Achilles Kapanidis
@achilleskap.bsky.social
📤 154
📥 85
📝 15
Professor of Biological Physics at Oxford.
pinned post!
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...
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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 ...
https://www.biorxiv.org/content/10.1101/2025.11.27.690701v1
about 2 months ago
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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/...
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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
https://academic.oup.com/nar/article/54/2/gkag001/8425301
6 days ago
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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...
loading . . .
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 ...
https://www.biorxiv.org/content/10.1101/2025.11.27.690701v1
about 2 months ago
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reposted by
Achilles Kapanidis
LUMICKS
about 2 months ago
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...
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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,...
https://www.nature.com/articles/s41594-025-01707-1
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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/...
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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
https://academic.oup.com/nar/article/53/19/gkaf1020/8285782
3 months ago
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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/...
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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
https://academic.oup.com/nar/article/53/17/gkaf857/8251898
4 months ago
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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.
add a skeleton here at some point
6 months ago
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The RNA helicase HrpA rescues collided ribosomes in E. coli: Molecular Cell
www.cell.com/molecular-ce...
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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 ...
https://www.cell.com/molecular-cell/fulltext/S1097-2765%2825%2900052-8
11 months ago
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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*!
add a skeleton here at some point
11 months ago
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reposted by
Achilles Kapanidis
LUMICKS
11 months ago
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
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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.
add a skeleton here at some point
11 months ago
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Fascinating...so much still to learn about bacterial mechanisms! Base-modified nucleotides mediate immune signaling in bacteria | Science
www.science.org/doi/10.1126/...
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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 ...
https://www.science.org/doi/10.1126/science.ads6055?utm_source=sfmc&utm_medium=email&utm_content=alert&utm_campaign=1stRelease&et_rid=17150066&et_cid=5536940
11 months ago
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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!
add a skeleton here at some point
11 months ago
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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
.
11 months ago
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