Achilles Kapanidis

Looking fwd to great discussions and brainstorming, Aaron! See you there!

We also link these new methods with past efforts in single-molecule DNA sequencing, and look at future challenges and opportunities for this new field.

A very enjoyable collaborative writing project with Sebastian Deindl, Laura Muras, Koushik Sreenivasa, Jagadish Hazra, John van Noort, and Chirlmin Joo.

From sequence to function: Bridging single-molecule kinetics and molecular diversity Biological function is fundamentally determined by nucleic acid and protein sequence. Beyond encoding genetic information, nucleic acids also display complex physicochemical parameters that shape stru...

Great to see our Science Review on emerging multiplexed single-molecule methods that use libraries to link sequence to dynamics. A fun collaborative writing project! From sequence to function: Bridging single-molecule kinetics and molecular diversity | Science www.science.org/doi/10.1126/...

Single-molecule experiments reveal NusG displaces transcription initiation factor σ70 from mature elongation complexes Abstract. The Escherichia coli transcription initiation factor σ70 was long believed to dissociate from RNA polymerase after promoter escape, following syn

Great work from the Mazumder lab, pointing out a new role for universal transcription factor NusG. Nice FCS and single-mol work as well! Single-molecule experiments reveal NusG displaces transcription initiation factor σ70 from mature elongation complexes url: academic.oup.com/nar/article/...

The concept work with libraries of DNA molecules that are immobilised on a surface, the interactions are explored, and then a short sequence on each DNA molecules is read via a new transient hybridization approach of "DNA seals" on DNA gaps.

Unraveling single-molecule reactions via multiplexed in-situ DNA sequencing DNA sequence regulates complex reactions and protein-DNA interactions, yet sequence effects remain poorly understood due to the lack of direct, high-throughput approaches to study sequence-dependence ...

New preprint! We share a new *DNA-only* method for single-molecule DNA sequencing, and use this cool tool to link single-molecule reactions/interactions to sequence. Big thanks🙏 to Jagadish Hazra @becs-andrews.bsky.social and all contributors since our 2016 start!
www.biorxiv.org/content/10.1...

Kinetic control of mammalian transcription elongation - Nature Structural & Molecular Biology By reconstituting and visualizing mammalian transcription elongation at the single-molecule level, Wang et al. dissected the effects of individual elongation factors on the speed of RNA polymerase II,...

A new NSMB study captured one of the clearest real-time views of how DNA transcribes to RNA with the LUMICKS C-Trap. 🧬
It reveals mechanism of action of the transcription machine: small disruptions can cause cancer, aging, etc.

Congrats to all the authors!
www.nature.com/articles/s41...

High-throughput single-virion DNA-PAINT reveals structural diversity, cooperativity, and flexibility during selective packaging in influenza Abstract. Influenza A, a negative-sense RNA virus, has a genome that consists of eight single-stranded RNA segments. Influenza co-infections can result in

Our work on influenza genome packaging using high-throughput single-virion DNA-PAINT is out in NAR! Packaging appears structurally diverse and flexible. Big thanks to Christoff & Qing (amazing effort)! A collab with @efodor.bsky.social, @nicolerobb.bsky.social academic.oup.com/nar/article/...

The displacement of the σ70 finger in initial transcription is highly heterogeneous and promoter-dependent Abstract. Most bacterial sigma factors (σ) contain a highly conserved structural module, the ‘σ-finger’, which forms a loop that protrudes towards the RNA

What controls how/when growing RNA unblocks the "door" to exit RNA polymerase? Brilliant duo Anna Wang and Abhishek Majumder led a study in my lab - now out in NAR - on this. *Sequence* matters a lot! Read on... Super smFRET/dynamics work as well. Excited! academic.oup.com/nar/article/...

DNA (once more) lights the way! Very excited re the fluorogenic saga manuscript - big congrats to @mirjamku.bsky.social (tremendous effort!) for leading this and to all the team of contributors.

A fantastic meeting, and this one looks even more special! Well done to Picoquant!

The RNA helicase HrpA rescues collided ribosomes in E. coli Antibiotics that inhibit ribosomes lead to collisions on mRNAs when upstream ribosomes catch up with stalled ones. Campbell et al. show that the HrpA protein in E. coli senses ribosome collisions and ...

The RNA helicase HrpA rescues collided ribosomes in E. coli: Molecular Cell www.cell.com/molecular-ce...

A wonderful meeting to share the latest developments on single-molecule research, network, and generate new ideas! Great invited speakers @sulianamanley.bsky.social @jungmannlab.bsky.social, David Rueda, Sebastian Diendl! Send us your Abstracts by *March 7th*!

Following the great success of the 2024 event, @ox.ac.uk and LUMICKS proudly present the second UK-Ireland symposium focusing on single-molecule research!

The abstract deadline, 7 March, is approaching fast. Secure a talk or poster by registering now > bit.ly/4gYPPpQ

So happy to see this AMR-related story from our 3-way collaboration!! Huge congrats to Alison + team, and thanks to @oxmartinschool.bsky.social for making it possible. Basic idea: deep "learning" ribosome distributions after antibiotic treatment rapidly classifies cells as resistant or not.

Wonderful achievement for Nic - what an amazing journey during the past few years for him! Dr Shiaelis, congratulations! Looking fwd to lots of success and discoveries in the years to come... Congrats to @nicolerobb.bsky.social as well, and big thanks to the examiners.

Base-modified nucleotides mediate immune signaling in bacteria Signaling from pathogen sensing to effector activation is a fundamental principle of cellular immunity. While cyclic (oligo)nucleotides have emerged as key signaling molecules, the existence of other ...

Fascinating...so much still to learn about bacterial mechanisms! Base-modified nucleotides mediate immune signaling in bacteria | Science www.science.org/doi/10.1126/...

Waiting for your abstracts by March 7! Join us with your recent stories for a "single-molecule festival" in mid-May... a lovely time to visit Oxford as well!

A DNA-PAINT protocol for the segment-specific detection of viral vRNPs. Virus particles are surface-immobilized, fixed, permeabilized and incubated with non-fluorescent barcoded probes, that bind to 20-50 different sequences on a viral RNA segment. All probes carry the same segment-specific oligonucleotide extension that is transiently bound by fluorescent imager strands. Several combinations of barcode extensions and imager strands can be used to sequentially to detect various gene segments in a single virus particle.

First BlueSky post + a breath of fresh air! Excited about our preprint on the packaging + structure of viral RNA segments in influenza virions: doi.org/10.1101/2025.... A saga from amazing Christof and Qing, and a great collaboration with @nicolerobb.bsky.social and @efodor.bsky.social.