE
  4. Bambara RA
  (2006 Oct 27). Mechanisms by which Bloom protein can disrupt recombination intermediates of Okazaki fragment maturation. J Biol Chem. 281, 32227-39.
• 1. Operario DJ
  2. Balakrishnan M
  3. Bambara RA
  4. Kim B
  (2006 Oct 27). Reduced dNTP interaction of human immunodeficiency virus type 1 reverse transcriptase promotes strand transfer. J Biol Chem. 281, 32113-21.
• 1. Huang J
  2. Li X
  3. Qiao T
  4. Bambara RA
  5. Hilf R
  6. Muyan M
  (2006 Jan 01). A tale of two estrogen receptors (ERs): how differential ER-estrogen responsive element interactions contribute to subtype-specific transcriptional responses. Nucl Recept Signal. 4, e015.