Achilles Kapanidis
@achilleskap.bsky.social
Professor of Biological Physics at Oxford.
Pinned
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...
www.science.org
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/...
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/...
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...
www.science.org
January 30, 2026 at 6:59 PM
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/...
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/...
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
academic.oup.com
January 15, 2026 at 10:34 AM
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/...
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...
www.biorxiv.org/content/10.1...
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 ...
www.biorxiv.org
December 5, 2025 at 12:04 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Achilles Kapanidis
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...
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...
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,...
www.nature.com
December 4, 2025 at 10:23 AM
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...
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...
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/...
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
academic.oup.com
October 16, 2025 at 4:58 PM
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/...
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/...
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
academic.oup.com
September 16, 2025 at 9:40 PM
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.
💡 Final PhD paper in NAR: A toolbox for fluorogenic DNA probes aka molecular lightbulbs!
🧬 Flexible in sequence, length, dye
🔬 Single-molecule imaging at μM conc.
🏃♀️➡️ Speeds up DNA-PAINT superres
🌟 No special optics
📄 academic.oup.com/nar/article/...
@kavlioxford.bsky.social @achilleskap.bsky.social
🧬 Flexible in sequence, length, dye
🔬 Single-molecule imaging at μM conc.
🏃♀️➡️ Speeds up DNA-PAINT superres
🌟 No special optics
📄 academic.oup.com/nar/article/...
@kavlioxford.bsky.social @achilleskap.bsky.social
Tunable fluorogenic DNA probes drive fast and high-resolution single-molecule fluorescence imaging
Abstract. A main limitation of single-molecule fluorescence (SMF) measurements is the ‘high concentration barrier’, describing the maximum concentration of
academic.oup.com
July 14, 2025 at 11:52 AM
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.
The RNA helicase HrpA rescues collided ribosomes in E. coli: Molecular Cell www.cell.com/molecular-ce...
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 ...
www.cell.com
March 6, 2025 at 6:47 PM
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
The abstract deadline, 7 March, is approaching fast. Secure a talk or poster by registering now > bit.ly/4gYPPpQ
March 4, 2025 at 2:29 PM
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*!
Reposted by Achilles Kapanidis
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
The abstract deadline, 7 March, is approaching fast. Secure a talk or poster by registering now > bit.ly/4gYPPpQ
February 24, 2025 at 2:52 PM
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
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.
Our work on rapid detection of antibiotic resistant and susceptible cells using ribosome phenotypes is out today! We used fluorescent imaging and changes in bacterial structure to classify single cells with high accuracy.
@achilleskap.bsky.social @oxmartinschool.bsky.social doi.org/10.1038/s420...
@achilleskap.bsky.social @oxmartinschool.bsky.social doi.org/10.1038/s420...
Ribosome phenotypes for rapid classification of antibiotic-susceptible and resistant strains of Escherichia coli - Communications Biology
Ribosome-targeting FISH probes reveal intracellular changes in response to antibiotics that can be used to train neural networks to rapidly classify Escherichia coli from clinical isolates as antibiot...
doi.org
February 28, 2025 at 7:01 PM
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.
Fascinating...so much still to learn about bacterial mechanisms! Base-modified nucleotides mediate immune signaling in bacteria | Science www.science.org/doi/10.1126/...
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 ...
www.science.org
February 21, 2025 at 10:44 AM
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!
The UK&Ireland single-molecule meeting 2025 will be held in Oxford on May 14 and 15 - deadline for abstract submission March 7 - submit one and join us! Here is the link:
lumicks.com/uk-single-mo...
lumicks.com/uk-single-mo...
UK Single-molecule Meeting 2025 – LUMICKS
lumicks.com
February 18, 2025 at 6:21 PM
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!
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.
February 17, 2025 at 3:07 PM
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.