Gene machines, one molecule at a time


Gene expression is the vital path that converts DNA information into functional proteins. Our group studies mechanisms and machines of gene expression using single-molecule biophysical methods and biochemistry. We observe single biomachines in real time, both "in vitro" and in living cells. We also develop single-molecule fluorescence methods, assays and DNA-based biosensors.

Our team is a Biological Physics research group within Condensed Matter Physics. We are also linked to the Doctoral Training Centre (DTC) and the Wellcome Trust graduate programme in structural biology.

News

  • Now we have a new webpage! Please visit our new homepage. Link.

  • Join us at Oxford for the 1st Single-Molecule Bacteriology meeting! Sept 9-12, 2018.

For more info follow this link: Link.

  • NEW STUDENTSHIP AVAILABLE!!
- We have an exciting new studentship available in the lab – we are looking for someone with an interest in using cutting edge microscopy to answer fundamental questions about the morphology and cellular interactions of RNA viruses. This is a 4 year, Royal Society-funded DPhil in Biophysics. For more info please see: Link.
  • April 2018:
- It has been a busy month for papers, check out our exciting new work on the E.coli RNA polymerase, published in Mol. Cell Link and Nature Communications Link.
- We also have two new papers uploaded on BioRxiv! Link and Link.
- Congratulations to Maabur for winning the Arthur H Cooke Memorial Prize, which is awarded for distinguished work by a first year research student in Condensed Matter Physics. Well done!!!
- We say goodbye to our two MPhys students Amy Kent and Joseph Dolphin and wish them the best of luck with their exams!
- Team Rapinidis is running the Oxford Town and Gown 10K, in aid of Muscular Dystrophy UK, on the 13th of May. Our team has grown since last year and we are all training hard. If you would like to donate to this great cause please see our Justgiving page below: Link.
  • February 2018:
- Nicole, Becky and Barak have just been to the 2018 Biophysical Society Meeting in San Francisco! We heard some great science, caught up with old friends and made some new ones.
  • December 2017:
- We all had a great time at the annual Kapanidis Christmas lunch! Merry Christmas everyone!!!
  • October 2017:
- Hello to our brand new DPhil student Jingwen Xiao, welcome to the group!
  • September 2017:
- Congratulations to Nicole Robb on being awarded a Royal Society Dorothy Hodgkin Fellowship! Link.
- We had a great time chatting to the public about our research at the Curiosity Carnival, thanks to everyone that helped out on the night!
  • August 2017:
- We bid farewell to Jonny Taylor, and wish him good luck with his PhD!
- A big welcome to our new post-docs Oliver Pambos and Abhishek Mazumder, to our rotation student Jingwen Xiao and to our new summer student Amy Kent.
- In other news Team Rapidnidis is busy preparing for our next challenge - the Oxford Half Marathon on the 8th of October!
  • July 2017:
- Farewell to Sophie Schuman, and good luck with your next rotation project. To say goodbye we went on a lab punting trip!
  • May 2017:
- Team Rapidnidis successfully completed the Oxford Town and Gown 10k! We raised over £300 for Muscular Dystrophy UK, thank you so much to everyone who donated money and supported us on the day, we had a great time and couldn't have done it without you!!
  • April 2017:
- Congratulations to Fede on the publication of his work in Biophys Journal: Link.
- On the 14th of May the Rapidnidis group will be running the Oxford Town and Gown 10k, in order to raise money for Muscular Dystrophy UK. If you would like to support this excellent cause please use the link below.

Link.

- We are all (mostly) training hard and looking forward to the race!!
  • March 2017:
- We have a new arrival - welcome to Hafez El Sayyed, who has joined the group as a post-doctoral researcher to work on tracking of RNAP in vivo.
- At the same time, we bid farewell to Mathew Stracy, and wish him the best of luck for his new position in the Biochemistry department, University of Oxford.
- And finally, photo of the month goes to Becky, pictured here using the Nanoimager!! (thanks to Micron, Oxford).
  • January 2017:
- Happy New Year everyone!!!
  • December 2016:
- Welcome to our new group members - we are very glad to have Jun Fan and Horst Steuer join the group as post-doctoral fellows as well as Maabur Sow who is doing his DPhil in the group!
- Congrats to Nicole Robb on the publication of her NAR paper : Link.
- We bid farewell to Angelina Scheck and and wish her the best of luck with the rest of her degree.
  • September 2016:
- Two new papers this month: our discovery of pausing in initial transcription is out in Molecular Cell. Well done to Diego Duchi, David Bauer and everyone who contributed! Link.
- More congrats to Anne Plochowietz for the first studies of single tRNA molecules in living bacteria, work that is now out in Nucleic Acids Research: Link
  • September 2016:
- Another warm welcome, this time to Barak Gilboa, who has joined us to work on single-molecule studies of transcription initiation mechanisms.
  • June 2016:
- A big welcome to Angelina Scheck and Jonny Taylor, who have joined the team for a few months to work on single-molecule 3-color FRET and virus tracking projects, respectively.
  • April 2016:
- A new arrival:Becky Andrews joined the group to do a DPhil on single-molecule studies of transcription. Welcome Becky!
  • March 2016:
- Graduations; 5 successful vivas in 4 months! Marko Sustarsic, Mat Stracy, Federico Garza de León, Peter May and Anne Plochowietz defended and now are Doctors of Philosophy! And farewell to Anne Plochowietz, Martin Kaller, Marko Sustarsic, and Peter May.
  • February 2016:
- The lab was represented by 4 talks in the Biophysical Society meeting in Los Angeles at the end of February.
  • January 2016:
- Wellcome Trust award to Achillefs Kapanidis for work on “molecular mechanisms and regulation of bacterial transcription in vivo”.
-There are several postdoctoral openings for biophysicists and biochemists, welcome to inquire informally regarding the posts.
  • December 2015
- Congratulations to Mat Stracy for his Cell Reports paper on Topo IV (with Pawel Zawadzki, and the Sherratt lab)! Link
  • October 2015:
- MRC (Medical Research Council) award to Achillefs Kapanidis on influenza transcription mechanisms.
- Micron Oxford has been awarded a renewal of its Strategic Award from the Wellcome Trust. Read the full story here.
  • September 2015:
- Congratulations to Anne on winning the PicoQuant student award for best talk at the 21st International Workshop on “Single Molecule Spectroscopy and Super-resolution Microscopy in the Life Sciences” in Berlin!
  • August 2015:
- Two new papers this month: Congratulations to Peter on his paper in PNAS about assembly, translocation, and activation of XerCD-dif recombination by FtsK translocase analyzed in real-time by FRET and two-color tethered fluorophore motion. Link
-Congratulations also to Mathew and Federico for their paper about live-cell superresolution microscopy revealing the organization of RNA polymerase in the bacterial nucleoid, which has also been published in PNAS. Link
-Our software DAOSTORM got ranked third in the category for high density images in a quantitative evaluation of software packages for single-molecule localization microscopy published in Nature Methods. Link Details about the software: Link.
  • May 2015:
- What a way to go! As we say farewell to Geraint, headed off to Illumina, congratulations are in order on the publication of his paper on conformational changes in DNA Polymerase I during DNA synthesis. Open Access Article
-Welcome to Matthew Tedaldi and Horst Steuer, who join us to work on the development of a portable single-molecule fluorescence imager.