PhD's & postdocs: dont miss the GRS partner conference, organized by @qmsmith.bsky.social & #AlbaGómez-Segalàs with lots of interaction opportunities and career mentorship:
⏰ June 27-28, 2026
🌍 Swiss Alpes (✈️ Geneva)
✅ APPLY now: deadline May 30.
www.grc.org/single-molec...

Don't miss the #GordonConference on 𝑺𝒊𝒏𝒈𝒍𝒆-𝒎𝒐𝒍𝒆𝒄𝒖𝒍𝒆 𝑨𝒑𝒑𝒓𝒐𝒂𝒄𝒉𝒆𝒔 𝒕𝒐 𝑩𝒊𝒐𝒍𝒐𝒈𝒚, organized by #KevinWelsher & me:
⏰ June 28 - July 3, 2026
🌍 in the Swiss Alpes (✈️ Geneva)
✅ APPLY now: deadline May 31.
We're 75% booked: register today & be there! 🙌
🕳️ 🧬🧪🧫 🔬🟩🟥🟩🟥🏋️‍♀️💥🪤 🍩 ... you get it... 😁

Has anyone had any luck using CDART from NCBI lately? It used to work really well for exploring domain architectures, but now seems broken... I guess InterPro is the closest replacement?

www.ncbi.nlm.nih.gov/Structure/le...

Structural basis of supercoiling-induced CRISPR–Cas9 off-target activity - Nature Cas9 structures explain topology sensing and off-target activation.

A new #Nature study from the Rueda and @alicepyne.bsky.social labs identifies the molecular mechanism of DNA supercoiling in CRISPR–Cas9 off-target activity.
www.nature.com/articles/s41...

Thanks for sharing our work @lumicks.bsky.social 🧬

Spent too much time in situ and forgot the level of detail you get with SPA 🍩
#cryoEM

PIs/group leaders, what was the most important aspect of the first paper your lab published

1️⃣ Establishing the lab's identity
2️⃣ Communicating an important discovery
3️⃣ Completing a project started as a postdoc
4️⃣ Other

📊 Show results

Some of my PhD work is now out in Nature!
www.nature.com/articles/s41...
Investigating the structural basis of off‑target Cas9 binding to supercoiled DNA with #AFM & cryo-EM. From my time in the lab of @alicepyne.bsky.social, in collaboration with @qmsmith.bsky.social and the team at the MRC LMS.

We turned DNA minicircles into diamond rings with Cas9 and uncovered mechanisms behind supercoiling induced Cas9 off-targeting! 🧬⭕️💍

Check out this thread that summaries the key findings! 🧵

bsky.app/profile/qmsm...

Structural basis of supercoiling-induced CRISPR–Cas9 off-target activity - Nature Cas9 structures explain topology sensing and off-target activation.

Nature research paper: Structural basis of supercoiling-induced CRISPR–Cas9 off-target activity

go.nature.com/4t39bk8

Extended this (map_salami) a bit - added a movie option which will generate a labeled movie (1080p or 4k) transitioning between all scenes, with a short rocking motion at each scene for depth perception:

Added a little script to chimerax-trimmings to automate the creation of panels for model-map fit figures.

It zones the map around (by default) 40aa parts of each chain (but doesn't cut in the middle of helices). Saves each as a png, metadata to csv.

Saves each view as a scene for tweaking views.

Proud to share the yeast telomerase structure, led by the talented @hongmiaohu.bsky.social in collaboration with the Wellinger and Chartrand labs. Discovered 37 years ago and took us nearly 7 years but totally worth the wait 😍.
www.science.org/doi/10.1126/...
www.youtube.com/watch?v=gFE4...

DNA shape explains crucial gene-therapy challenges Researchers at Imperial College London, the MRC Laboratory of Medical Sciences (LMS), and the University of Sheffield have shown that the physical tw...

Research from Imperial, @mrc-lms.bsky.social, &
@sheffielduni.bsky.social reveals that the twisting of DNA could play a role in correcting CRISPR errors. 🧬

The team captured interactions between CRISPR and DNA, providing insights that could help eradicate errors.
www.imperial.ac.uk/news/article...

Structural basis of supercoiling-induced CRISPR–Cas9 off-target activity @nature.com @qmsmith.bsky.social @alicepyne.bsky.social @imperialmed.bsky.social
www.nature.com/articles/s41...

Thank you Pablo - the Cas9 Diamond Ring structure is truly remarkable! 🧬⭕️💍

Supercoiling not only brings DNA to life (and makes it dance) but also changes how key proteins such as #CRISPR interact with it. Thanks @qmsmith.bsky.social for the brilliant collaboration, Sylvia for developing an amazing new #imageanalysis pipeline & @eddierollins.bsky.social for beautiful #AFM.

Thanks Toby - I appreciate it! 🥳

Thanks Noura! 🥳

Excited to share our story published today @nature.com!

🔗 www.nature.com/articles/s41...

Read about how we uncover the molecular mechanisms that enable Cas9 to bind and cleave negatively supercoiled ((-)SC) off-targets!

Have a quick read of some of the key events in the thread below🧵:

11/11 Big thanks for the support during my PhD: @mrc-lms.bsky.social @imperialcollegeldn.bsky.social, @sheffielduni.bsky.social, Royce @ Sheffield & LonCEM.

10/11 The next steps following this story is exciting! Huge congrats to amazing collaborats: Sylvia, Ric, @eddierollins.bsky.social, @adamjalal.bsky.social, Deborah, @kylelmorris.bsky.social & amazing mentorship from @alicepyne.bsky.social & David!

9/11 Finally, we used smFRET to capture HNH dynamics. We see high FRET on-targets bound to (-)SC DNA. Off-targets show HNH dynamics, which explains our structural observations and current high-fidelity Cas9 variants still exhibit off-targets on (-)SC DNA!

8/11 How about off-targets? We observe new non-canonical mismatches across the protospacer, highlighting broad diversity of mismatch types when the DNA is (-)SC.

7/11 Additionally, we observe that the HNH domain engages with a 15 Å swing closer to the target strand scissile phosphate when bound to (-)SC DNA. We suggest that this is the reason for accelerated cleavage activity observed with (-)SC substrates. ⏩

6/11 Next, we performed Cryo-EM to determine how Cas9 engages (-)SC substrate at an atomistic level! We observe a beautiful density of the entire DNA minicircle Cas9 complex - which we term the ‘Diamond Ring’. 🧬💍

These are a series of Atomic Force Microscopy snapshots, showing relaxed (left), negatively supercoiled (middle) and negatively supercoiled Cas9 complexes (right).

5/11 To gain structural insight into how Cas9 engages with these (-)SC minicircles, we collaborated with the @alicepyne.bsky.social lab to perform AFM. We observe structural defects with (-)SC DNA minicircles that are resolved upon Cas9 binding! ✅

4/11 We have addressed this by developing programmable (-)SC DNA minicircles. 🧬⭕

We observe that (-)SC accelerates off-target cleavage, generally 100-fold faster than previously reported linear off-target cleavage rates. ⏩

3/11 DNA topology has been shown to modulate CRISPR off-target activity. Yet, the molecular mechanism behind this has been unclear because of the lack of structural information of Cas9 bound to this type of substrate. 💡

2/11 CRISPR Cas9 has paved the way as a successful therapeutic tool. However, off-target editing still poses a great barrier to safe therapeutic applications. ❌