Ghodke, Harshad

Overview

Using a multidisciplinary approach combining genetics, molecular biology, biochemistry and single-molecule biophysics, I study how cells conduct DNA repair and maintain genomic integrity.

Top Publications

Year	Title
2019	Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells Published in Biophysical Journal
2019	Nuclease dead Cas9 is a programmable roadblock for DNA replication Published in Scientific Reports
2019	Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response Published in eLife
2018	Single-molecule live-cell imaging of bacterial DNA repair and damage tolerance Published in Biochemical Society Transactions
2018	The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage Published in Nature Communications
2014	Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates Published in Proceedings of the National Academy of Sciences of USA
2012	Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair Published in Proceedings of the National Academy of Sciences of USA

Research Areas

Research Overview

DNA is the blueprint of life. It contains all the information that cells need to live and reproduce. Unfortunately, cellular metabolism as well as exposure to the environment can result in damage to the DNA. Unrepaired DNA damage can be fatal and correcting damage in genomic DNA is essential for the continued proliferation of cellular life. DNA damage can impede fundamental cellular activities such as DNA replication, transcription and recombination. My research focuses on how cells identify damage in genomic DNA, and correct it.

Specifically, I am interested in understanding the structural and biochemical properties of DNA repair proteins that allow these factors to recognise sites of DNA damage, recruit downstream repair factors and handoff damage sites for further processing.

Understanding how DNA repair proteins act inside individual bacterial cells is important to understand how antimicrobial resistance evolves in response to DNA damaging antibiotics. Similarly, in case of humans, DNA repair activities lead to cancer therapeutic resistance.

To understand how cells conduct DNA repair, we have pioneered cutting-edge microscopy approaches that allow us to 'see' individual proteins inside living cells. Using lasers, high-resolution microscopes and fluorescently tagged DNA repair factors, we can monitor where DNA repair occurs inside cells for the first time. These methods allowed us to not only characterise key properties of protein-DNA interactions inside cells, but also to propose new models that describe how DNA repair occurs in a rapidly changing cellular environment.

Beyond resulting in high-impact papers this research is establishing novel methodologies and assembling an unprecedented look into how cells maintain genomic integrity. These approaches allow us to identify key sub-complexes and assemblies that can be targeted to mitigate antibiotic resistance. Ultimately, this work is critical to identify novel therapeutics that can prolong the use of antibiotics in a post-antibiotic era.

Available as Research Supervisor

Available for Collaborative Projects

Member Of

Molecular Horizons Research Fellow 2020 -
Illawarra Health and Medical Research Institute Research Fellow 2015 -

Selected Publications

Journal Article

Year	Title
2021	Single-molecule studies of helicases and translocases in prokaryotic genome-maintenance pathways Published In DNA Repair
2020	Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells Published In Biophysical Journal
2020	Modulation of DNA polymerase IV activity by UmuD and RecA* observed by single-molecule time-lapse microscopy
2020	Nuclease dead Cas9 is a programmable roadblock for DNA replication Published In Scientific Reports
2020	RecFOR epistasis group: RecF and RecO have distinct localizations and functions in Escherichia coli Published In Nucleic Acids Research
2020	Single-molecule imaging reveals molecular coupling between transcription and DNA repair in live cells
2020	Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair
2020	Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response Published In eLife
2020	Spy-ing on Cas9: Single-molecule tools reveal the enzymology of Cas9 Published In Current Opinion in Biomedical Engineering
2020	The effects of mCI inhibition on RecA activity Published In FASEB JOURNAL
2020	Single-molecule imaging reveals molecular coupling between transcription and DNA repair machinery in live cells Published In Nature Communications
2020	Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair Published In Nucleic Acids Research
2020	Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair Published In Nature Communications
2019	Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells Published In Biophysical Journal
2019	Modulation of DNA polymerase IV activity by UmuD and RecA* observed by single-molecule time-lapse microscopy
2019	Nuclease dead Cas9 is a programmable roadblock for DNA replication Published In Scientific Reports
2019	RecFOR epistasis group: RecF and RecO have distinct localizations and functions in Escherichia coli Published In Nucleic Acids Research
2019	Single-molecule imaging reveals molecular coupling between transcription and DNA repair in live cells
2019	Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair
2019	Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response Published In eLife
2019	Spy-ing on Cas9: Single-molecule tools reveal the enzymology of Cas9 Published In Current Opinion in Biomedical Engineering
2019	The effects of mCI inhibition on RecA activity Published In FASEB JOURNAL
2018	Anisotropic functionalization of upconversion nanoparticles Published In Chemical Science
2018	Design of DNA rolling-circle templates with controlled fork topology to study mechanisms of DNA replication Published In Analytical Biochemistry
2018	Resolving the Gordian Knot: Srs2 Strips Intermediates Formed during Homologous Recombination Published In Trends in Biochemical Sciences
2018	Single-molecule live-cell imaging of bacterial DNA repair and damage tolerance Published In Biochemical Society Transactions
2018	Spatial and temporal organization of RecA in theEscherichia coliDNA-damage response
2018	The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage Published In Nature Communications
2016	Single-molecule specific mislocalization of red fluorescent proteins in live Escherichia coli Published In Biophysical Journal
2015	ISBatch: a batch-processing platform for data analysis and exploration of live-cell single-molecule microscopy images and other hierarchical datasets Published In Molecular Biosystems
2015	Regulation of mutagenic DNA polymerase V activation in space and time Published In PLoS Genetics
2014	Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology Published In BMC Biophysics
2014	Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates Published In Proceedings of the National Academy of Sciences of USA
2013	Backbone-branched DNA building blocks for facile angular control in nanostructures Published In ACS Nano
2013	Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes Published In Nucleic Acids Research
2013	The Shu complex interacts with Rad51 through the Rad51 paralogues Rad55–Rad57 to mediate error-free recombination Published In Nucleic Acids Research
2012	Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair Published In Proceedings of the National Academy of Sciences of USA
2011	Single molecule studies of physiologically relevant telomeric tails reveal POT1 mechanism for promoting G-quadruplex unfolding Published In Journal of Biological Chemistry
2010	Direct visualization of joining of DNA fragments by LigIIIβ using atomic force microscopy Published In Biophysical Journal
2010	Room temperature synthesis of titanium dioxide nanoparticles of different phases in water in oil microemulsion Published In Colloids and Surfaces A: Physicochemical and Engineering Aspects
2007	The I-tetraplex building block: Rational design and controlled fabrication of robust 1D DNA scaffolds through non-Watson-Crick interactions Published In Angewandte Chemie - International Edition
2007	The I¿Tetraplex Building Block: Rational Design and Controlled Fabrication of Robust 1D DNA Scaffolds through Non¿Watson¿Crick Interactions Published In Angewandte Chemie

Chapter

Year	Title
2022	Biochemical and single-molecule techniques to study accessory helicase resolution of R-loop proteins at stalled replication forks Published In Methods in Enzymology Publisher Elsevier

Conference Paper

Year	Title
2015	Watching eukaryotic nucleotide excision repair: one molecule at a time Published In DNA REPAIR
2014	Watching Nucleotide Excision Repair Proteins: One Molecule at a Time. Published In ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
2013	WT UV-DDB Performs a 3D Search on DNA whereas the XP-E Mutant (K244E DDB2) Mutant Slides Published In BIOPHYSICAL JOURNAL
2012	Watching Nucleotide Excision Repair, One Molecule at a Time Published In ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
2010	Direct Visualization Of Joining of DNA Fragments By LigIII beta Using Atomic Force Microscopy Published In BIOPHYSICAL JOURNAL
2007	New design paradigms: Tetraplex building blocks for structural DNA nanotechnology Published In JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Investigator On

Year	Title
2021 - 2024	Structures to Solve Conflicts of DNA Replication and RNA Transcription Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2020 - 2021	Antibiotic resistance: combining microscopy, microfluidics and genomics to target bacterial DNA repair pathways Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2020 - 2021	Creation and Repair of Postreplicative DNA Gaps Awarded by: National Institute of Health (NIH) Funding Scheme: Grant

Available as Research Supervisor

Potential Supervision Topics

Problems at the interface of DNA repair, replication, recombination and transcription

Advisees

Graduate Advising Relationship

Degree	Research Title	Advisee
Doctor of Philosophy	The role of translesion DNA synthesis in the development of antibiotic resistance	Cherry, Megan
Doctor of Philosophy	Dynamic Iinteractions of E. coli Accessory Helicases Rep and UvrD with Stalled Replication Forks	Whinn, Kelsey
Doctor of Philosophy	Investigating the role of recombination mediator proteins in the formation and resolution of single-strand gaps during the E. coli DNA damage response using single molecule live cell imaging. Studying replication-transcription conflicts at the singl...	Sharma, Nischal

Professional Service Activities

Molecular Horizons Seminar Committee Member 2018 -
School of Chemistry Safety Committee Member 2015 - 2018

Education And Training

Ph.D., University of Pittsburgh/Carnegie Mellon, Molecular Biophysics and Structural Biology 2009 - 2013
M.S. in Chemical Engineering, Carnegie Mellon University, Chemical Engineering 2007 - 2008
B.E. in Chemical Engineering, Indian Institute of Technology - Bombay, Chemical Engineering 2003 - 2007

Keywords

DNA repair
biochemistry
single-molecule biophysics
single-molecule fluorescence

Full Name

Harshad Ghodke

Mailing Address

42.216 Molecular Horizons

University of Wollongong

Wollongong

NSW

2522

Australia

Located In Facility

Molecular Horizons

Orcid Id

http://orcid.org/0000-0002-6628-876X (confirmed)

Top Publications

Year	Title
2019	Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells Published in Biophysical Journal
2019	Nuclease dead Cas9 is a programmable roadblock for DNA replication Published in Scientific Reports
2019	Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response Published in eLife
2018	Single-molecule live-cell imaging of bacterial DNA repair and damage tolerance Published in Biochemical Society Transactions
2018	The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage Published in Nature Communications
2014	Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates Published in Proceedings of the National Academy of Sciences of USA
2012	Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair Published in Proceedings of the National Academy of Sciences of USA

Research Areas

Research Overview

DNA is the blueprint of life. It contains all the information that cells need to live and reproduce. Unfortunately, cellular metabolism as well as exposure to the environment can result in damage to the DNA. Unrepaired DNA damage can be fatal and correcting damage in genomic DNA is essential for the continued proliferation of cellular life. DNA damage can impede fundamental cellular activities such as DNA replication, transcription and recombination. My research focuses on how cells identify damage in genomic DNA, and correct it.

Specifically, I am interested in understanding the structural and biochemical properties of DNA repair proteins that allow these factors to recognise sites of DNA damage, recruit downstream repair factors and handoff damage sites for further processing.

Understanding how DNA repair proteins act inside individual bacterial cells is important to understand how antimicrobial resistance evolves in response to DNA damaging antibiotics. Similarly, in case of humans, DNA repair activities lead to cancer therapeutic resistance.

To understand how cells conduct DNA repair, we have pioneered cutting-edge microscopy approaches that allow us to 'see' individual proteins inside living cells. Using lasers, high-resolution microscopes and fluorescently tagged DNA repair factors, we can monitor where DNA repair occurs inside cells for the first time. These methods allowed us to not only characterise key properties of protein-DNA interactions inside cells, but also to propose new models that describe how DNA repair occurs in a rapidly changing cellular environment.

Beyond resulting in high-impact papers this research is establishing novel methodologies and assembling an unprecedented look into how cells maintain genomic integrity. These approaches allow us to identify key sub-complexes and assemblies that can be targeted to mitigate antibiotic resistance. Ultimately, this work is critical to identify novel therapeutics that can prolong the use of antibiotics in a post-antibiotic era.

Member Of

Molecular Horizons Research Fellow 2020 -
Illawarra Health and Medical Research Institute Research Fellow 2015 -

Selected Publications

Journal Article

Year	Title
2021	Single-molecule studies of helicases and translocases in prokaryotic genome-maintenance pathways Published In DNA Repair
2020	Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells Published In Biophysical Journal
2020	Modulation of DNA polymerase IV activity by UmuD and RecA* observed by single-molecule time-lapse microscopy
2020	Nuclease dead Cas9 is a programmable roadblock for DNA replication Published In Scientific Reports
2020	RecFOR epistasis group: RecF and RecO have distinct localizations and functions in Escherichia coli Published In Nucleic Acids Research
2020	Single-molecule imaging reveals molecular coupling between transcription and DNA repair in live cells
2020	Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair
2020	Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response Published In eLife
2020	Spy-ing on Cas9: Single-molecule tools reveal the enzymology of Cas9 Published In Current Opinion in Biomedical Engineering
2020	The effects of mCI inhibition on RecA activity Published In FASEB JOURNAL
2020	Single-molecule imaging reveals molecular coupling between transcription and DNA repair machinery in live cells Published In Nature Communications
2020	Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair Published In Nucleic Acids Research
2020	Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair Published In Nature Communications
2019	Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells Published In Biophysical Journal
2019	Modulation of DNA polymerase IV activity by UmuD and RecA* observed by single-molecule time-lapse microscopy
2019	Nuclease dead Cas9 is a programmable roadblock for DNA replication Published In Scientific Reports
2019	RecFOR epistasis group: RecF and RecO have distinct localizations and functions in Escherichia coli Published In Nucleic Acids Research
2019	Single-molecule imaging reveals molecular coupling between transcription and DNA repair in live cells
2019	Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair
2019	Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response Published In eLife
2019	Spy-ing on Cas9: Single-molecule tools reveal the enzymology of Cas9 Published In Current Opinion in Biomedical Engineering
2019	The effects of mCI inhibition on RecA activity Published In FASEB JOURNAL
2018	Anisotropic functionalization of upconversion nanoparticles Published In Chemical Science
2018	Design of DNA rolling-circle templates with controlled fork topology to study mechanisms of DNA replication Published In Analytical Biochemistry
2018	Resolving the Gordian Knot: Srs2 Strips Intermediates Formed during Homologous Recombination Published In Trends in Biochemical Sciences
2018	Single-molecule live-cell imaging of bacterial DNA repair and damage tolerance Published In Biochemical Society Transactions
2018	Spatial and temporal organization of RecA in theEscherichia coliDNA-damage response
2018	The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage Published In Nature Communications
2016	Single-molecule specific mislocalization of red fluorescent proteins in live Escherichia coli Published In Biophysical Journal
2015	ISBatch: a batch-processing platform for data analysis and exploration of live-cell single-molecule microscopy images and other hierarchical datasets Published In Molecular Biosystems
2015	Regulation of mutagenic DNA polymerase V activation in space and time Published In PLoS Genetics
2014	Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology Published In BMC Biophysics
2014	Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates Published In Proceedings of the National Academy of Sciences of USA
2013	Backbone-branched DNA building blocks for facile angular control in nanostructures Published In ACS Nano
2013	Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes Published In Nucleic Acids Research
2013	The Shu complex interacts with Rad51 through the Rad51 paralogues Rad55–Rad57 to mediate error-free recombination Published In Nucleic Acids Research
2012	Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair Published In Proceedings of the National Academy of Sciences of USA
2011	Single molecule studies of physiologically relevant telomeric tails reveal POT1 mechanism for promoting G-quadruplex unfolding Published In Journal of Biological Chemistry
2010	Direct visualization of joining of DNA fragments by LigIIIβ using atomic force microscopy Published In Biophysical Journal
2010	Room temperature synthesis of titanium dioxide nanoparticles of different phases in water in oil microemulsion Published In Colloids and Surfaces A: Physicochemical and Engineering Aspects
2007	The I-tetraplex building block: Rational design and controlled fabrication of robust 1D DNA scaffolds through non-Watson-Crick interactions Published In Angewandte Chemie - International Edition
2007	The I¿Tetraplex Building Block: Rational Design and Controlled Fabrication of Robust 1D DNA Scaffolds through Non¿Watson¿Crick Interactions Published In Angewandte Chemie

Chapter

Year	Title
2022	Biochemical and single-molecule techniques to study accessory helicase resolution of R-loop proteins at stalled replication forks Published In Methods in Enzymology Publisher Elsevier

Conference Paper

Year	Title
2015	Watching eukaryotic nucleotide excision repair: one molecule at a time Published In DNA REPAIR
2014	Watching Nucleotide Excision Repair Proteins: One Molecule at a Time. Published In ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
2013	WT UV-DDB Performs a 3D Search on DNA whereas the XP-E Mutant (K244E DDB2) Mutant Slides Published In BIOPHYSICAL JOURNAL
2012	Watching Nucleotide Excision Repair, One Molecule at a Time Published In ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
2010	Direct Visualization Of Joining of DNA Fragments By LigIII beta Using Atomic Force Microscopy Published In BIOPHYSICAL JOURNAL
2007	New design paradigms: Tetraplex building blocks for structural DNA nanotechnology Published In JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Investigator On

Year	Title
2021 - 2024	Structures to Solve Conflicts of DNA Replication and RNA Transcription Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2020 - 2021	Antibiotic resistance: combining microscopy, microfluidics and genomics to target bacterial DNA repair pathways Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2020 - 2021	Creation and Repair of Postreplicative DNA Gaps Awarded by: National Institute of Health (NIH) Funding Scheme: Grant

Potential Supervision Topics

Problems at the interface of DNA repair, replication, recombination and transcription

Advisees

Graduate Advising Relationship

Degree	Research Title	Advisee
Doctor of Philosophy	The role of translesion DNA synthesis in the development of antibiotic resistance	Cherry, Megan
Doctor of Philosophy	Dynamic Iinteractions of E. coli Accessory Helicases Rep and UvrD with Stalled Replication Forks	Whinn, Kelsey
Doctor of Philosophy	Investigating the role of recombination mediator proteins in the formation and resolution of single-strand gaps during the E. coli DNA damage response using single molecule live cell imaging. Studying replication-transcription conflicts at the singl...	Sharma, Nischal

Professional Service Activities

Molecular Horizons Seminar Committee Member 2018 -
School of Chemistry Safety Committee Member 2015 - 2018

Education And Training

Ph.D., University of Pittsburgh/Carnegie Mellon, Molecular Biophysics and Structural Biology 2009 - 2013
M.S. in Chemical Engineering, Carnegie Mellon University, Chemical Engineering 2007 - 2008
B.E. in Chemical Engineering, Indian Institute of Technology - Bombay, Chemical Engineering 2003 - 2007

Keywords

DNA repair
biochemistry
single-molecule biophysics
single-molecule fluorescence

Full Name

Harshad Ghodke

Mailing Address

42.216 Molecular Horizons

University of Wollongong

Wollongong

NSW

2522

Australia

Located In Facility

Molecular Horizons

Orcid Id

http://orcid.org/0000-0002-6628-876X (confirmed)

Overview

Overview

Top Publications

Research Areas

Research Overview

Available as Research Supervisor

Affiliation

Available for Collaborative Projects

Member Of

Publications

Selected Publications

Journal Article

Chapter

Conference Paper

Funding

Investigator On

Supervision

Available as Research Supervisor

Potential Supervision Topics

Advisees

Graduate Advising Relationship

Service

Professional Service Activities

Background

Education And Training

Keywords

Contact

Full Name

Mailing Address

Located In Facility

Identity

Orcid Id

Overview

Top Publications

Research Areas

Research Overview

Affiliation

Member Of

Publications

Selected Publications

Journal Article

Chapter

Conference Paper

Funding

Investigator On

Supervision

Potential Supervision Topics

Advisees

Graduate Advising Relationship

Service

Professional Service Activities

Background

Education And Training

Keywords

Contact

Full Name

Mailing Address

Located In Facility

Identity

Orcid Id

Visualisations

Research Areas