Linda B Bloom

Linda B Bloom,

Professor

Department: MD-BIOCHEM / MOLECULAR BIOL
Business Phone: (352) 294-8379
Business Email: lbloom@ufl.edu

Teaching Profile

Courses Taught
2013-2023
BCH6040 Research Discussion in Biochemistry and Molecular Biology
2016-2023
GMS5905 Special Topics in Biomedical Sciences
2013-2014,2016-2023
GMS6001 Fundamentals of Biomedical Sciences I
2009-2012,2020
BCH6905 Independent Studies in Biochemistry and Molecular Biology
2009-2012,2020
BCH6971 Research for Master’s Thesis
2009-2012,2020
BCH6910 Supervised Research
2015-2019,2021
BCH6747 Structural Biology/Advanced Physical Biochemistry: Spectroscopy and Hydrodynamics
2014-2019,2021-2022
BCH6415 Advanced Molecular and Cell Biology
2014-2019,2021-2022
BCH6740 Physical Biochemistry/Structural Biology
2018
GMS7980 Research for Doctoral Dissertation
2018
GMS7979 Advanced Research
2018
MCB7979 Advanced Research
2018
MCB7980 Research for Doctoral Dissertation
2014-2015
BCH4024 Introduction to Biochemistry and Molecular Biology
2015,2021
BCH4905 Biochemistry Senior Research
2013,2021
GMS6003 Fundamentals of Graduate Research and Professional Development
2007-2010,2012
BCH6936 Biochemistry Seminar
2012
BCH7979 Advanced Research
2021-2022
BCH7515 Structural Biology/Advanced Physical Biochemistry: Kinetics and Thermodynamics

Research Profile

Open Researcher and Contributor ID (ORCID)

0000-0002-6075-4387

Publications

2021
Alternative complexes formed by the Escherichia coli clamp loader accessory protein HolC (x) with replication protein HolD (ψ) and repair protein YoaA.
DNA repair. 100 [DOI] 10.1016/j.dnarep.2020.103006. [PMID] 33582602.
2021
Potassium Glutamate and Glycine Betaine Induce Self-Assembly of the PCNA and β-Sliding Clamps.
Biophysical journal. 120(1):73-85 [DOI] 10.1016/j.bpj.2020.11.013. [PMID] 33221249.
2021
The SOS Error-Prone DNA Polymerase V Mutasome and β-Sliding Clamp Acting in Concert on Undamaged DNA and during Translesion Synthesis.
Cells. 10(5) [DOI] 10.3390/cells10051083. [PMID] 34062858.
2020
Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity.
Scientific reports. 10(1) [DOI] 10.1038/s41598-019-55118-6. [PMID] 32015389.
2019
Investigation of the Possible Pharmacologically Active Forms of the Nicotinic Acetylcholine Receptor Agonist Anabaseine.
Marine drugs. 17(11) [DOI] 10.3390/md17110614. [PMID] 31671780.
2018
Photophysical characterization of interchromophoric interactions between rhodamine dyes conjugated to proteins.
Methods and applications in fluorescence. 6(4) [DOI] 10.1088/2050-6120/aad20f. [PMID] 29985159.
2018
Secretory granule protein chromogranin B (CHGB) forms an anion channel in membranes.
Life science alliance. 1(5) [DOI] 10.26508/lsa.201800139. [PMID] 30456382.
2017
Electrostatic Interactions at the Dimer Interface Stabilize the E. coli β Sliding Clamp.
Biophysical journal. 113(4):794-804 [DOI] 10.1016/j.bpj.2017.06.057. [PMID] 28834716.
2017
Mechanism of opening a sliding clamp.
Nucleic acids research. 45(17):10178-10189 [DOI] 10.1093/nar/gkx665. [PMID] 28973453.
2016
Solution structure of an “open” E. coli Pol III clamp loader sliding clamp complex.
Journal of structural biology. 194(3):272-81 [DOI] 10.1016/j.jsb.2016.03.003. [PMID] 26968362.
2015
Kinetic analysis of PCNA clamp binding and release in the clamp loading reaction catalyzed by Saccharomyces cerevisiae replication factor C.
Biochimica et biophysica acta. 1854(1):31-8 [DOI] 10.1016/j.bbapap.2014.09.019. [PMID] 25450506.
2015
Solution study of the Escherichia coli DNA polymerase III clamp loader reveals the location of the dynamic ψχ heterodimer.
Structural dynamics (Melville, N.Y.). 2(5) [DOI] 10.1063/1.4927407. [PMID] 26798827.
2014
Human Ap Endonuclease Inefficiently Removes Abasic Sites Within G4 Structures Compared To Duplex Dna
Nucleic acids research. 42(12):7708-7719 [DOI] 10.1093/nar/gku417. [PMID] 24848015.
2014
Intrinsic stability and oligomerization dynamics of DNA processivity clamps.
Nucleic acids research. 42(10):6476-86 [DOI] 10.1093/nar/gku255. [PMID] 24728995.
2014
The ATP sites of AAA+ clamp loaders work together as a switch to assemble clamps on DNA.
The Journal of biological chemistry. 289(9):5537-48 [DOI] 10.1074/jbc.M113.541466. [PMID] 24436332.
2014
The interplay of primer-template DNA phosphorylation status and single-stranded DNA binding proteins in directing clamp loaders to the appropriate polarity of DNA.
Nucleic acids research. 42(16):10655-67 [DOI] 10.1093/nar/gku774. [PMID] 25159615.
2013
A novel function for the conserved glutamate residue in the walker B motif of replication factor C.
Genes. 4(2):134-51 [DOI] 10.3390/genes4020134. [PMID] 23946885.
2013
The β sliding clamp closes around DNA prior to release by the Escherichia coli clamp loader γ complex.
The Journal of biological chemistry. 288(2):1162-70 [DOI] 10.1074/jbc.M112.406231. [PMID] 23161545.
2012
E. Coli and S. Cerevisiae Clamp Loaders, Gamma Complex and Rfc, Actively Close Clamps
The FASEB's Journal. 26
2012
Effect of Quadruplex Dna Formation On Repair of Endogenous Dna Damage
The FASEB's Journal. 26
2012
Improved solubility of replication factor C (RFC) Walker A mutants.
Protein expression and purification. 83(2):135-44 [DOI] 10.1016/j.pep.2012.03.010. [PMID] 22469630.
2012
Replication factor C is a more effective proliferating cell nuclear antigen (PCNA) opener than the checkpoint clamp loader, Rad24-RFC.
The Journal of biological chemistry. 287(3):2203-9 [DOI] 10.1074/jbc.C111.318899. [PMID] 22115746.
2012
S. Cerevisiae Rfc Walker a and Arginine Finger Mutants Are Defective in Clamp Opening and Binding
The FASEB's Journal. 26
2012
Sliding clamps: an open and shut case?
Current biology : CB. 22(5):R157-60 [DOI] 10.1016/j.cub.2012.01.029. [PMID] 22401895.
2011
The Escherichia coli clamp loader can actively pry open the β-sliding clamp.
The Journal of biological chemistry. 286(49):42704-42714 [DOI] 10.1074/jbc.M111.268169. [PMID] 21971175.
2009
A slow ATP-induced conformational change limits the rate of DNA binding but not the rate of beta clamp binding by the escherichia coli gamma complex clamp loader.
The Journal of biological chemistry. 284(46):32147-57 [DOI] 10.1074/jbc.M109.045997. [PMID] 19759003.
2009
Loading clamps for DNA replication and repair.
DNA repair. 8(5):570-8 [DOI] 10.1016/j.dnarep.2008.12.014. [PMID] 19213612.
2009
Temporal correlation of DNA binding, ATP hydrolysis, and clamp release in the clamp loading reaction catalyzed by the Escherichia coli gamma complex.
Biochemistry. 48(36):8516-27 [DOI] 10.1021/bi900912a. [PMID] 19663416.
2007
A function for the psi subunit in loading the Escherichia coli DNA polymerase sliding clamp.
The Journal of biological chemistry. 282(10):7035-45 [PMID] 17210572.
2007
Pre-steady-state kinetic characterization of the AP endonuclease activity of human AP endonuclease 1.
The Journal of biological chemistry. 282(42):30577-85 [PMID] 17724035.
2007
Slow base excision by human alkyladenine DNA glycosylase limits the rate of formation of AP sites and AP endonuclease 1 does not stimulate base excision.
DNA repair. 6(1):71-81 [PMID] 17018265.
2007
Structure/function analysis of the interaction of adenomatous polyposis coli with DNA polymerase beta and its implications for base excision repair.
Biochemistry. 46(49):13961-74 [PMID] 17999539.
2006
Dynamics of loading the Escherichia coli DNA polymerase processivity clamp.
Critical reviews in biochemistry and molecular biology. 41(3):179-208 [PMID] 16760017.
2006
Dynamics of nucleotide incorporation: snapshots revealed by 2-aminopurine fluorescence studies.
Biochemistry. 45(9):2836-44 [PMID] 16503638.
2006
Multiplexed DNA sequencing-by-synthesis.
Analytical biochemistry. 348(1):127-38 [PMID] 16289447.
2005
The efficiency of hypoxanthine excision by alkyladenine DNA glycosylase is altered by changes in nearest neighbor bases.
DNA repair. 4(10):1088-98 [PMID] 15990363.
2004
Contribution of a conserved phenylalanine residue to the activity of Escherichia coli uracil DNA glycosylase.
DNA repair. 3(10):1273-83 [PMID] 15336623.
2004
Increased dNTP binding affinity reveals a nonprocessive role for Escherichia coli beta clamp with DNA polymerase IV.
The Journal of biological chemistry. 279(32):33047-50 [PMID] 15210708.
2004
Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: I. Two distinct activities for individual ATP sites in the gamma complex.
The Journal of biological chemistry. 279(6):4376-85 [PMID] 14610067.
2004
Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: II. Uncoupling the beta and DNA binding activities of the gamma complex.
The Journal of biological chemistry. 279(6):4386-93 [PMID] 14610068.
2003
Mechanism of loading the Escherichia coli DNA polymerase III beta sliding clamp on DNA. Bona fide primer/templates preferentially trigger the gamma complex to hydrolyze ATP and load the clamp.
The Journal of biological chemistry. 278(12):10033-40 [PMID] 12519754.
2002
Effects of hydrogen bonding within a damaged base pair on the activity of wild type and DNA-intercalating mutants of human alkyladenine DNA glycosylase.
The Journal of biological chemistry. 277(35):31673-8 [PMID] 12077143.
2002
Long-patch base excision repair of apurinic/apyrimidinic site DNA is decreased in mouse embryonic fibroblast cell lines treated with plumbagin: involvement of cyclin-dependent kinase inhibitor p21Waf-1/Cip-1.
Oncogene. 21(38):5912-22 [PMID] 12185591.
2001
A sliding clamp monkey wrench.
Nature structural biology. 8(10):829-31 [PMID] 11573082.
2001
Base excision and DNA binding activities of human alkyladenine DNA glycosylase are sensitive to the base paired with a lesion.
The Journal of biological chemistry. 276(16):13379-87 [PMID] 11278716.
2000
A model for Escherichia coli DNA polymerase III holoenzyme assembly at primer/template ends. DNA triggers a change in binding specificity of the gamma complex clamp loader.
The Journal of biological chemistry. 275(4):3006-15 [PMID] 10644772.
2000
Molecular mechanism and energetics of clamp assembly in Escherichia coli. The role of ATP hydrolysis when gamma complex loads beta on DNA.
The Journal of biological chemistry. 275(37):28413-20 [PMID] 10874049.
1999
Division of labor–sequential ATP hydrolysis drives assembly of a DNA polymerase sliding clamp around DNA.
The EMBO journal. 18(18):5131-44 [PMID] 10487764.
1998
Exonuclease-polymerase active site partitioning of primer-template DNA strands and equilibrium Mg2+ binding properties of bacteriophage T4 DNA polymerase.
Biochemistry. 37(28):10144-55 [PMID] 9665720.
1998
Pre-steady state analysis of the assembly of wild type and mutant circular clamps of Escherichia coli DNA polymerase III onto DNA.
The Journal of biological chemistry. 273(38):24564-74 [PMID] 9733751.
1998
Stopped-flow fluorescence study of precatalytic primer strand base-unstacking transitions in the exonuclease cleft of bacteriophage T4 DNA polymerase.
Biochemistry. 37(28):10156-63 [PMID] 9665721.
1998
The proofreading pathway of bacteriophage T4 DNA polymerase.
The Journal of biological chemistry. 273(36):22969-76 [PMID] 9722519.
1997
Fidelity of Escherichia coli DNA polymerase III holoenzyme. The effects of beta, gamma complex processivity proteins and epsilon proofreading exonuclease on nucleotide misincorporation efficiencies.
The Journal of biological chemistry. 272(44):27919-30 [PMID] 9346941.
1996
Base analog and neighboring base effects on substrate specificity of recombinant human G:T mismatch-specific thymine DNA-glycosylase.
Biochemistry. 35(39):12926-32 [PMID] 8841138.
1996
Dynamics of loading the beta sliding clamp of DNA polymerase III onto DNA.
The Journal of biological chemistry. 271(48):30699-708 [PMID] 8940047.
1995
Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies.
Methods in enzymology. 262:232-56 [PMID] 8594351.
1994
Nucleotide insertion and primer extension at abasic template sites in different sequence contexts.
Annals of the New York Academy of Sciences. 726:132-42; discussion 142 [PMID] 8092671.
1994
Pre-steady-state kinetic analysis of sequence-dependent nucleotide excision by the 3′-exonuclease activity of bacteriophage T4 DNA polymerase.
Biochemistry. 33(24):7576-86 [PMID] 8011623.
1993
Biochemical basis of DNA replication fidelity.
Critical reviews in biochemistry and molecular biology. 28(2):83-126 [PMID] 8485987.
1993
Effect of a template-located 2′,2′-difluorodeoxycytidine on the kinetics and fidelity of base insertion by Klenow (3′–>5’exonuclease-) fragment.
Cancer research. 53(19):4582-7 [PMID] 8402631.
1993
Influence of 5′-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment.
Biochemistry. 32(41):11247-58 [PMID] 8218190.
1993
Ionization of bromouracil and fluorouracil stimulates base mispairing frequencies with guanine.
The Journal of biological chemistry. 268(21):15935-43 [PMID] 7688001.
1993
Kinetics of deoxyribonucleotide insertion and extension at abasic template lesions in different sequence contexts using HIV-1 reverse transcriptase.
The Journal of biological chemistry. 268(31):23567-72 [PMID] 7693691.

Grants

Aug 2022 ACTIVE
How SSB Regulates YoaA-chis Function in DNA Damage Repair
Role: Other
Funding: NATL INST OF HLTH NIEHS
Sep 2021 ACTIVE
Mechanisms and Functions of Iron-Sulfur Helicases in DNA repair
Role: Principal Investigator
Funding: NATL INST OF HLTH NIGMS
Aug 2018 ACTIVE
Mechanisms of SSB in Coordinating DNA Replication and Repair
Role: Principal Investigator
Funding: NATL SCIENCE FOU
Jun 2018 – May 2021
Dissecting the Mechanism of a Phage-encoded Clamp Loader Inhibitor
Role: Principal Investigator
Funding: NATL INST OF HLTH NIAID
Jun 2012 – May 2016
The dynamics of replication processivity factors (Subrecipient with Arizona State University
Role: Principal Investigator
Funding: ARIZONA STATE UNIVERSITY via NATL SCIENCE FOU

Contact Details

Phones:
Business:
(352) 294-8379
Emails:
Business:
lbloom@ufl.edu
Addresses:
Business Mailing:
1200 NEWELL DRIVE
1200 NEWELL DR
DEPARTMENT OF BIOCHEMISTRY AND MOLECULAR BIO
GAINESVILLE FL 326103012
Business Street:
R3-165 ARB
GAINESVILLE FL 326100245