Single-molecule Biophysics @ UOW

The latest activities of the van Oijen lab

Our Group

Group Leader:

Prof. Antoine van Oijen

Antoine van Oijen obtained his BSc and PhD degrees in the Netherlands, where he was trained as a physicist.  A growing fascination for biology resulted in him moving to the USA and establishing a research group at Harvard Medical School. Subsequently, he was appointed as full professor at Groningen University in the Netherlands where he established a thriving biophysics research program focused on the development of single-molecule visualization techniques and their applications in basic and applied science. Recently, he moved to the UOW and was awarded a prestigious Laureate Fellowship by the Australian Research Council to further develop biophysical approaches to visualize the molecular processes that define life.

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☏ +61 2 42 21 4780 

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Research Fellows:

Dr. Andrew Robinson (sub-group leader)

Students: Sarah Henrikus, Megan Cherry, Thomas Armstrong, Liam McClure (honours).

Andrew completed his undergraduate and graduate studies at Macquarie University, Sydney, followed by postdoc positions at the University of Wollongong and the University of Groningen. He returned to Wollongong as a Research Fellow and Sub-group Leader in 2016. Andrew’s group uses single-molecule fluorescence imaging and experimental evolution to study error-prone DNA polymerases,and their role(s) in the evolution of antibiotic resistance. The group is also identifying proteins within the DNA replication and repair of bacteria that are potential novel drug targets.

✉ andrewr@uow.edu.au

☏ +61 2 4221 4735

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Dr. Bishnu Paudel

Bishnu acquired his PhD degree from the Imperial College London, where he applied a powerful single-molecule fluorescence resonance energy transfer (smFRET) method to study ribozyme folding dynamics. He is highly fascinated to use and extend this technique to understand basic underlying mechanism of nucleic acid-protein interactions. Therefore, he joined the van Oijen group in 2015 where he studies mechanism and importance of nucleic acid-protein interactions in several biological processes. For example, action of ATP-dependent chromatin remodeler during DNA remodeling and the role of G-quadruplex structure present at the telomeric end while telomerase is extending it.

✉ paudel@uowmail.edu.au

☏ +61 2 4221 5122

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Lisanne Spenkelink

Lisanne obtained her undergraduate degree in Experimental Physics at the University of Groningen, the Netherlands. She has always had an interest in biology and therefore joined the van Oijen Single-molecule Biophysics group in 2013 for her PhD, working on the visualisation of protein dynamics in DNA replication. She enjoyed this work (and Wollongong) so much that she decided to stay on as an Associate Research Fellow (from 2017-present) working on the single-molecule visualisation of DNA replication in Eukaryotes.

✉ Lisanne@uow.edu.au

☏ +61 2 4221 5748

Dr. Harshad Ghodke (sub-group leader)

Students: Han Ho, Kelsey Whinn (honours).

Harshad was trained as a chemical engineer but decided to switch fields in 2009 when he started a PhD with the van Houten lab at the University of Pittsburgh to study human nucleotide excision repair pathways. In 2014 joined the van Oijen lab and now oversees his own DNA repair sub-group that uses a combination of in vitro and in vivo single-molecule techniques to tackle questions related to 1. Transcription-coupled nucleotide excision repair 2. Visualizing recombination intermediates in cells, and 3. Developing single-molecule tools to study fork-stalling. Harshad is looking for students so please contact him if you are interested.

✉ harshad@uow.edu.au

☏ +61 2 4221 5122

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Dr. Jacob Lewis

Jacob completed his undergraduate studies in Medical Biotechnology with Honours at the University of Wollongong, before completing his PhD in the laboratory of Professor Nicholas Dixon. There, he used a combination of traditional biochemical and single-molecule techniques to investigate the structural dynamics and interactions of the E. coli DNA replication machinery. He joined the van Oijen group in mid 2016, tasked with developing new single-molecule based approaches to understand details of how DNA replication works in Eukaryotes.

✉ jacobl@uow.edu.au

☏ +61 2 4221 5122

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Graduate Students:

Han Ngoc Ho

Han did a bachelor in Chemistry in Melbourne before befriending Escherichia coli early on his PhD program in the van Oijen lab. Using single-molecule live-cell imaging, he is studying how RNA polymerase acts as the guardian of the genome during transcription by detecting DNA damage on its path and recruiting the DNA repair machinery.

Supervision: Prof. Antoine van Oijen, Dr. Harshad Ghodke

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☏ +61 2 4221 5748

Sarah Henrikus

For Sarah’s B. Sc. in Chemistry she studied dual-use fluorescent probes at Saarland University, Germany. Her Master’s at University of Groningen, focused on stabilization of fluorescent proteins. Then in 2016, she chose a PhD in the van Oijen lab to study the DNA damage and repair pathways that grant access of proteins to damaged DNA in vivo.

Supervision: Dr. Andrew Robinson, Prof. Antoine van Oijen

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☏ +61 2 4221 5748

Nicholas Marzano

For my PhD I am developing novel approaches to study the mechanistic details of molecular chaperones using single-molecule techniques. By looking at chaperones one at a time, we can gain a better understanding of how they prevent protein aggregation- A process that underpins many diseases such as Parkinson’s and motor neuron disease.

Supervision: Prof. Antoine van Oijen, A. Prof. Heath Ecroyd, Dr. Bishnu Paudel

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☏ +61 4 2100 6437

Gurleen Kaur

Gurleen completed her Bachelor of Science in chemistry at UOW. She completed an Honour’s project involving the development of single-molecule tools to fluorescently visualise single-stranded DNA production. For her PhD project she is investigating proteins involved in E. coli DNA damage and repair systems.

Supervisor(s): Prof. Antoine van Oijen, Dr. Andrew Robinson and Dr. Jacob Lewis

✉ gk980@uowmail.edu.au

☏ +61 2 4221 5748

Varsha Natarajan

Varsha did her Bachelor’s in Biotechnology and her Master’s in Biophysics before starting a PhD with the van Oijen lab. She is working to elucidate the mechanisms of eukaryotic DNA replication using Saccharomyces cerevisiae as a model. Varsha uses both fluorescence and forced-based single-molecule approaches to probe this complex process.

Supervision: Prof. Antoine van Oijen, Prof. Nicholas Dixon

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☏ +61 2 4221 5748

Megan Cherry

Upon completing a B.Sc. in Chemistry at MIT, Megan pursued a Topmaster in Nanoscience at the University of Groningen, where she became interested in antibiotic resistance within microfluidics. As a PhD student, Megan works as a member of the in vivo subgroup to investigate the role of TLS polymerases and induced mutagenesis in antibiotic resistance.

Supervision: Dr. Andrew Robinson, Prof. Antoine van Oijen 

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☏ +61 2 4221 5748

Stefan Müller

After finishing his Bachelor’s in physics, working on ultra cold neutrons, at the Technical University of Munich, Germany, Stefan became interested in Biophysics. For his Master’s he studied microtubule-associated proteins by using single molecule microscopy. His PhD-Project focusses on single-molecule imaging of the eukaryotic replisome.

Supervision: Prof. Antoine van Oijen, Prof Nicholas Dixon

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☏ +61 2 4221 5748

Caitlin Johnston

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Richard Spinks

After obtaining his B. Sc. in medical biotechnology from UOW, Richard took an interest in our specialised microscopy and spent his honours year studying DNA replication at the single-molecule level. He enjoyed this work so much that, in 2017, he started a PhD to develop single-molecule methods to probe the coordination principles of the replisome.

Supervison: Prof. Antoine van Oijen, Prof. Nicholas Dixon

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☏ +61 2 4221 5748

Thomas Armstrong

After completing his Bachelor’s in Medical Biotechnology at UOW, Tom undertook an Honour’s project as part of the in vivo subgroup studying TLS polymerases at the single-molecule level. He is now continuing this project in the form of a PhD, further studying TLS polymerases and single-strand gap repair in E. coli.

Supervison: Dr. Andrew Robinson, Prof. Antoine van Oijen

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☏ +61 2 4221 5748

Alumni of the van Oijen lab:

  • Enrico Monachino – PhD 2013-2018 – Currently having a rest somewhere in Italy…
  • Flynn Hill – postdoc 2013-2017 – Currently an education data analyst within UOW, Wollongong, Australia.
  • Karl Duderstadt – postdoc 2011-2014 – Currently a group leader at Max Planck Institute of Biochemistry, Martinsried, Germany.
  • Nathan Tanner – PhD/postdoc 2006-2011 – Currently a research scientist New England Biolabs, Ipswich, USA.